id string | task_type string | pipeline string | difficulty string | num_hops int64 | question string | context string | reasoning_chain dict | answer string | choices list | modalities list | modality_data list | evidence list | metadata unknown | path_confidence_score float64 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
co_coun_00109 | counterfactual | coding_variant | hard | 4 | If CCND1 were knocked out, its physical interaction with AR would be lost. Which disease association of AR could therefore be indirectly affected? | CCND1 GENE_ENCODES_PROTEIN CCND1 -> CCND1 PROTEIN_PHYSICALLY_INTERACTS_WITH AR -> AR GENE_ENCODES_PROTEIN AR -> AR GENE_ASSOCIATED_WITH_DISEASE glioma | {
"steps": [
{
"hop": 1,
"source_node_id": "CCND1",
"source_node_type": "GENE",
"source_node_label": "CCND1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "595"... | glioma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CCND1",
"source_db": "UniProt",
"payload": {
"accession": "P24385",
"sequence": "MEHQLLCCEVETIRRAYPDANLLNDRVLRAMLKAEETCAPSVSYFKCVQKEVLPSMRKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIR... | [
{
"source_db": "bridge",
"source_id": "595",
"text": "CCND1 GENE_ENCODES_PROTEIN CCND1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "367",
"text": "CCND1 PROTEIN_PHYSICALLY_INTERACTS_WITH AR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "CCND1",
"interaction_partner": "AR",
"affected_target": "glioma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.68606 |
co_coun_00110 | counterfactual | coding_variant | hard | 4 | If PTEN were knocked out, its physical interaction with EGFR would be lost. Which pathway of EGFR could therefore be indirectly affected? | PTEN GENE_ENCODES_PROTEIN PTEN -> PTEN PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_PARTICIPATES_IN_PATHWAY PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling | {
"steps": [
{
"hop": 1,
"source_node_id": "PTEN",
"source_node_type": "GENE",
"source_node_label": "PTEN",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5728",... | PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PTEN",
"source_db": "UniProt",
"payload": {
"accession": "P60484",
"sequence": "MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVM... | [
{
"source_db": "bridge",
"source_id": "5728",
"text": "PTEN GENE_ENCODES_PROTEIN PTEN",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "PTEN PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "PTEN",
"interaction_partner": "EGFR",
"affected_target": "PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00111 | counterfactual | coding_variant | hard | 4 | If CHEK2 were knocked out, its physical interaction with CDKN1A would be lost. Which disease association of CDKN1A could therefore be indirectly affected? | CHEK2 GENE_ENCODES_PROTEIN CHEK2 -> CHEK2 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN1A -> CDKN1A GENE_ENCODES_PROTEIN CDKN1A -> CDKN1A GENE_ASSOCIATED_WITH_DISEASE cardiomyopathy | {
"steps": [
{
"hop": 1,
"source_node_id": "CHEK2",
"source_node_type": "GENE",
"source_node_label": "CHEK2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1120... | cardiomyopathy | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "bridge",
"source_id": "11200",
"text": "CHEK2 GENE_ENCODES_PROTEIN CHEK2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1026",
"text": "CHEK2 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN1A",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "CHEK2",
"interaction_partner": "CDKN1A",
"affected_target": "cardiomyopathy",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.769359 |
co_coun_00112 | counterfactual | coding_variant | hard | 3 | If ATM were knocked out, the BASC complex (BRCA1-associated genome surveillance complex) complex would lose one of its members, indirectly affecting MSH6, another member of the same complex. Which disease association of MSH6 could therefore be indirectly affected? | ATM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> MSH6 PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> MSH6 GENE_ASSOCIATED_WITH_DISEASE risk-taking behaviour | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "CORU... | risk-taking behaviour | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "OmniPath",
"source_id": "CORUM:433",
"text": "ATM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex)",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "MSH6",
"text": "MSH6 PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-ass... | {
"knocked_out_gene": "ATM",
"disrupted_complex": "BASC complex (BRCA1-associated genome surveillance complex)",
"complex_partner": "MSH6",
"affected_target": "risk-taking behaviour",
"target_kind": "disease",
"mechanism": "complex"
} | 0.740141 |
co_coun_00113 | counterfactual | coding_variant | hard | 4 | If C9orf72 were knocked out, its physical interaction with MYC would be lost. Which pathway of MYC could therefore be indirectly affected? | C9orf72 GENE_ENCODES_PROTEIN C9orf72 -> C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH MYC -> MYC GENE_ENCODES_PROTEIN MYC -> MYC GENE_PARTICIPATES_IN_PATHWAY Constitutive Signaling by NOTCH1 PEST Domain Mutants | {
"steps": [
{
"hop": 1,
"source_node_id": "C9orf72",
"source_node_type": "GENE",
"source_node_label": "C9orf72",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "... | Constitutive Signaling by NOTCH1 PEST Domain Mutants | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "C9orf72",
"source_db": "UniProt",
"payload": {
"accession": "Q96LT7",
"sequence": "MSTLCPPPSPAVAKTEIALSGKSPLLAATFAYWDNILGPRVRHIWAPKTEQVLLSDGEITFLANHTLNGEILRNAESGAIDVKFFVLSEKGVIIVSLIFDGNWNGDRSTYGLSIILPQTELSFYLPLHRVC... | [
{
"source_db": "bridge",
"source_id": "203228",
"text": "C9orf72 GENE_ENCODES_PROTEIN C9orf72",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4609",
"text": "C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH MYC",
"confidence": 0.9
},
{
"source_db": "bridge",
"... | {
"knocked_out_gene": "C9orf72",
"interaction_partner": "MYC",
"affected_target": "Constitutive Signaling by NOTCH1 PEST Domain Mutants",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00114 | counterfactual | coding_variant | hard | 3 | If ATM were knocked out, the ATM / ATR / BARD1 / BRCA1... complex would lose one of its members, indirectly affecting BARD1, another member of the same complex. Which disease association of BARD1 could therefore be indirectly affected? | ATM PROTEIN_MEMBER_OF_COMPLEX ATM / ATR / BARD1 / BRCA1... -> BARD1 PROTEIN_MEMBER_OF_COMPLEX ATM / ATR / BARD1 / BRCA1... -> BARD1 GENE_ASSOCIATED_WITH_DISEASE trachea squamous cell carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Comp... | trachea squamous cell carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC6143",
"text": "ATM PROTEIN_MEMBER_OF_COMPLEX ATM / ATR / BARD1 / BRCA1...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BARD1",
"text": "BARD1 PROTEIN_MEMBER_OF_COMPLEX ATM / ATR / BARD1 / BRCA1...",
"confidence... | {
"knocked_out_gene": "ATM",
"disrupted_complex": "ATM / ATR / BARD1 / BRCA1...",
"complex_partner": "BARD1",
"affected_target": "trachea squamous cell carcinoma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.569586 |
co_coun_00115 | counterfactual | coding_variant | hard | 4 | If CDK1 were knocked out, its physical interaction with CDKN1A would be lost. Which disease association of CDKN1A could therefore be indirectly affected? | CDK1 GENE_ENCODES_PROTEIN CDK1 -> CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN1A -> CDKN1A GENE_ENCODES_PROTEIN CDKN1A -> CDKN1A GENE_ASSOCIATED_WITH_DISEASE palmar fibromatosis | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK1",
"source_node_type": "GENE",
"source_node_label": "CDK1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "983",
... | palmar fibromatosis | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK1",
"source_db": "UniProt",
"payload": {
"accession": "P06493",
"sequence": "MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNL... | [
{
"source_db": "bridge",
"source_id": "983",
"text": "CDK1 GENE_ENCODES_PROTEIN CDK1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1026",
"text": "CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN1A",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"knocked_out_gene": "CDK1",
"interaction_partner": "CDKN1A",
"affected_target": "palmar fibromatosis",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.695235 |
co_coun_00116 | counterfactual | coding_variant | hard | 4 | If DNMT3A were knocked out, its physical interaction with CDH1 would be lost. Which disease association of CDH1 could therefore be indirectly affected? | DNMT3A GENE_ENCODES_PROTEIN DNMT3A -> DNMT3A PROTEIN_PHYSICALLY_INTERACTS_WITH CDH1 -> CDH1 GENE_ENCODES_PROTEIN CDH1 -> CDH1 GENE_ASSOCIATED_WITH_DISEASE prostate adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "DNMT3A",
"source_node_type": "GENE",
"source_node_label": "DNMT3A",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "17... | prostate adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "DNMT3A",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y6K1",
"sequence": "MPAMPSSGPGDTSSSAAEREEDRKDGEEQEEPRGKEERQEPSTTARKVGRPGRKRKHPPVESGDTPKDPAVISKSPSMAQDSGASELLPNGDLEKRSEPQPEEGSPAGGQKGGAPAEGEGAAETLPEASRAV... | [
{
"source_db": "bridge",
"source_id": "1788",
"text": "DNMT3A GENE_ENCODES_PROTEIN DNMT3A",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "999",
"text": "DNMT3A PROTEIN_PHYSICALLY_INTERACTS_WITH CDH1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"knocked_out_gene": "DNMT3A",
"interaction_partner": "CDH1",
"affected_target": "prostate adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.684547 |
co_coun_00117 | counterfactual | coding_variant | hard | 3 | If PMS2 were knocked out, the BLM / BRCA1 / EXO1 / MLH1... complex would lose one of its members, indirectly affecting BLM, another member of the same complex. Which disease association of BLM could therefore be indirectly affected? | PMS2 PROTEIN_MEMBER_OF_COMPLEX BLM / BRCA1 / EXO1 / MLH1... -> BLM PROTEIN_MEMBER_OF_COMPLEX BLM / BRCA1 / EXO1 / MLH1... -> BLM GENE_ASSOCIATED_WITH_DISEASE lung sclerosing hemangioma | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Co... | lung sclerosing hemangioma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PMS2",
"source_db": "UniProt",
"payload": {
"accession": "P54278",
"sequence": "MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTR... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC6768",
"text": "PMS2 PROTEIN_MEMBER_OF_COMPLEX BLM / BRCA1 / EXO1 / MLH1...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BLM",
"text": "BLM PROTEIN_MEMBER_OF_COMPLEX BLM / BRCA1 / EXO1 / MLH1...",
"confidence": ... | {
"knocked_out_gene": "PMS2",
"disrupted_complex": "BLM / BRCA1 / EXO1 / MLH1...",
"complex_partner": "BLM",
"affected_target": "lung sclerosing hemangioma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.569966 |
co_coun_00118 | counterfactual | coding_variant | hard | 4 | If CDKN2A were knocked out, its physical interaction with AR would be lost. Which disease association of AR could therefore be indirectly affected? | CDKN2A GENE_ENCODES_PROTEIN CDKN2A -> CDKN2A PROTEIN_PHYSICALLY_INTERACTS_WITH AR -> AR GENE_ENCODES_PROTEIN AR -> AR GENE_ASSOCIATED_WITH_DISEASE angiosarcoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CDKN2A",
"source_node_type": "GENE",
"source_node_label": "CDKN2A",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "10... | angiosarcoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDKN2A",
"source_db": "UniProt",
"payload": {
"accession": "Q8N726",
"sequence": "MVRRFLVTLRIRRACGPPRVRVFVVHIPRLTGEWAAPGAPAAVALVLMLLRSQRLGQQPLPRRPGHDDGQRPSGGAAAAPRRGAQLRRPRHSHPTRARRCPGGLPGHAGGAAPGRGAAGRARCLGPSARGPG... | [
{
"source_db": "bridge",
"source_id": "1029",
"text": "CDKN2A GENE_ENCODES_PROTEIN CDKN2A",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "367",
"text": "CDKN2A PROTEIN_PHYSICALLY_INTERACTS_WITH AR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "CDKN2A",
"interaction_partner": "AR",
"affected_target": "angiosarcoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.671296 |
co_coun_00119 | counterfactual | coding_variant | hard | 4 | If TP53 were knocked out, its physical interaction with CDKN2A would be lost. Which disease association of CDKN2A could therefore be indirectly affected? | TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN2A -> CDKN2A GENE_ENCODES_PROTEIN CDKN2A -> CDKN2A GENE_ASSOCIATED_WITH_DISEASE schwannoma | {
"steps": [
{
"hop": 1,
"source_node_id": "TP53",
"source_node_type": "GENE",
"source_node_label": "TP53",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "7157",... | schwannoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "bridge",
"source_id": "7157",
"text": "TP53 GENE_ENCODES_PROTEIN TP53",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1029",
"text": "TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN2A",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "TP53",
"interaction_partner": "CDKN2A",
"affected_target": "schwannoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.674969 |
co_coun_00120 | counterfactual | coding_variant | hard | 4 | If CCND1 were knocked out, its physical interaction with CDKN2A would be lost. Which disease association of CDKN2A could therefore be indirectly affected? | CCND1 GENE_ENCODES_PROTEIN CCND1 -> CCND1 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN2A -> CDKN2A GENE_ENCODES_PROTEIN CDKN2A -> CDKN2A GENE_ASSOCIATED_WITH_DISEASE mesenchymal chondrosarcoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CCND1",
"source_node_type": "GENE",
"source_node_label": "CCND1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "595"... | mesenchymal chondrosarcoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CCND1",
"source_db": "UniProt",
"payload": {
"accession": "P24385",
"sequence": "MEHQLLCCEVETIRRAYPDANLLNDRVLRAMLKAEETCAPSVSYFKCVQKEVLPSMRKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIR... | [
{
"source_db": "bridge",
"source_id": "595",
"text": "CCND1 GENE_ENCODES_PROTEIN CCND1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1029",
"text": "CCND1 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN2A",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "CCND1",
"interaction_partner": "CDKN2A",
"affected_target": "mesenchymal chondrosarcoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.671799 |
co_coun_00121 | counterfactual | coding_variant | hard | 4 | If ABL1 were knocked out, its physical interaction with ERBB2 would be lost. Which pathway of ERBB2 could therefore be indirectly affected? | ABL1 GENE_ENCODES_PROTEIN ABL1 -> ABL1 PROTEIN_PHYSICALLY_INTERACTS_WITH ERBB2 -> ERBB2 GENE_ENCODES_PROTEIN ERBB2 -> ERBB2 GENE_PARTICIPATES_IN_PATHWAY Downregulation of ERBB2:ERBB3 signaling | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL1",
"source_node_type": "GENE",
"source_node_label": "ABL1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "25",
... | Downregulation of ERBB2:ERBB3 signaling | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL1",
"source_db": "UniProt",
"payload": {
"accession": "P00519",
"sequence": "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSR... | [
{
"source_db": "bridge",
"source_id": "25",
"text": "ABL1 GENE_ENCODES_PROTEIN ABL1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2064",
"text": "ABL1 PROTEIN_PHYSICALLY_INTERACTS_WITH ERBB2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "ABL1",
"interaction_partner": "ERBB2",
"affected_target": "Downregulation of ERBB2:ERBB3 signaling",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00122 | counterfactual | coding_variant | hard | 4 | If KMT2D were knocked out, its physical interaction with AR would be lost. Which disease association of AR could therefore be indirectly affected? | KMT2D GENE_ENCODES_PROTEIN KMT2D -> KMT2D PROTEIN_PHYSICALLY_INTERACTS_WITH AR -> AR GENE_ENCODES_PROTEIN AR -> AR GENE_ASSOCIATED_WITH_DISEASE breast ductal adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2D",
"source_node_type": "GENE",
"source_node_label": "KMT2D",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "8085... | breast ductal adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2D",
"source_db": "UniProt",
"payload": {
"accession": "O14686",
"sequence": "MDSQKLAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSSGSPRLQETPQDCSGGPVRRCALCNCGEPSLHGQRELRRFELPFDWPRCPVVSPGGSPGPNEAVLPSEDLSQIGFPEGLTPAHLGEPG... | [
{
"source_db": "bridge",
"source_id": "8085",
"text": "KMT2D GENE_ENCODES_PROTEIN KMT2D",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "367",
"text": "KMT2D PROTEIN_PHYSICALLY_INTERACTS_WITH AR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "KMT2D",
"interaction_partner": "AR",
"affected_target": "breast ductal adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.721863 |
co_coun_00123 | counterfactual | coding_variant | hard | 4 | If AXL were knocked out, its physical interaction with EGFR would be lost. Which disease association of EGFR could therefore be indirectly affected? | AXL GENE_ENCODES_PROTEIN AXL -> AXL PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_ASSOCIATED_WITH_DISEASE angiosarcoma | {
"steps": [
{
"hop": 1,
"source_node_id": "AXL",
"source_node_type": "GENE",
"source_node_label": "AXL",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "558",
... | angiosarcoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AXL",
"source_db": "UniProt",
"payload": {
"accession": "P30530",
"sequence": "MAWRCPRMGRVPLAWCLALCGWACMAPRGTQAEESPFVGNPGNITGARGLTGTLRCQLQVQGEPPEVHWLRDGQILELADSTQTQVPLGEDEQDDWIVVSQLRITSLQLSDTGQYQCLVFLGHQTFVSQPGYVGL... | [
{
"source_db": "bridge",
"source_id": "558",
"text": "AXL GENE_ENCODES_PROTEIN AXL",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "AXL PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "E... | {
"knocked_out_gene": "AXL",
"interaction_partner": "EGFR",
"affected_target": "angiosarcoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.674097 |
co_coun_00124 | counterfactual | coding_variant | hard | 4 | If TARDBP were knocked out, its physical interaction with FUS would be lost. Which disease association of FUS could therefore be indirectly affected? | TARDBP GENE_ENCODES_PROTEIN TARDBP -> TARDBP PROTEIN_PHYSICALLY_INTERACTS_WITH FUS -> FUS GENE_ENCODES_PROTEIN FUS -> FUS GENE_ASSOCIATED_WITH_DISEASE small cell lung carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "TARDBP",
"source_node_type": "GENE",
"source_node_label": "TARDBP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "23... | small cell lung carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TARDBP",
"source_db": "UniProt",
"payload": {
"accession": "Q13148",
"sequence": "MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLM... | [
{
"source_db": "bridge",
"source_id": "23435",
"text": "TARDBP GENE_ENCODES_PROTEIN TARDBP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2521",
"text": "TARDBP PROTEIN_PHYSICALLY_INTERACTS_WITH FUS",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "TARDBP",
"interaction_partner": "FUS",
"affected_target": "small cell lung carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.606775 |
co_coun_00125 | counterfactual | coding_variant | hard | 4 | If MYC were knocked out, its physical interaction with POLD1 would be lost. Which disease association of POLD1 could therefore be indirectly affected? | MYC GENE_ENCODES_PROTEIN MYC -> MYC PROTEIN_PHYSICALLY_INTERACTS_WITH POLD1 -> POLD1 GENE_ENCODES_PROTEIN POLD1 -> POLD1 GENE_ASSOCIATED_WITH_DISEASE primary central nervous system lymphoma | {
"steps": [
{
"hop": 1,
"source_node_id": "MYC",
"source_node_type": "GENE",
"source_node_label": "MYC",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4609",
... | primary central nervous system lymphoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MYC",
"source_db": "UniProt",
"payload": {
"accession": "P01106",
"sequence": "MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD... | [
{
"source_db": "bridge",
"source_id": "4609",
"text": "MYC GENE_ENCODES_PROTEIN MYC",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5424",
"text": "MYC PROTEIN_PHYSICALLY_INTERACTS_WITH POLD1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "MYC",
"interaction_partner": "POLD1",
"affected_target": "primary central nervous system lymphoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.710502 |
co_coun_00126 | counterfactual | coding_variant | hard | 4 | If SOX2 were knocked out, its physical interaction with CTNNB1 would be lost. Which disease association of CTNNB1 could therefore be indirectly affected? | SOX2 GENE_ENCODES_PROTEIN SOX2 -> SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1 -> CTNNB1 GENE_ENCODES_PROTEIN CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE parathyroid gland adenoma | {
"steps": [
{
"hop": 1,
"source_node_id": "SOX2",
"source_node_type": "GENE",
"source_node_label": "SOX2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "6657",... | parathyroid gland adenoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SOX2",
"source_db": "UniProt",
"payload": {
"accession": "P48431",
"sequence": "MYNMMETELKPPGPQQTSGGGGGNSTAAAAGGNQKNSPDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKTLMKKDKYTLPGGLLAP... | [
{
"source_db": "bridge",
"source_id": "6657",
"text": "SOX2 GENE_ENCODES_PROTEIN SOX2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1499",
"text": "SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "SOX2",
"interaction_partner": "CTNNB1",
"affected_target": "parathyroid gland adenoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.674043 |
co_coun_00127 | counterfactual | coding_variant | hard | 4 | If NRAS were knocked out, its physical interaction with PIK3CA would be lost. Which disease association of PIK3CA could therefore be indirectly affected? | NRAS GENE_ENCODES_PROTEIN NRAS -> NRAS PROTEIN_PHYSICALLY_INTERACTS_WITH PIK3CA -> PIK3CA GENE_ENCODES_PROTEIN PIK3CA -> PIK3CA GENE_ASSOCIATED_WITH_DISEASE malignant glioma | {
"steps": [
{
"hop": 1,
"source_node_id": "NRAS",
"source_node_type": "GENE",
"source_node_label": "NRAS",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4893",... | malignant glioma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NRAS",
"source_db": "UniProt",
"payload": {
"accession": "P01111",
"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELA... | [
{
"source_db": "bridge",
"source_id": "4893",
"text": "NRAS GENE_ENCODES_PROTEIN NRAS",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5290",
"text": "NRAS PROTEIN_PHYSICALLY_INTERACTS_WITH PIK3CA",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "NRAS",
"interaction_partner": "PIK3CA",
"affected_target": "malignant glioma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.731112 |
co_coun_00128 | counterfactual | coding_variant | hard | 4 | If C9orf72 were knocked out, its physical interaction with SQSTM1 would be lost. Which disease association of SQSTM1 could therefore be indirectly affected? | C9orf72 GENE_ENCODES_PROTEIN C9orf72 -> C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH SQSTM1 -> SQSTM1 GENE_ENCODES_PROTEIN SQSTM1 -> SQSTM1 GENE_ASSOCIATED_WITH_DISEASE osteoarthritis, hip | {
"steps": [
{
"hop": 1,
"source_node_id": "C9orf72",
"source_node_type": "GENE",
"source_node_label": "C9orf72",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "... | osteoarthritis, hip | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "C9orf72",
"source_db": "UniProt",
"payload": {
"accession": "Q96LT7",
"sequence": "MSTLCPPPSPAVAKTEIALSGKSPLLAATFAYWDNILGPRVRHIWAPKTEQVLLSDGEITFLANHTLNGEILRNAESGAIDVKFFVLSEKGVIIVSLIFDGNWNGDRSTYGLSIILPQTELSFYLPLHRVC... | [
{
"source_db": "bridge",
"source_id": "203228",
"text": "C9orf72 GENE_ENCODES_PROTEIN C9orf72",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "8878",
"text": "C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH SQSTM1",
"confidence": 0.9
},
{
"source_db": "bridge",
... | {
"knocked_out_gene": "C9orf72",
"interaction_partner": "SQSTM1",
"affected_target": "osteoarthritis, hip",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.684191 |
co_coun_00129 | counterfactual | coding_variant | hard | 4 | If ABI1 were knocked out, its physical interaction with EGFR would be lost. Which disease association of EGFR could therefore be indirectly affected? | ABI1 GENE_ENCODES_PROTEIN ABI1 -> ABI1 PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_ASSOCIATED_WITH_DISEASE pleural mesothelioma | {
"steps": [
{
"hop": 1,
"source_node_id": "ABI1",
"source_node_type": "GENE",
"source_node_label": "ABI1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "10006"... | pleural mesothelioma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABI1",
"source_db": "UniProt",
"payload": {
"accession": "Q8IZP0",
"sequence": "MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKALEETKAYTTQSLASVAYQINALANNVLQLLDIQASQLRRMESSINHISQTVDIHKEKVARREIGILTTNKNTSRTHKIIAPANMERPV... | [
{
"source_db": "bridge",
"source_id": "10006",
"text": "ABI1 GENE_ENCODES_PROTEIN ABI1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "ABI1 PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"knocked_out_gene": "ABI1",
"interaction_partner": "EGFR",
"affected_target": "pleural mesothelioma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.677811 |
co_coun_00130 | counterfactual | coding_variant | hard | 4 | If SOX2 were knocked out, its physical interaction with DDX41 would be lost. Which pathway of DDX41 could therefore be indirectly affected? | SOX2 GENE_ENCODES_PROTEIN SOX2 -> SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH DDX41 -> DDX41 GENE_ENCODES_PROTEIN DDX41 -> DDX41 GENE_PARTICIPATES_IN_PATHWAY STING mediated induction of host immune responses | {
"steps": [
{
"hop": 1,
"source_node_id": "SOX2",
"source_node_type": "GENE",
"source_node_label": "SOX2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "6657",... | STING mediated induction of host immune responses | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SOX2",
"source_db": "UniProt",
"payload": {
"accession": "P48431",
"sequence": "MYNMMETELKPPGPQQTSGGGGGNSTAAAAGGNQKNSPDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKTLMKKDKYTLPGGLLAP... | [
{
"source_db": "bridge",
"source_id": "6657",
"text": "SOX2 GENE_ENCODES_PROTEIN SOX2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "51428",
"text": "SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH DDX41",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "SOX2",
"interaction_partner": "DDX41",
"affected_target": "STING mediated induction of host immune responses",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00131 | counterfactual | coding_variant | hard | 4 | If BRIP1 were knocked out, its physical interaction with BARD1 would be lost. Which disease association of BARD1 could therefore be indirectly affected? | BRIP1 GENE_ENCODES_PROTEIN BRIP1 -> BRIP1 PROTEIN_PHYSICALLY_INTERACTS_WITH BARD1 -> BARD1 GENE_ENCODES_PROTEIN BARD1 -> BARD1 GENE_ASSOCIATED_WITH_DISEASE colon medullary carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "BRIP1",
"source_node_type": "GENE",
"source_node_label": "BRIP1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "8399... | colon medullary carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRIP1",
"source_db": "UniProt",
"payload": {
"accession": "Q9BX63",
"sequence": "MSSMWSEYTIGGVKIYFPYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLALLCSALAWQQSLSGKPADEGVSEKAEVQLSCCCACHSKDFTNNDMNQGTSRHFNYPSTPPSERNGTSSTCQDSPEKTT... | [
{
"source_db": "bridge",
"source_id": "83990",
"text": "BRIP1 GENE_ENCODES_PROTEIN BRIP1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "580",
"text": "BRIP1 PROTEIN_PHYSICALLY_INTERACTS_WITH BARD1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "BRIP1",
"interaction_partner": "BARD1",
"affected_target": "colon medullary carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.605831 |
co_coun_00132 | counterfactual | coding_variant | hard | 4 | If SQSTM1 were knocked out, its physical interaction with SOX2 would be lost. Which disease association of SOX2 could therefore be indirectly affected? | SQSTM1 GENE_ENCODES_PROTEIN SQSTM1 -> SQSTM1 PROTEIN_PHYSICALLY_INTERACTS_WITH SOX2 -> SOX2 GENE_ENCODES_PROTEIN SOX2 -> SOX2 GENE_ASSOCIATED_WITH_DISEASE microphthalmia, isolated, with coloboma | {
"steps": [
{
"hop": 1,
"source_node_id": "SQSTM1",
"source_node_type": "GENE",
"source_node_label": "SQSTM1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "88... | microphthalmia, isolated, with coloboma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SQSTM1",
"source_db": "UniProt",
"payload": {
"accession": "Q13501",
"sequence": "MASLTVKAYLLGKEDAAREIRRFSFCCSPEPEAEAEAAAGPGPCERLLSRVAALFPALRPGGFQAHYRDEDGDLVAFSSDEELTMAMSYVKDDIFRIYIKEKKECRRDHRPPCAQEAPRNMVHPNVICDGCN... | [
{
"source_db": "bridge",
"source_id": "8878",
"text": "SQSTM1 GENE_ENCODES_PROTEIN SQSTM1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "6657",
"text": "SQSTM1 PROTEIN_PHYSICALLY_INTERACTS_WITH SOX2",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "SQSTM1",
"interaction_partner": "SOX2",
"affected_target": "microphthalmia, isolated, with coloboma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.729456 |
co_coun_00133 | counterfactual | coding_variant | hard | 4 | If MAPK1 were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | MAPK1 GENE_ENCODES_PROTEIN MAPK1 -> MAPK1 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE breast-ovarian cancer, familial, susceptibility to, 2 | {
"steps": [
{
"hop": 1,
"source_node_id": "MAPK1",
"source_node_type": "GENE",
"source_node_label": "MAPK1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5594... | breast-ovarian cancer, familial, susceptibility to, 2 | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MAPK1",
"source_db": "UniProt",
"payload": {
"accession": "P28482",
"sequence": "MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQI... | [
{
"source_db": "bridge",
"source_id": "5594",
"text": "MAPK1 GENE_ENCODES_PROTEIN MAPK1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "MAPK1 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "MAPK1",
"interaction_partner": "BRCA1",
"affected_target": "breast-ovarian cancer, familial, susceptibility to, 2",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.746179 |
co_coun_00134 | counterfactual | coding_variant | hard | 3 | If CHEK2 were knocked out, the ATM / ATR / BLM / BRCA1... complex would lose one of its members, indirectly affecting ATM, another member of the same complex. Which disease association of ATM could therefore be indirectly affected? | CHEK2 PROTEIN_MEMBER_OF_COMPLEX ATM / ATR / BLM / BRCA1... -> ATM PROTEIN_MEMBER_OF_COMPLEX ATM / ATR / BLM / BRCA1... -> ATM GENE_ASSOCIATED_WITH_DISEASE testicular seminoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CHEK2",
"source_node_type": "GENE",
"source_node_label": "CHEK2",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | testicular seminoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC6924",
"text": "CHEK2 PROTEIN_MEMBER_OF_COMPLEX ATM / ATR / BLM / BRCA1...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "ATM",
"text": "ATM PROTEIN_MEMBER_OF_COMPLEX ATM / ATR / BLM / BRCA1...",
"confidence": 1
... | {
"knocked_out_gene": "CHEK2",
"disrupted_complex": "ATM / ATR / BLM / BRCA1...",
"complex_partner": "ATM",
"affected_target": "testicular seminoma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.652013 |
co_coun_00135 | counterfactual | coding_variant | hard | 4 | If CDK1 were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | CDK1 GENE_ENCODES_PROTEIN CDK1 -> CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE anaplastic oligodendroglioma | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK1",
"source_node_type": "GENE",
"source_node_label": "CDK1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "983",
... | anaplastic oligodendroglioma | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK1",
"source_db": "UniProt",
"payload": {
"accession": "P06493",
"sequence": "MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNL... | [
{
"source_db": "bridge",
"source_id": "983",
"text": "CDK1 GENE_ENCODES_PROTEIN CDK1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "CDK1",
"interaction_partner": "BRCA1",
"affected_target": "anaplastic oligodendroglioma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.67102 |
co_coun_00136 | counterfactual | coding_variant | hard | 3 | If AURKB were knocked out, the AURKB / BIRC7 / BRCA1 / MAPRE1... complex would lose one of its members, indirectly affecting BRCA1, another member of the same complex. Which disease association of BRCA1 could therefore be indirectly affected? | AURKB PROTEIN_MEMBER_OF_COMPLEX AURKB / BIRC7 / BRCA1 / MAPRE1... -> BRCA1 PROTEIN_MEMBER_OF_COMPLEX AURKB / BIRC7 / BRCA1 / MAPRE1... -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE mantle cell lymphoma | {
"steps": [
{
"hop": 1,
"source_node_id": "AURKB",
"source_node_type": "GENE",
"source_node_label": "AURKB",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | mantle cell lymphoma | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AURKB",
"source_db": "UniProt",
"payload": {
"accession": "Q96GD4",
"sequence": "MAQKENSYPWPYGRQTAPSGLSTLPQRVLRKEPVTPSALVLMSRSNVQPTAAPGQKVMENSSGTPDILTRHFTIDDFEIGRPLGKGKFGNVYLAREKKSHFIVALKVLFKSQIEKEGVEHQLRREIEIQAHLH... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC4217",
"text": "AURKB PROTEIN_MEMBER_OF_COMPLEX AURKB / BIRC7 / BRCA1 / MAPRE1...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX AURKB / BIRC7 / BRCA1 / MAPRE1...",
... | {
"knocked_out_gene": "AURKB",
"disrupted_complex": "AURKB / BIRC7 / BRCA1 / MAPRE1...",
"complex_partner": "BRCA1",
"affected_target": "mantle cell lymphoma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.654461 |
co_coun_00137 | counterfactual | coding_variant | hard | 4 | If BRCA1 were knocked out, its physical interaction with AR would be lost. Which disease association of AR could therefore be indirectly affected? | BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 PROTEIN_PHYSICALLY_INTERACTS_WITH AR -> AR GENE_ENCODES_PROTEIN AR -> AR GENE_ASSOCIATED_WITH_DISEASE Familial prostate cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA1",
"source_node_type": "GENE",
"source_node_label": "BRCA1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "672"... | Familial prostate cancer | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "bridge",
"source_id": "672",
"text": "BRCA1 GENE_ENCODES_PROTEIN BRCA1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "367",
"text": "BRCA1 PROTEIN_PHYSICALLY_INTERACTS_WITH AR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "BRCA1",
"interaction_partner": "AR",
"affected_target": "Familial prostate cancer",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.819337 |
co_coun_00138 | counterfactual | coding_variant | hard | 4 | If RET were knocked out, its physical interaction with EGFR would be lost. Which pathway of EGFR could therefore be indirectly affected? | RET GENE_ENCODES_PROTEIN RET -> RET PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_PARTICIPATES_IN_PATHWAY NOTCH3 Activation and Transmission of Signal to the Nucleus | {
"steps": [
{
"hop": 1,
"source_node_id": "RET",
"source_node_type": "GENE",
"source_node_label": "RET",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5979",
... | NOTCH3 Activation and Transmission of Signal to the Nucleus | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RET",
"source_db": "UniProt",
"payload": {
"accession": "P07949",
"sequence": "MAKATSGAAGLRLLLLLLLPLLGKVALGLYFSRDAYWEKLYVDQAAGTPLLYVHALRDAPEEVPSFRLGQHLYGTYRTRLHENNWICIQEDTGLLYLNRSLDHSSWEKLSVRNRGFPLLTVYLKVFLSPTSLREG... | [
{
"source_db": "bridge",
"source_id": "5979",
"text": "RET GENE_ENCODES_PROTEIN RET",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "RET PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "... | {
"knocked_out_gene": "RET",
"interaction_partner": "EGFR",
"affected_target": "NOTCH3 Activation and Transmission of Signal to the Nucleus",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00139 | counterfactual | coding_variant | hard | 4 | If SOX2 were knocked out, its physical interaction with AKT1 would be lost. Which disease association of AKT1 could therefore be indirectly affected? | SOX2 GENE_ENCODES_PROTEIN SOX2 -> SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1 -> AKT1 GENE_ENCODES_PROTEIN AKT1 -> AKT1 GENE_ASSOCIATED_WITH_DISEASE thyroid gland undifferentiated (anaplastic) carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "SOX2",
"source_node_type": "GENE",
"source_node_label": "SOX2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "6657",... | thyroid gland undifferentiated (anaplastic) carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SOX2",
"source_db": "UniProt",
"payload": {
"accession": "P48431",
"sequence": "MYNMMETELKPPGPQQTSGGGGGNSTAAAAGGNQKNSPDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKTLMKKDKYTLPGGLLAP... | [
{
"source_db": "bridge",
"source_id": "6657",
"text": "SOX2 GENE_ENCODES_PROTEIN SOX2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "207",
"text": "SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "SOX2",
"interaction_partner": "AKT1",
"affected_target": "thyroid gland undifferentiated (anaplastic) carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.678692 |
co_coun_00140 | counterfactual | coding_variant | hard | 4 | If ABL1 were knocked out, its physical interaction with CTNNB1 would be lost. Which disease association of CTNNB1 could therefore be indirectly affected? | ABL1 GENE_ENCODES_PROTEIN ABL1 -> ABL1 PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1 -> CTNNB1 GENE_ENCODES_PROTEIN CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE ovarian microcystic stromal tumor | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL1",
"source_node_type": "GENE",
"source_node_label": "ABL1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "25",
... | ovarian microcystic stromal tumor | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL1",
"source_db": "UniProt",
"payload": {
"accession": "P00519",
"sequence": "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSR... | [
{
"source_db": "bridge",
"source_id": "25",
"text": "ABL1 GENE_ENCODES_PROTEIN ABL1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1499",
"text": "ABL1 PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "ABL1",
"interaction_partner": "CTNNB1",
"affected_target": "ovarian microcystic stromal tumor",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.721645 |
co_coun_00141 | counterfactual | coding_variant | hard | 4 | If CREBBP were knocked out, its physical interaction with RXRA would be lost. Which disease association of RXRA could therefore be indirectly affected? | CREBBP GENE_ENCODES_PROTEIN CREBBP -> CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH RXRA -> RXRA GENE_ENCODES_PROTEIN RXRA -> RXRA GENE_ASSOCIATED_WITH_DISEASE T-cell non-Hodgkin lymphoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CREBBP",
"source_node_type": "GENE",
"source_node_label": "CREBBP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "13... | T-cell non-Hodgkin lymphoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CREBBP",
"source_db": "UniProt",
"payload": {
"accession": "Q92793",
"sequence": "MAENLLDGPPNPKRAKLSSPGFSANDSTDFGSLFDLENDLPDELIPNGGELGLLNSGNLVPDAASKHKQLSELLRGGSGSSINPGIGNVSASSPVQQGLGGQAQGQPNSANMASLSAMGKSPLSQGDSSAPS... | [
{
"source_db": "bridge",
"source_id": "1387",
"text": "CREBBP GENE_ENCODES_PROTEIN CREBBP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "6256",
"text": "CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH RXRA",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "CREBBP",
"interaction_partner": "RXRA",
"affected_target": "T-cell non-Hodgkin lymphoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.720458 |
co_coun_00142 | counterfactual | coding_variant | hard | 4 | If CTNNA1 were knocked out, its physical interaction with CDH1 would be lost. Which disease association of CDH1 could therefore be indirectly affected? | CTNNA1 GENE_ENCODES_PROTEIN CTNNA1 -> CTNNA1 PROTEIN_PHYSICALLY_INTERACTS_WITH CDH1 -> CDH1 GENE_ENCODES_PROTEIN CDH1 -> CDH1 GENE_ASSOCIATED_WITH_DISEASE salivary gland carcinoma ex pleomorphic adenoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CTNNA1",
"source_node_type": "GENE",
"source_node_label": "CTNNA1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "14... | salivary gland carcinoma ex pleomorphic adenoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CTNNA1",
"source_db": "UniProt",
"payload": {
"accession": "P35221",
"sequence": "MTAVHAGNINFKWDPKSLEIRTLAVERLLEPLVTQVTTLVNTNSKGPSNKKRGRSKKAHVLAASVEQATENFLEKGDKIAKESQFLKEELVAAVEDVRKQGDLMKAAAGEFADDPCSSVKRGNMVRAARALL... | [
{
"source_db": "bridge",
"source_id": "1495",
"text": "CTNNA1 GENE_ENCODES_PROTEIN CTNNA1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "999",
"text": "CTNNA1 PROTEIN_PHYSICALLY_INTERACTS_WITH CDH1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"knocked_out_gene": "CTNNA1",
"interaction_partner": "CDH1",
"affected_target": "salivary gland carcinoma ex pleomorphic adenoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00143 | counterfactual | coding_variant | medium | 3 | If ERG were knocked out, the ribonucleoprotein complex complex would lose one of its members, indirectly affecting ACTB, another member of the same complex. Which pathway of ACTB could therefore be indirectly affected? | ERG PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex -> ACTB PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex -> ACTB GENE_PARTICIPATES_IN_PATHWAY Sensory processing of sound by inner hair cells of the cochlea | {
"steps": [
{
"hop": 1,
"source_node_id": "ERG",
"source_node_type": "GENE",
"source_node_label": "ERG",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Comp... | Sensory processing of sound by inner hair cells of the cochlea | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ERG",
"source_db": "UniProt",
"payload": {
"accession": "P11308",
"sequence": "MASTIKEALSVVSEDQSLFECAYGTPHLAKTEMTASSSSDYGQTSKMSPRVPQQDWLSQPPARVTIKMECNPSQVNGSRNSPDECSVAKGGKMVGSPDTVGMNYGSYMEEKHMPPPNMTTNERRVIVPADPTLWS... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC393",
"text": "ERG PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "ACTB",
"text": "ACTB PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex",
"confidence": 1
},... | {
"knocked_out_gene": "ERG",
"disrupted_complex": "ribonucleoprotein complex",
"complex_partner": "ACTB",
"affected_target": "Sensory processing of sound by inner hair cells of the cochlea",
"target_kind": "pathway",
"mechanism": "complex"
} | 1 |
co_coun_00144 | counterfactual | coding_variant | hard | 4 | If PALB2 were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | PALB2 GENE_ENCODES_PROTEIN PALB2 -> PALB2 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE head and neck carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "PALB2",
"source_node_type": "GENE",
"source_node_label": "PALB2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "7972... | head and neck carcinoma | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PALB2",
"source_db": "UniProt",
"payload": {
"accession": "Q86YC2",
"sequence": "MDEPPGKPLSCEEKEKLKEKLAFLKREYSKTLARLQRAQRAEKIKHSIKKTVEEQDCLSQQDLSPQLKHSEPKNKICVYDKLHIKTHLDEETGEKTSITLDVGPESFNPGDGPGGLPIQRTDDTQEHFPHRVS... | [
{
"source_db": "bridge",
"source_id": "79728",
"text": "PALB2 GENE_ENCODES_PROTEIN PALB2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "PALB2 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "PALB2",
"interaction_partner": "BRCA1",
"affected_target": "head and neck carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670797 |
co_coun_00145 | counterfactual | coding_variant | hard | 4 | If ESR1 were knocked out, its physical interaction with KMT2D would be lost. Which disease association of KMT2D could therefore be indirectly affected? | ESR1 GENE_ENCODES_PROTEIN ESR1 -> ESR1 PROTEIN_PHYSICALLY_INTERACTS_WITH KMT2D -> KMT2D GENE_ENCODES_PROTEIN KMT2D -> KMT2D GENE_ASSOCIATED_WITH_DISEASE choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "ESR1",
"source_node_type": "GENE",
"source_node_label": "ESR1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2099",... | choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ESR1",
"source_db": "UniProt",
"payload": {
"accession": "P03372",
"sequence": "MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANAQVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLEN... | [
{
"source_db": "bridge",
"source_id": "2099",
"text": "ESR1 GENE_ENCODES_PROTEIN ESR1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "8085",
"text": "ESR1 PROTEIN_PHYSICALLY_INTERACTS_WITH KMT2D",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"knocked_out_gene": "ESR1",
"interaction_partner": "KMT2D",
"affected_target": "choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00146 | counterfactual | coding_variant | hard | 4 | If BIN1 were knocked out, its physical interaction with MYC would be lost. Which disease association of MYC could therefore be indirectly affected? | BIN1 GENE_ENCODES_PROTEIN BIN1 -> BIN1 PROTEIN_PHYSICALLY_INTERACTS_WITH MYC -> MYC GENE_ENCODES_PROTEIN MYC -> MYC GENE_ASSOCIATED_WITH_DISEASE colon adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "BIN1",
"source_node_type": "GENE",
"source_node_label": "BIN1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "274",
... | colon adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BIN1",
"source_db": "UniProt",
"payload": {
"accession": "O00499",
"sequence": "MAEMGSKGVTAGKIASNVQKKLTRAQEKVLQKLGKADETKDEQFEQCVQNFNKQLTEGTRLQKDLRTYLASVKAMHEASKKLNECLQEVYEPDWPGRDEANKIAENNDLLWMDYHQKLVDQALLTMDTYLGQFP... | [
{
"source_db": "bridge",
"source_id": "274",
"text": "BIN1 GENE_ENCODES_PROTEIN BIN1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4609",
"text": "BIN1 PROTEIN_PHYSICALLY_INTERACTS_WITH MYC",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "BIN1",
"interaction_partner": "MYC",
"affected_target": "colon adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.678763 |
co_coun_00147 | counterfactual | coding_variant | hard | 4 | If C9orf72 were knocked out, its physical interaction with KRAS would be lost. Which disease association of KRAS could therefore be indirectly affected? | C9orf72 GENE_ENCODES_PROTEIN C9orf72 -> C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH KRAS -> KRAS GENE_ENCODES_PROTEIN KRAS -> KRAS GENE_ASSOCIATED_WITH_DISEASE small intestine adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "C9orf72",
"source_node_type": "GENE",
"source_node_label": "C9orf72",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "... | small intestine adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "C9orf72",
"source_db": "UniProt",
"payload": {
"accession": "Q96LT7",
"sequence": "MSTLCPPPSPAVAKTEIALSGKSPLLAATFAYWDNILGPRVRHIWAPKTEQVLLSDGEITFLANHTLNGEILRNAESGAIDVKFFVLSEKGVIIVSLIFDGNWNGDRSTYGLSIILPQTELSFYLPLHRVC... | [
{
"source_db": "bridge",
"source_id": "203228",
"text": "C9orf72 GENE_ENCODES_PROTEIN C9orf72",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "3845",
"text": "C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH KRAS",
"confidence": 0.9
},
{
"source_db": "bridge",
... | {
"knocked_out_gene": "C9orf72",
"interaction_partner": "KRAS",
"affected_target": "small intestine adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.723262 |
co_coun_00148 | counterfactual | coding_variant | hard | 4 | If PGR were knocked out, its physical interaction with MAPK1 would be lost. Which disease association of MAPK1 could therefore be indirectly affected? | PGR GENE_ENCODES_PROTEIN PGR -> PGR PROTEIN_PHYSICALLY_INTERACTS_WITH MAPK1 -> MAPK1 GENE_ENCODES_PROTEIN MAPK1 -> MAPK1 GENE_ASSOCIATED_WITH_DISEASE hypertrophic cardiomyopathy | {
"steps": [
{
"hop": 1,
"source_node_id": "PGR",
"source_node_type": "GENE",
"source_node_label": "PGR",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5241",
... | hypertrophic cardiomyopathy | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PGR",
"source_db": "UniProt",
"payload": {
"accession": "P06401",
"sequence": "MTELKAKGPRAPHVAGGPPSPEVGSPLLCRPAAGPFPGSQTSDTLPEVSAIPISLDGLLFPRPCQGQDPSDEKTQDQQSLSDVEGAYSRAEATRGAGGSSSSPPEKDSGLLDSVLDTLLAPSGPGQSQPSPPACE... | [
{
"source_db": "bridge",
"source_id": "5241",
"text": "PGR GENE_ENCODES_PROTEIN PGR",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5594",
"text": "PGR PROTEIN_PHYSICALLY_INTERACTS_WITH MAPK1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "PGR",
"interaction_partner": "MAPK1",
"affected_target": "hypertrophic cardiomyopathy",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.778994 |
co_coun_00149 | counterfactual | coding_variant | hard | 4 | If CDK6 were knocked out, its physical interaction with CCND1 would be lost. Which disease association of CCND1 could therefore be indirectly affected? | CDK6 GENE_ENCODES_PROTEIN CDK6 -> CDK6 PROTEIN_PHYSICALLY_INTERACTS_WITH CCND1 -> CCND1 GENE_ENCODES_PROTEIN CCND1 -> CCND1 GENE_ASSOCIATED_WITH_DISEASE Miyoshi myopathy | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK6",
"source_node_type": "GENE",
"source_node_label": "CDK6",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1021",... | Miyoshi myopathy | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK6",
"source_db": "UniProt",
"payload": {
"accession": "Q00534",
"sequence": "MEKDGLCRADQQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVQTGEEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTVSRTDRETKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLD... | [
{
"source_db": "bridge",
"source_id": "1021",
"text": "CDK6 GENE_ENCODES_PROTEIN CDK6",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "595",
"text": "CDK6 PROTEIN_PHYSICALLY_INTERACTS_WITH CCND1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "CDK6",
"interaction_partner": "CCND1",
"affected_target": "Miyoshi myopathy",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.531567 |
co_coun_00150 | counterfactual | coding_variant | medium | 3 | If ATM were knocked out, the ATM / ATR / BARD1 / BRCA1... complex would lose one of its members, indirectly affecting BARD1, another member of the same complex. Which disease association of BARD1 could therefore be indirectly affected? | ATM PROTEIN_MEMBER_OF_COMPLEX ATM / ATR / BARD1 / BRCA1... -> BARD1 PROTEIN_MEMBER_OF_COMPLEX ATM / ATR / BARD1 / BRCA1... -> BARD1 GENE_ASSOCIATED_WITH_DISEASE BARD1-related cancer predisposition | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Comp... | BARD1-related cancer predisposition | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC6143",
"text": "ATM PROTEIN_MEMBER_OF_COMPLEX ATM / ATR / BARD1 / BRCA1...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BARD1",
"text": "BARD1 PROTEIN_MEMBER_OF_COMPLEX ATM / ATR / BARD1 / BRCA1...",
"confidence... | {
"knocked_out_gene": "ATM",
"disrupted_complex": "ATM / ATR / BARD1 / BRCA1...",
"complex_partner": "BARD1",
"affected_target": "BARD1-related cancer predisposition",
"target_kind": "disease",
"mechanism": "complex"
} | 0.868693 |
co_coun_00151 | counterfactual | coding_variant | hard | 4 | If PGR were knocked out, its physical interaction with MAPK1 would be lost. Which disease association of MAPK1 could therefore be indirectly affected? | PGR GENE_ENCODES_PROTEIN PGR -> PGR PROTEIN_PHYSICALLY_INTERACTS_WITH MAPK1 -> MAPK1 GENE_ENCODES_PROTEIN MAPK1 -> MAPK1 GENE_ASSOCIATED_WITH_DISEASE microcephaly | {
"steps": [
{
"hop": 1,
"source_node_id": "PGR",
"source_node_type": "GENE",
"source_node_label": "PGR",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5241",
... | microcephaly | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PGR",
"source_db": "UniProt",
"payload": {
"accession": "P06401",
"sequence": "MTELKAKGPRAPHVAGGPPSPEVGSPLLCRPAAGPFPGSQTSDTLPEVSAIPISLDGLLFPRPCQGQDPSDEKTQDQQSLSDVEGAYSRAEATRGAGGSSSSPPEKDSGLLDSVLDTLLAPSGPGQSQPSPPACE... | [
{
"source_db": "bridge",
"source_id": "5241",
"text": "PGR GENE_ENCODES_PROTEIN PGR",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5594",
"text": "PGR PROTEIN_PHYSICALLY_INTERACTS_WITH MAPK1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "PGR",
"interaction_partner": "MAPK1",
"affected_target": "microcephaly",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.763205 |
co_coun_00152 | counterfactual | coding_variant | hard | 4 | If ACTB were knocked out, its physical interaction with ESR1 would be lost. Which disease association of ESR1 could therefore be indirectly affected? | ACTB GENE_ENCODES_PROTEIN ACTB -> ACTB PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1 -> ESR1 GENE_ENCODES_PROTEIN ESR1 -> ESR1 GENE_ASSOCIATED_WITH_DISEASE Braxton-Hicks contractions | {
"steps": [
{
"hop": 1,
"source_node_id": "ACTB",
"source_node_type": "GENE",
"source_node_label": "ACTB",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "60",
... | Braxton-Hicks contractions | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACTB",
"source_db": "UniProt",
"payload": {
"accession": "P60709",
"sequence": "MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYV... | [
{
"source_db": "bridge",
"source_id": "60",
"text": "ACTB GENE_ENCODES_PROTEIN ACTB",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2099",
"text": "ACTB PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "ACTB",
"interaction_partner": "ESR1",
"affected_target": "Braxton-Hicks contractions",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.687281 |
co_coun_00153 | counterfactual | coding_variant | hard | 3 | If FBXO7 were knocked out, the ubiquitin ligase complex complex would lose one of its members, indirectly affecting BARD1, another member of the same complex. Which disease association of BARD1 could therefore be indirectly affected? | FBXO7 PROTEIN_MEMBER_OF_COMPLEX ubiquitin ligase complex -> BARD1 PROTEIN_MEMBER_OF_COMPLEX ubiquitin ligase complex -> BARD1 GENE_ASSOCIATED_WITH_DISEASE rectum adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "FBXO7",
"source_node_type": "GENE",
"source_node_label": "FBXO7",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | rectum adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FBXO7",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y3I1",
"sequence": "MRLRVRLLKRTWPLEVPETEPTLGHLRSHLRQSLLCTWGYSSNTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPAPNIPSSTDSEHSSLQNNEQPSLATSSNQTSMQDEQPSDSFQGQAAQSGV... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC933",
"text": "FBXO7 PROTEIN_MEMBER_OF_COMPLEX ubiquitin ligase complex",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BARD1",
"text": "BARD1 PROTEIN_MEMBER_OF_COMPLEX ubiquitin ligase complex",
"confidence": 1
... | {
"knocked_out_gene": "FBXO7",
"disrupted_complex": "ubiquitin ligase complex",
"complex_partner": "BARD1",
"affected_target": "rectum adenocarcinoma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.652013 |
co_coun_00154 | counterfactual | coding_variant | hard | 3 | If BRCA1 were knocked out, the BRCA1-cABL complex complex would lose one of its members, indirectly affecting ABL1, another member of the same complex. Which disease association of ABL1 could therefore be indirectly affected? | BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-cABL complex -> ABL1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-cABL complex -> ABL1 GENE_ASSOCIATED_WITH_DISEASE dermatofibrosarcoma protuberans | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA1",
"source_node_type": "GENE",
"source_node_label": "BRCA1",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | dermatofibrosarcoma protuberans | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "OmniPath",
"source_id": "CORUM:2811",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-cABL complex",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "ABL1",
"text": "ABL1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-cABL complex",
"confidence": 1
},
{
"source... | {
"knocked_out_gene": "BRCA1",
"disrupted_complex": "BRCA1-cABL complex",
"complex_partner": "ABL1",
"affected_target": "dermatofibrosarcoma protuberans",
"target_kind": "disease",
"mechanism": "complex"
} | 0.826062 |
co_coun_00155 | counterfactual | coding_variant | hard | 3 | If FBXO7 were knocked out, the ubiquitin ligase complex complex would lose one of its members, indirectly affecting BARD1, another member of the same complex. Which disease association of BARD1 could therefore be indirectly affected? | FBXO7 PROTEIN_MEMBER_OF_COMPLEX ubiquitin ligase complex -> BARD1 PROTEIN_MEMBER_OF_COMPLEX ubiquitin ligase complex -> BARD1 GENE_ASSOCIATED_WITH_DISEASE head and neck squamous cell carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "FBXO7",
"source_node_type": "GENE",
"source_node_label": "FBXO7",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | head and neck squamous cell carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FBXO7",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y3I1",
"sequence": "MRLRVRLLKRTWPLEVPETEPTLGHLRSHLRQSLLCTWGYSSNTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPAPNIPSSTDSEHSSLQNNEQPSLATSSNQTSMQDEQPSDSFQGQAAQSGV... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC933",
"text": "FBXO7 PROTEIN_MEMBER_OF_COMPLEX ubiquitin ligase complex",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BARD1",
"text": "BARD1 PROTEIN_MEMBER_OF_COMPLEX ubiquitin ligase complex",
"confidence": 1
... | {
"knocked_out_gene": "FBXO7",
"disrupted_complex": "ubiquitin ligase complex",
"complex_partner": "BARD1",
"affected_target": "head and neck squamous cell carcinoma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.65418 |
co_coun_00156 | counterfactual | coding_variant | medium | 3 | If BLM were knocked out, the BLM / BRCA1 / CDK1 / EXO1... complex would lose one of its members, indirectly affecting CDK1, another member of the same complex. Which pathway of CDK1 could therefore be indirectly affected? | BLM PROTEIN_MEMBER_OF_COMPLEX BLM / BRCA1 / CDK1 / EXO1... -> CDK1 PROTEIN_MEMBER_OF_COMPLEX BLM / BRCA1 / CDK1 / EXO1... -> CDK1 GENE_PARTICIPATES_IN_PATHWAY Phosphorylation of Emi1 | {
"steps": [
{
"hop": 1,
"source_node_id": "BLM",
"source_node_type": "GENE",
"source_node_label": "BLM",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Comp... | Phosphorylation of Emi1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BLM",
"source_db": "UniProt",
"payload": {
"accession": "P54132",
"sequence": "MAAVPQNNLQEQLERHSARTLNNKLSLSKPKFSGFTFKKKTSSDNNVSVTNVSVAKTPVLRNKDVNVTEDFSFSEPLPNTTNQQRVKDFFKNAPAGQETQRGGSKSLLPDFLQTPKEVVCTTQNTPTVKKSRDTA... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC9341",
"text": "BLM PROTEIN_MEMBER_OF_COMPLEX BLM / BRCA1 / CDK1 / EXO1...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "CDK1",
"text": "CDK1 PROTEIN_MEMBER_OF_COMPLEX BLM / BRCA1 / CDK1 / EXO1...",
"confidence":... | {
"knocked_out_gene": "BLM",
"disrupted_complex": "BLM / BRCA1 / CDK1 / EXO1...",
"complex_partner": "CDK1",
"affected_target": "Phosphorylation of Emi1",
"target_kind": "pathway",
"mechanism": "complex"
} | 1 |
co_coun_00157 | counterfactual | coding_variant | hard | 3 | If ATM were knocked out, the BASC complex (BRCA1-associated genome surveillance complex) complex would lose one of its members, indirectly affecting BLM, another member of the same complex. Which disease association of BLM could therefore be indirectly affected? | ATM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> BLM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> BLM GENE_ASSOCIATED_WITH_DISEASE hereditary cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "CORU... | hereditary cancer | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "OmniPath",
"source_id": "CORUM:433",
"text": "ATM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex)",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BLM",
"text": "BLM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-assoc... | {
"knocked_out_gene": "ATM",
"disrupted_complex": "BASC complex (BRCA1-associated genome surveillance complex)",
"complex_partner": "BLM",
"affected_target": "hereditary cancer",
"target_kind": "disease",
"mechanism": "complex"
} | 0.554704 |
co_coun_00158 | counterfactual | coding_variant | hard | 4 | If AR were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | AR GENE_ENCODES_PROTEIN AR -> AR PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE invasive ductal breast carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "AR",
"source_node_type": "GENE",
"source_node_label": "AR",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "367",
... | invasive ductal breast carcinoma | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AR",
"source_db": "UniProt",
"payload": {
"accession": "P10275",
"sequence": "MEVQLGLGRVYPRPPSKTYRGAFQNLFQSVREVIQNPGPRHPEAASAAPPGASLLLLQQQQQQQQQQQQQQQQQQQQQQQETSPRQQQQQQGEDGSPQAHRRGPTGYLVLDEEQQPSQPQSALECHPERGCVPEPG... | [
{
"source_db": "bridge",
"source_id": "367",
"text": "AR GENE_ENCODES_PROTEIN AR",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "AR PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "BRCA... | {
"knocked_out_gene": "AR",
"interaction_partner": "BRCA1",
"affected_target": "invasive ductal breast carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.748463 |
co_coun_00159 | counterfactual | coding_variant | hard | 4 | If CREBBP were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | CREBBP GENE_ENCODES_PROTEIN CREBBP -> CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE Malignant Neoplasms | {
"steps": [
{
"hop": 1,
"source_node_id": "CREBBP",
"source_node_type": "GENE",
"source_node_label": "CREBBP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "13... | Malignant Neoplasms | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CREBBP",
"source_db": "UniProt",
"payload": {
"accession": "Q92793",
"sequence": "MAENLLDGPPNPKRAKLSSPGFSANDSTDFGSLFDLENDLPDELIPNGGELGLLNSGNLVPDAASKHKQLSELLRGGSGSSINPGIGNVSASSPVQQGLGGQAQGQPNSANMASLSAMGKSPLSQGDSSAPS... | [
{
"source_db": "bridge",
"source_id": "1387",
"text": "CREBBP GENE_ENCODES_PROTEIN CREBBP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "CREBBP",
"interaction_partner": "BRCA1",
"affected_target": "Malignant Neoplasms",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.845194 |
co_coun_00160 | counterfactual | coding_variant | hard | 4 | If SNCA were knocked out, its physical interaction with MAPT would be lost. Which disease association of MAPT could therefore be indirectly affected? | SNCA GENE_ENCODES_PROTEIN SNCA -> SNCA PROTEIN_PHYSICALLY_INTERACTS_WITH MAPT -> MAPT GENE_ENCODES_PROTEIN MAPT -> MAPT GENE_ASSOCIATED_WITH_DISEASE ovarian carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "SNCA",
"source_node_type": "GENE",
"source_node_label": "SNCA",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "6622",... | ovarian carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SNCA",
"source_db": "UniProt",
"payload": {
"accession": "P37840",
"sequence": "MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKNEEGAPQEGILEDMPVDPDNEAYEMPSEEGYQ... | [
{
"source_db": "bridge",
"source_id": "6622",
"text": "SNCA GENE_ENCODES_PROTEIN SNCA",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4137",
"text": "SNCA PROTEIN_PHYSICALLY_INTERACTS_WITH MAPT",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "SNCA",
"interaction_partner": "MAPT",
"affected_target": "ovarian carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.652042 |
co_coun_00161 | counterfactual | coding_variant | hard | 3 | If MLH1 were knocked out, the BASC complex (BRCA1-associated genome surveillance complex) complex would lose one of its members, indirectly affecting BRCA1, another member of the same complex. Which disease association of BRCA1 could therefore be indirectly affected? | MLH1 PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> BRCA1 PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE Hematologic Neoplasms | {
"steps": [
{
"hop": 1,
"source_node_id": "MLH1",
"source_node_type": "GENE",
"source_node_label": "MLH1",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "CO... | Hematologic Neoplasms | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "OmniPath",
"source_id": "CORUM:433",
"text": "MLH1 PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex)",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-... | {
"knocked_out_gene": "MLH1",
"disrupted_complex": "BASC complex (BRCA1-associated genome surveillance complex)",
"complex_partner": "BRCA1",
"affected_target": "Hematologic Neoplasms",
"target_kind": "disease",
"mechanism": "complex"
} | 0.67679 |
co_coun_00162 | counterfactual | coding_variant | hard | 4 | If CD44 were knocked out, its physical interaction with ERBB4 would be lost. Which disease association of ERBB4 could therefore be indirectly affected? | CD44 GENE_ENCODES_PROTEIN CD44 -> CD44 PROTEIN_PHYSICALLY_INTERACTS_WITH ERBB4 -> ERBB4 GENE_ENCODES_PROTEIN ERBB4 -> ERBB4 GENE_ASSOCIATED_WITH_DISEASE combined hepatocellular carcinoma and cholangiocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CD44",
"source_node_type": "GENE",
"source_node_label": "CD44",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "960",
... | combined hepatocellular carcinoma and cholangiocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD44",
"source_db": "UniProt",
"payload": {
"accession": "P16070",
"sequence": "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTD... | [
{
"source_db": "bridge",
"source_id": "960",
"text": "CD44 GENE_ENCODES_PROTEIN CD44",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2066",
"text": "CD44 PROTEIN_PHYSICALLY_INTERACTS_WITH ERBB4",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "CD44",
"interaction_partner": "ERBB4",
"affected_target": "combined hepatocellular carcinoma and cholangiocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00163 | counterfactual | coding_variant | hard | 3 | If MYC were knocked out, the ACTL6A / ARID1A / ARID1B / ARID2... complex would lose one of its members, indirectly affecting BRCA1, another member of the same complex. Which disease association of BRCA1 could therefore be indirectly affected? | MYC PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2... -> BRCA1 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2... -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE ovarian serous surface papillary adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "MYC",
"source_node_type": "GENE",
"source_node_label": "MYC",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Comp... | ovarian serous surface papillary adenocarcinoma | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MYC",
"source_db": "UniProt",
"payload": {
"accession": "P01106",
"sequence": "MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC5233",
"text": "MYC PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2...",
... | {
"knocked_out_gene": "MYC",
"disrupted_complex": "ACTL6A / ARID1A / ARID1B / ARID2...",
"complex_partner": "BRCA1",
"affected_target": "ovarian serous surface papillary adenocarcinoma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.692868 |
co_coun_00164 | counterfactual | coding_variant | hard | 4 | If CDK6 were knocked out, its physical interaction with CDKN2A would be lost. Which disease association of CDKN2A could therefore be indirectly affected? | CDK6 GENE_ENCODES_PROTEIN CDK6 -> CDK6 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN2A -> CDKN2A GENE_ENCODES_PROTEIN CDKN2A -> CDKN2A GENE_ASSOCIATED_WITH_DISEASE Richter transformation | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK6",
"source_node_type": "GENE",
"source_node_label": "CDK6",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1021",... | Richter transformation | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK6",
"source_db": "UniProt",
"payload": {
"accession": "Q00534",
"sequence": "MEKDGLCRADQQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVQTGEEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTVSRTDRETKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLD... | [
{
"source_db": "bridge",
"source_id": "1021",
"text": "CDK6 GENE_ENCODES_PROTEIN CDK6",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1029",
"text": "CDK6 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN2A",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "CDK6",
"interaction_partner": "CDKN2A",
"affected_target": "Richter transformation",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.672046 |
co_coun_00165 | counterfactual | coding_variant | hard | 4 | If BRCA1 were knocked out, its physical interaction with JAK2 would be lost. Which pathway of JAK2 could therefore be indirectly affected? | BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2 -> JAK2 GENE_ENCODES_PROTEIN JAK2 -> JAK2 GENE_PARTICIPATES_IN_PATHWAY Signaling by Erythropoietin | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA1",
"source_node_type": "GENE",
"source_node_label": "BRCA1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "672"... | Signaling by Erythropoietin | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "bridge",
"source_id": "672",
"text": "BRCA1 GENE_ENCODES_PROTEIN BRCA1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "3717",
"text": "BRCA1 PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "BRCA1",
"interaction_partner": "JAK2",
"affected_target": "Signaling by Erythropoietin",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00166 | counterfactual | coding_variant | hard | 4 | If ALK were knocked out, its physical interaction with JAK2 would be lost. Which disease association of JAK2 could therefore be indirectly affected? | ALK GENE_ENCODES_PROTEIN ALK -> ALK PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2 -> JAK2 GENE_ENCODES_PROTEIN JAK2 -> JAK2 GENE_ASSOCIATED_WITH_DISEASE skin infection | {
"steps": [
{
"hop": 1,
"source_node_id": "ALK",
"source_node_type": "GENE",
"source_node_label": "ALK",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "238",
... | skin infection | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ALK",
"source_db": "UniProt",
"payload": {
"accession": "Q9UM73",
"sequence": "MGAIGLLWLLPLLLSTAAVGSGMGTGQRAGSPAAGPPLQPREPLSYSRLQRKSLAVDFVVPSLFRVYARDLLLPPSSSELKAGRPEARGSLALDCAPLLRLLGPAPGVSWTAGSPAPAEARTLSRVLKGGSVRKL... | [
{
"source_db": "bridge",
"source_id": "238",
"text": "ALK GENE_ENCODES_PROTEIN ALK",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "3717",
"text": "ALK PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "J... | {
"knocked_out_gene": "ALK",
"interaction_partner": "JAK2",
"affected_target": "skin infection",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.693803 |
co_coun_00167 | counterfactual | coding_variant | hard | 4 | If TP53 were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE extramammary Paget disease | {
"steps": [
{
"hop": 1,
"source_node_id": "TP53",
"source_node_type": "GENE",
"source_node_label": "TP53",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "7157",... | extramammary Paget disease | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "bridge",
"source_id": "7157",
"text": "TP53 GENE_ENCODES_PROTEIN TP53",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "TP53",
"interaction_partner": "BRCA1",
"affected_target": "extramammary Paget disease",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00168 | counterfactual | coding_variant | hard | 4 | If BLM were knocked out, its physical interaction with MYC would be lost. Which disease association of MYC could therefore be indirectly affected? | BLM GENE_ENCODES_PROTEIN BLM -> BLM PROTEIN_PHYSICALLY_INTERACTS_WITH MYC -> MYC GENE_ENCODES_PROTEIN MYC -> MYC GENE_ASSOCIATED_WITH_DISEASE adrenal cortex carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "BLM",
"source_node_type": "GENE",
"source_node_label": "BLM",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "641",
... | adrenal cortex carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BLM",
"source_db": "UniProt",
"payload": {
"accession": "P54132",
"sequence": "MAAVPQNNLQEQLERHSARTLNNKLSLSKPKFSGFTFKKKTSSDNNVSVTNVSVAKTPVLRNKDVNVTEDFSFSEPLPNTTNQQRVKDFFKNAPAGQETQRGGSKSLLPDFLQTPKEVVCTTQNTPTVKKSRDTA... | [
{
"source_db": "bridge",
"source_id": "641",
"text": "BLM GENE_ENCODES_PROTEIN BLM",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4609",
"text": "BLM PROTEIN_PHYSICALLY_INTERACTS_WITH MYC",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "MY... | {
"knocked_out_gene": "BLM",
"interaction_partner": "MYC",
"affected_target": "adrenal cortex carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.618844 |
co_coun_00169 | counterfactual | coding_variant | hard | 4 | If ACTB were knocked out, its physical interaction with ERBB2 would be lost. Which disease association of ERBB2 could therefore be indirectly affected? | ACTB GENE_ENCODES_PROTEIN ACTB -> ACTB PROTEIN_PHYSICALLY_INTERACTS_WITH ERBB2 -> ERBB2 GENE_ENCODES_PROTEIN ERBB2 -> ERBB2 GENE_ASSOCIATED_WITH_DISEASE breast adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "ACTB",
"source_node_type": "GENE",
"source_node_label": "ACTB",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "60",
... | breast adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACTB",
"source_db": "UniProt",
"payload": {
"accession": "P60709",
"sequence": "MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYV... | [
{
"source_db": "bridge",
"source_id": "60",
"text": "ACTB GENE_ENCODES_PROTEIN ACTB",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2064",
"text": "ACTB PROTEIN_PHYSICALLY_INTERACTS_WITH ERBB2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "ACTB",
"interaction_partner": "ERBB2",
"affected_target": "breast adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.811268 |
co_coun_00170 | counterfactual | coding_variant | hard | 4 | If CBL were knocked out, its physical interaction with CTNNB1 would be lost. Which pathway of CTNNB1 could therefore be indirectly affected? | CBL GENE_ENCODES_PROTEIN CBL -> CBL PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1 -> CTNNB1 GENE_ENCODES_PROTEIN CTNNB1 -> CTNNB1 GENE_PARTICIPATES_IN_PATHWAY Formation of definitive endoderm | {
"steps": [
{
"hop": 1,
"source_node_id": "CBL",
"source_node_type": "GENE",
"source_node_label": "CBL",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "867",
... | Formation of definitive endoderm | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CBL",
"source_db": "UniProt",
"payload": {
"accession": "P22681",
"sequence": "MAGNVKKSSGAGGGSGSGGSGSGGLIGLMKDAFQPHHHHHHHLSPHPPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKE... | [
{
"source_db": "bridge",
"source_id": "867",
"text": "CBL GENE_ENCODES_PROTEIN CBL",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1499",
"text": "CBL PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "CBL",
"interaction_partner": "CTNNB1",
"affected_target": "Formation of definitive endoderm",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00171 | counterfactual | coding_variant | hard | 4 | If AFP were knocked out, its physical interaction with PTEN would be lost. Which disease association of PTEN could therefore be indirectly affected? | AFP GENE_ENCODES_PROTEIN AFP -> AFP PROTEIN_PHYSICALLY_INTERACTS_WITH PTEN -> PTEN GENE_ENCODES_PROTEIN PTEN -> PTEN GENE_ASSOCIATED_WITH_DISEASE Macrocephaly/autism syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "AFP",
"source_node_type": "GENE",
"source_node_label": "AFP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "174",
... | Macrocephaly/autism syndrome | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AFP",
"source_db": "UniProt",
"payload": {
"accession": "P02771",
"sequence": "MKWVESIFLIFLLNFTESRTLHRNEYGIASILDSYQCTAEISLADLATIFFAQFVQEATYKEVSKMVKDALTAIEKPTGDEQSSGCLENQLPAFLEELCHEKEILEKYGHSDCCSQSEEGRHNCFLAHKKPTPAS... | [
{
"source_db": "bridge",
"source_id": "174",
"text": "AFP GENE_ENCODES_PROTEIN AFP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5728",
"text": "AFP PROTEIN_PHYSICALLY_INTERACTS_WITH PTEN",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "P... | {
"knocked_out_gene": "AFP",
"interaction_partner": "PTEN",
"affected_target": "Macrocephaly/autism syndrome",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00172 | counterfactual | coding_variant | hard | 4 | If BCL2 were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | BCL2 GENE_ENCODES_PROTEIN BCL2 -> BCL2 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE acute myeloid leukemia | {
"steps": [
{
"hop": 1,
"source_node_id": "BCL2",
"source_node_type": "GENE",
"source_node_label": "BCL2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "596",
... | acute myeloid leukemia | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BCL2",
"source_db": "UniProt",
"payload": {
"accession": "P10415",
"sequence": "MAHAGRTGYDNREIVMKYIHYKLSQRGYEWDAGDVGAAPPGAAPAPGIFSSQPGHTPHPAASRDPVARTSPLQTPAAPGAAAGPALSPVPPVVHLTLRQAGDDFSRRYRRDFAEMSSQLHLTPFTARGRFATVV... | [
{
"source_db": "bridge",
"source_id": "596",
"text": "BCL2 GENE_ENCODES_PROTEIN BCL2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "BCL2 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "BCL2",
"interaction_partner": "BRCA1",
"affected_target": "acute myeloid leukemia",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.685056 |
co_coun_00173 | counterfactual | coding_variant | hard | 4 | If BRCA2 were knocked out, its physical interaction with BCL2 would be lost. Which disease association of BCL2 could therefore be indirectly affected? | BRCA2 GENE_ENCODES_PROTEIN BRCA2 -> BRCA2 PROTEIN_PHYSICALLY_INTERACTS_WITH BCL2 -> BCL2 GENE_ENCODES_PROTEIN BCL2 -> BCL2 GENE_ASSOCIATED_WITH_DISEASE Genu varum | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA2",
"source_node_type": "GENE",
"source_node_label": "BRCA2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "675"... | Genu varum | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA2",
"source_db": "UniProt",
"payload": {
"accession": "P51587",
"sequence": "MPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPYNSEPAEESEHKNNNYEPNLFKTPQRKPSYNQLASTPIIFKEQGLTLPLYQSPVKELDKFKLDLGRNVPNSRHKSLRTVKTKMDQADDVSCP... | [
{
"source_db": "bridge",
"source_id": "675",
"text": "BRCA2 GENE_ENCODES_PROTEIN BRCA2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "596",
"text": "BRCA2 PROTEIN_PHYSICALLY_INTERACTS_WITH BCL2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"knocked_out_gene": "BRCA2",
"interaction_partner": "BCL2",
"affected_target": "Genu varum",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.658605 |
co_coun_00174 | counterfactual | coding_variant | hard | 4 | If ALK were knocked out, its physical interaction with JAK2 would be lost. Which disease association of JAK2 could therefore be indirectly affected? | ALK GENE_ENCODES_PROTEIN ALK -> ALK PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2 -> JAK2 GENE_ENCODES_PROTEIN JAK2 -> JAK2 GENE_ASSOCIATED_WITH_DISEASE CD4+/CD56+ hematodermic neoplasm | {
"steps": [
{
"hop": 1,
"source_node_id": "ALK",
"source_node_type": "GENE",
"source_node_label": "ALK",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "238",
... | CD4+/CD56+ hematodermic neoplasm | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ALK",
"source_db": "UniProt",
"payload": {
"accession": "Q9UM73",
"sequence": "MGAIGLLWLLPLLLSTAAVGSGMGTGQRAGSPAAGPPLQPREPLSYSRLQRKSLAVDFVVPSLFRVYARDLLLPPSSSELKAGRPEARGSLALDCAPLLRLLGPAPGVSWTAGSPAPAEARTLSRVLKGGSVRKL... | [
{
"source_db": "bridge",
"source_id": "238",
"text": "ALK GENE_ENCODES_PROTEIN ALK",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "3717",
"text": "ALK PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "J... | {
"knocked_out_gene": "ALK",
"interaction_partner": "JAK2",
"affected_target": "CD4+/CD56+ hematodermic neoplasm",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670909 |
co_coun_00175 | counterfactual | coding_variant | hard | 4 | If CDK1 were knocked out, its physical interaction with BARD1 would be lost. Which disease association of BARD1 could therefore be indirectly affected? | CDK1 GENE_ENCODES_PROTEIN CDK1 -> CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH BARD1 -> BARD1 GENE_ENCODES_PROTEIN BARD1 -> BARD1 GENE_ASSOCIATED_WITH_DISEASE acinar lung adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK1",
"source_node_type": "GENE",
"source_node_label": "CDK1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "983",
... | acinar lung adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK1",
"source_db": "UniProt",
"payload": {
"accession": "P06493",
"sequence": "MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNL... | [
{
"source_db": "bridge",
"source_id": "983",
"text": "CDK1 GENE_ENCODES_PROTEIN CDK1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "580",
"text": "CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH BARD1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "CDK1",
"interaction_partner": "BARD1",
"affected_target": "acinar lung adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.605831 |
co_coun_00176 | counterfactual | coding_variant | medium | 3 | If ESR1 were knocked out, the ACTL6A / ARID1A / ARID1B / ARID2... complex would lose one of its members, indirectly affecting TP53, another member of the same complex. Which pathway of TP53 could therefore be indirectly affected? | ESR1 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2... -> TP53 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2... -> TP53 GENE_PARTICIPATES_IN_PATHWAY Oncogene Induced Senescence | {
"steps": [
{
"hop": 1,
"source_node_id": "ESR1",
"source_node_type": "GENE",
"source_node_label": "ESR1",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Co... | Oncogene Induced Senescence | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ESR1",
"source_db": "UniProt",
"payload": {
"accession": "P03372",
"sequence": "MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANAQVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLEN... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC5233",
"text": "ESR1 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "TP53",
"text": "TP53 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2...",
... | {
"knocked_out_gene": "ESR1",
"disrupted_complex": "ACTL6A / ARID1A / ARID1B / ARID2...",
"complex_partner": "TP53",
"affected_target": "Oncogene Induced Senescence",
"target_kind": "pathway",
"mechanism": "complex"
} | 1 |
co_coun_00177 | counterfactual | coding_variant | hard | 4 | If APC were knocked out, its physical interaction with CTNNB1 would be lost. Which disease association of CTNNB1 could therefore be indirectly affected? | APC GENE_ENCODES_PROTEIN APC -> APC PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1 -> CTNNB1 GENE_ENCODES_PROTEIN CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE prostate cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "324",
... | prostate cancer | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APC",
"source_db": "UniProt",
"payload": {
"accession": "P25054",
"sequence": "MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLE... | [
{
"source_db": "bridge",
"source_id": "324",
"text": "APC GENE_ENCODES_PROTEIN APC",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1499",
"text": "APC PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "APC",
"interaction_partner": "CTNNB1",
"affected_target": "prostate cancer",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.734847 |
co_coun_00178 | counterfactual | coding_variant | hard | 4 | If VCP were knocked out, its physical interaction with PARK7 would be lost. Which disease association of PARK7 could therefore be indirectly affected? | VCP GENE_ENCODES_PROTEIN VCP -> VCP PROTEIN_PHYSICALLY_INTERACTS_WITH PARK7 -> PARK7 GENE_ENCODES_PROTEIN PARK7 -> PARK7 GENE_ASSOCIATED_WITH_DISEASE amyotrophic lateral sclerosis-parkinsonism-dementia complex | {
"steps": [
{
"hop": 1,
"source_node_id": "VCP",
"source_node_type": "GENE",
"source_node_label": "VCP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "7415",
... | amyotrophic lateral sclerosis-parkinsonism-dementia complex | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "VCP",
"source_db": "UniProt",
"payload": {
"accession": "P55072",
"sequence": "MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYL... | [
{
"source_db": "bridge",
"source_id": "7415",
"text": "VCP GENE_ENCODES_PROTEIN VCP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "11315",
"text": "VCP PROTEIN_PHYSICALLY_INTERACTS_WITH PARK7",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "VCP",
"interaction_partner": "PARK7",
"affected_target": "amyotrophic lateral sclerosis-parkinsonism-dementia complex",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.705596 |
co_coun_00179 | counterfactual | coding_variant | hard | 4 | If RET were knocked out, its physical interaction with EGFR would be lost. Which disease association of EGFR could therefore be indirectly affected? | RET GENE_ENCODES_PROTEIN RET -> RET PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_ASSOCIATED_WITH_DISEASE salivary gland cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "RET",
"source_node_type": "GENE",
"source_node_label": "RET",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5979",
... | salivary gland cancer | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RET",
"source_db": "UniProt",
"payload": {
"accession": "P07949",
"sequence": "MAKATSGAAGLRLLLLLLLPLLGKVALGLYFSRDAYWEKLYVDQAAGTPLLYVHALRDAPEEVPSFRLGQHLYGTYRTRLHENNWICIQEDTGLLYLNRSLDHSSWEKLSVRNRGFPLLTVYLKVFLSPTSLREG... | [
{
"source_db": "bridge",
"source_id": "5979",
"text": "RET GENE_ENCODES_PROTEIN RET",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "RET PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "... | {
"knocked_out_gene": "RET",
"interaction_partner": "EGFR",
"affected_target": "salivary gland cancer",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00180 | counterfactual | coding_variant | hard | 4 | If VCP were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | VCP GENE_ENCODES_PROTEIN VCP -> VCP PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE intellectual disability | {
"steps": [
{
"hop": 1,
"source_node_id": "VCP",
"source_node_type": "GENE",
"source_node_label": "VCP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "7415",
... | intellectual disability | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "VCP",
"source_db": "UniProt",
"payload": {
"accession": "P55072",
"sequence": "MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYL... | [
{
"source_db": "bridge",
"source_id": "7415",
"text": "VCP GENE_ENCODES_PROTEIN VCP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "VCP PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "... | {
"knocked_out_gene": "VCP",
"interaction_partner": "BRCA1",
"affected_target": "intellectual disability",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.721803 |
co_coun_00181 | counterfactual | coding_variant | hard | 3 | If ESR1 were knocked out, the ACTL6A / ARID1A / ARID1B / ARID2... complex would lose one of its members, indirectly affecting BRCA1, another member of the same complex. Which disease association of BRCA1 could therefore be indirectly affected? | ESR1 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2... -> BRCA1 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2... -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE Mental Depression | {
"steps": [
{
"hop": 1,
"source_node_id": "ESR1",
"source_node_type": "GENE",
"source_node_label": "ESR1",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Co... | Mental Depression | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ESR1",
"source_db": "UniProt",
"payload": {
"accession": "P03372",
"sequence": "MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANAQVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLEN... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC5233",
"text": "ESR1 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2...",
... | {
"knocked_out_gene": "ESR1",
"disrupted_complex": "ACTL6A / ARID1A / ARID1B / ARID2...",
"complex_partner": "BRCA1",
"affected_target": "Mental Depression",
"target_kind": "disease",
"mechanism": "complex"
} | 0.697953 |
co_coun_00182 | counterfactual | coding_variant | hard | 4 | If BRAF were knocked out, its physical interaction with AKT1 would be lost. Which pathway of AKT1 could therefore be indirectly affected? | BRAF GENE_ENCODES_PROTEIN BRAF -> BRAF PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1 -> AKT1 GENE_ENCODES_PROTEIN AKT1 -> AKT1 GENE_PARTICIPATES_IN_PATHWAY KSRP (KHSRP) binds and destabilizes mRNA | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "673",
... | KSRP (KHSRP) binds and destabilizes mRNA | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRAF",
"source_db": "UniProt",
"payload": {
"accession": "P15056",
"sequence": "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEHIEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTVTSSSSSSLSVLPSS... | [
{
"source_db": "bridge",
"source_id": "673",
"text": "BRAF GENE_ENCODES_PROTEIN BRAF",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "207",
"text": "BRAF PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "BRAF",
"interaction_partner": "AKT1",
"affected_target": "KSRP (KHSRP) binds and destabilizes mRNA",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00183 | counterfactual | coding_variant | hard | 4 | If BRCA1 were knocked out, its physical interaction with JAK2 would be lost. Which disease association of JAK2 could therefore be indirectly affected? | BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2 -> JAK2 GENE_ENCODES_PROTEIN JAK2 -> JAK2 GENE_ASSOCIATED_WITH_DISEASE gout | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA1",
"source_node_type": "GENE",
"source_node_label": "BRCA1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "672"... | gout | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "bridge",
"source_id": "672",
"text": "BRCA1 GENE_ENCODES_PROTEIN BRCA1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "3717",
"text": "BRCA1 PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "BRCA1",
"interaction_partner": "JAK2",
"affected_target": "gout",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.705222 |
co_coun_00184 | counterfactual | coding_variant | hard | 4 | If RXRA were knocked out, its physical interaction with ESR1 would be lost. Which disease association of ESR1 could therefore be indirectly affected? | RXRA GENE_ENCODES_PROTEIN RXRA -> RXRA PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1 -> ESR1 GENE_ENCODES_PROTEIN ESR1 -> ESR1 GENE_ASSOCIATED_WITH_DISEASE uterine carcinosarcoma | {
"steps": [
{
"hop": 1,
"source_node_id": "RXRA",
"source_node_type": "GENE",
"source_node_label": "RXRA",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "6256",... | uterine carcinosarcoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RXRA",
"source_db": "UniProt",
"payload": {
"accession": "P19793",
"sequence": "MDTKHFLPLDFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMASFTKHI... | [
{
"source_db": "bridge",
"source_id": "6256",
"text": "RXRA GENE_ENCODES_PROTEIN RXRA",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2099",
"text": "RXRA PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "RXRA",
"interaction_partner": "ESR1",
"affected_target": "uterine carcinosarcoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.722524 |
co_coun_00185 | counterfactual | coding_variant | hard | 4 | If MAPK1 were knocked out, its physical interaction with SNCA would be lost. Which disease association of SNCA could therefore be indirectly affected? | MAPK1 GENE_ENCODES_PROTEIN MAPK1 -> MAPK1 PROTEIN_PHYSICALLY_INTERACTS_WITH SNCA -> SNCA GENE_ENCODES_PROTEIN SNCA -> SNCA GENE_ASSOCIATED_WITH_DISEASE Alzheimer disease | {
"steps": [
{
"hop": 1,
"source_node_id": "MAPK1",
"source_node_type": "GENE",
"source_node_label": "MAPK1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5594... | Alzheimer disease | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MAPK1",
"source_db": "UniProt",
"payload": {
"accession": "P28482",
"sequence": "MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQI... | [
{
"source_db": "bridge",
"source_id": "5594",
"text": "MAPK1 GENE_ENCODES_PROTEIN MAPK1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "6622",
"text": "MAPK1 PROTEIN_PHYSICALLY_INTERACTS_WITH SNCA",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "MAPK1",
"interaction_partner": "SNCA",
"affected_target": "Alzheimer disease",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.533233 |
co_coun_00186 | counterfactual | coding_variant | hard | 4 | If AR were knocked out, its physical interaction with CCND1 would be lost. Which disease association of CCND1 could therefore be indirectly affected? | AR GENE_ENCODES_PROTEIN AR -> AR PROTEIN_PHYSICALLY_INTERACTS_WITH CCND1 -> CCND1 GENE_ENCODES_PROTEIN CCND1 -> CCND1 GENE_ASSOCIATED_WITH_DISEASE cataract | {
"steps": [
{
"hop": 1,
"source_node_id": "AR",
"source_node_type": "GENE",
"source_node_label": "AR",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "367",
... | cataract | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AR",
"source_db": "UniProt",
"payload": {
"accession": "P10275",
"sequence": "MEVQLGLGRVYPRPPSKTYRGAFQNLFQSVREVIQNPGPRHPEAASAAPPGASLLLLQQQQQQQQQQQQQQQQQQQQQQQETSPRQQQQQQGEDGSPQAHRRGPTGYLVLDEEQQPSQPQSALECHPERGCVPEPG... | [
{
"source_db": "bridge",
"source_id": "367",
"text": "AR GENE_ENCODES_PROTEIN AR",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "595",
"text": "AR PROTEIN_PHYSICALLY_INTERACTS_WITH CCND1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "CCND... | {
"knocked_out_gene": "AR",
"interaction_partner": "CCND1",
"affected_target": "cataract",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.582518 |
co_coun_00187 | counterfactual | coding_variant | hard | 4 | If CDK1 were knocked out, its physical interaction with SOX2 would be lost. Which pathway of SOX2 could therefore be indirectly affected? | CDK1 GENE_ENCODES_PROTEIN CDK1 -> CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH SOX2 -> SOX2 GENE_ENCODES_PROTEIN SOX2 -> SOX2 GENE_PARTICIPATES_IN_PATHWAY Transcriptional regulation of pluripotent stem cells | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK1",
"source_node_type": "GENE",
"source_node_label": "CDK1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "983",
... | Transcriptional regulation of pluripotent stem cells | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK1",
"source_db": "UniProt",
"payload": {
"accession": "P06493",
"sequence": "MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNL... | [
{
"source_db": "bridge",
"source_id": "983",
"text": "CDK1 GENE_ENCODES_PROTEIN CDK1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "6657",
"text": "CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH SOX2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "CDK1",
"interaction_partner": "SOX2",
"affected_target": "Transcriptional regulation of pluripotent stem cells",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00188 | counterfactual | coding_variant | hard | 4 | If ERBB2 were knocked out, its physical interaction with CBL would be lost. Which disease association of CBL could therefore be indirectly affected? | ERBB2 GENE_ENCODES_PROTEIN ERBB2 -> ERBB2 PROTEIN_PHYSICALLY_INTERACTS_WITH CBL -> CBL GENE_ENCODES_PROTEIN CBL -> CBL GENE_ASSOCIATED_WITH_DISEASE yolk sac tumor | {
"steps": [
{
"hop": 1,
"source_node_id": "ERBB2",
"source_node_type": "GENE",
"source_node_label": "ERBB2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2064... | yolk sac tumor | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ERBB2",
"source_db": "UniProt",
"payload": {
"accession": "P04626",
"sequence": "MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGAS... | [
{
"source_db": "bridge",
"source_id": "2064",
"text": "ERBB2 GENE_ENCODES_PROTEIN ERBB2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "867",
"text": "ERBB2 PROTEIN_PHYSICALLY_INTERACTS_WITH CBL",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"knocked_out_gene": "ERBB2",
"interaction_partner": "CBL",
"affected_target": "yolk sac tumor",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.605831 |
co_coun_00189 | counterfactual | coding_variant | hard | 4 | If MLH1 were knocked out, its physical interaction with PMS2 would be lost. Which disease association of PMS2 could therefore be indirectly affected? | MLH1 GENE_ENCODES_PROTEIN MLH1 -> MLH1 PROTEIN_PHYSICALLY_INTERACTS_WITH PMS2 -> PMS2 GENE_ENCODES_PROTEIN PMS2 -> PMS2 GENE_ASSOCIATED_WITH_DISEASE nodal marginal zone B-cell lymphoma | {
"steps": [
{
"hop": 1,
"source_node_id": "MLH1",
"source_node_type": "GENE",
"source_node_label": "MLH1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4292",... | nodal marginal zone B-cell lymphoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "bridge",
"source_id": "4292",
"text": "MLH1 GENE_ENCODES_PROTEIN MLH1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5395",
"text": "MLH1 PROTEIN_PHYSICALLY_INTERACTS_WITH PMS2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "MLH1",
"interaction_partner": "PMS2",
"affected_target": "nodal marginal zone B-cell lymphoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.605831 |
co_coun_00190 | counterfactual | coding_variant | hard | 4 | If MAPK1 were knocked out, its physical interaction with BCL2 would be lost. Which disease association of BCL2 could therefore be indirectly affected? | MAPK1 GENE_ENCODES_PROTEIN MAPK1 -> MAPK1 PROTEIN_PHYSICALLY_INTERACTS_WITH BCL2 -> BCL2 GENE_ENCODES_PROTEIN BCL2 -> BCL2 GENE_ASSOCIATED_WITH_DISEASE follicular lymphoma | {
"steps": [
{
"hop": 1,
"source_node_id": "MAPK1",
"source_node_type": "GENE",
"source_node_label": "MAPK1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5594... | follicular lymphoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MAPK1",
"source_db": "UniProt",
"payload": {
"accession": "P28482",
"sequence": "MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQI... | [
{
"source_db": "bridge",
"source_id": "5594",
"text": "MAPK1 GENE_ENCODES_PROTEIN MAPK1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "596",
"text": "MAPK1 PROTEIN_PHYSICALLY_INTERACTS_WITH BCL2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "MAPK1",
"interaction_partner": "BCL2",
"affected_target": "follicular lymphoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00191 | counterfactual | coding_variant | hard | 4 | If MSH2 were knocked out, its physical interaction with TP53 would be lost. Which disease association of TP53 could therefore be indirectly affected? | MSH2 GENE_ENCODES_PROTEIN MSH2 -> MSH2 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_ASSOCIATED_WITH_DISEASE carcinoma of esophagus | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH2",
"source_node_type": "GENE",
"source_node_label": "MSH2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4436",... | carcinoma of esophagus | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH2",
"source_db": "UniProt",
"payload": {
"accession": "P43246",
"sequence": "MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDI... | [
{
"source_db": "bridge",
"source_id": "4436",
"text": "MSH2 GENE_ENCODES_PROTEIN MSH2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "MSH2 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "MSH2",
"interaction_partner": "TP53",
"affected_target": "carcinoma of esophagus",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.73005 |
co_coun_00192 | counterfactual | coding_variant | hard | 4 | If AFP were knocked out, its physical interaction with CREBBP would be lost. Which disease association of CREBBP could therefore be indirectly affected? | AFP GENE_ENCODES_PROTEIN AFP -> AFP PROTEIN_PHYSICALLY_INTERACTS_WITH CREBBP -> CREBBP GENE_ENCODES_PROTEIN CREBBP -> CREBBP GENE_ASSOCIATED_WITH_DISEASE endometrial endometrioid adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "AFP",
"source_node_type": "GENE",
"source_node_label": "AFP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "174",
... | endometrial endometrioid adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AFP",
"source_db": "UniProt",
"payload": {
"accession": "P02771",
"sequence": "MKWVESIFLIFLLNFTESRTLHRNEYGIASILDSYQCTAEISLADLATIFFAQFVQEATYKEVSKMVKDALTAIEKPTGDEQSSGCLENQLPAFLEELCHEKEILEKYGHSDCCSQSEEGRHNCFLAHKKPTPAS... | [
{
"source_db": "bridge",
"source_id": "174",
"text": "AFP GENE_ENCODES_PROTEIN AFP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1387",
"text": "AFP PROTEIN_PHYSICALLY_INTERACTS_WITH CREBBP",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "AFP",
"interaction_partner": "CREBBP",
"affected_target": "endometrial endometrioid adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.720458 |
co_coun_00193 | counterfactual | coding_variant | hard | 4 | If MSH2 were knocked out, its physical interaction with CHEK2 would be lost. Which disease association of CHEK2 could therefore be indirectly affected? | MSH2 GENE_ENCODES_PROTEIN MSH2 -> MSH2 PROTEIN_PHYSICALLY_INTERACTS_WITH CHEK2 -> CHEK2 GENE_ENCODES_PROTEIN CHEK2 -> CHEK2 GENE_ASSOCIATED_WITH_DISEASE appendix adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH2",
"source_node_type": "GENE",
"source_node_label": "MSH2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4436",... | appendix adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH2",
"source_db": "UniProt",
"payload": {
"accession": "P43246",
"sequence": "MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDI... | [
{
"source_db": "bridge",
"source_id": "4436",
"text": "MSH2 GENE_ENCODES_PROTEIN MSH2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "11200",
"text": "MSH2 PROTEIN_PHYSICALLY_INTERACTS_WITH CHEK2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "MSH2",
"interaction_partner": "CHEK2",
"affected_target": "appendix adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00194 | counterfactual | coding_variant | hard | 4 | If AKT1 were knocked out, its physical interaction with MTOR would be lost. Which disease association of MTOR could therefore be indirectly affected? | AKT1 GENE_ENCODES_PROTEIN AKT1 -> AKT1 PROTEIN_PHYSICALLY_INTERACTS_WITH MTOR -> MTOR GENE_ENCODES_PROTEIN MTOR -> MTOR GENE_ASSOCIATED_WITH_DISEASE ovarian granulosa cell tumor | {
"steps": [
{
"hop": 1,
"source_node_id": "AKT1",
"source_node_type": "GENE",
"source_node_label": "AKT1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "207",
... | ovarian granulosa cell tumor | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AKT1",
"source_db": "UniProt",
"payload": {
"accession": "P31749",
"sequence": "MSDVAIVKEGWLHKRGEYIKTWRPRYFLLKNDGTFIGYKERPQDVDQREAPLNNFSVAQCQLMKTERPRPNTFIIRCLQWTTVIERTFHVETPEEREEWTTAIQTVADGLKKQEEEEMDFRSGSPSDNSGAEEM... | [
{
"source_db": "bridge",
"source_id": "207",
"text": "AKT1 GENE_ENCODES_PROTEIN AKT1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2475",
"text": "AKT1 PROTEIN_PHYSICALLY_INTERACTS_WITH MTOR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "AKT1",
"interaction_partner": "MTOR",
"affected_target": "ovarian granulosa cell tumor",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.672631 |
co_coun_00195 | counterfactual | coding_variant | hard | 4 | If MAPK1 were knocked out, its physical interaction with MAPT would be lost. Which disease association of MAPT could therefore be indirectly affected? | MAPK1 GENE_ENCODES_PROTEIN MAPK1 -> MAPK1 PROTEIN_PHYSICALLY_INTERACTS_WITH MAPT -> MAPT GENE_ENCODES_PROTEIN MAPT -> MAPT GENE_ASSOCIATED_WITH_DISEASE Atypical progressive supranuclear palsy | {
"steps": [
{
"hop": 1,
"source_node_id": "MAPK1",
"source_node_type": "GENE",
"source_node_label": "MAPK1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5594... | Atypical progressive supranuclear palsy | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MAPK1",
"source_db": "UniProt",
"payload": {
"accession": "P28482",
"sequence": "MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQI... | [
{
"source_db": "bridge",
"source_id": "5594",
"text": "MAPK1 GENE_ENCODES_PROTEIN MAPK1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4137",
"text": "MAPK1 PROTEIN_PHYSICALLY_INTERACTS_WITH MAPT",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "MAPK1",
"interaction_partner": "MAPT",
"affected_target": "Atypical progressive supranuclear palsy",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.849577 |
co_coun_00196 | counterfactual | coding_variant | hard | 4 | If KMT2D were knocked out, its physical interaction with ESR1 would be lost. Which disease association of ESR1 could therefore be indirectly affected? | KMT2D GENE_ENCODES_PROTEIN KMT2D -> KMT2D PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1 -> ESR1 GENE_ENCODES_PROTEIN ESR1 -> ESR1 GENE_ASSOCIATED_WITH_DISEASE adenomyosis | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2D",
"source_node_type": "GENE",
"source_node_label": "KMT2D",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "8085... | adenomyosis | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2D",
"source_db": "UniProt",
"payload": {
"accession": "O14686",
"sequence": "MDSQKLAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSSGSPRLQETPQDCSGGPVRRCALCNCGEPSLHGQRELRRFELPFDWPRCPVVSPGGSPGPNEAVLPSEDLSQIGFPEGLTPAHLGEPG... | [
{
"source_db": "bridge",
"source_id": "8085",
"text": "KMT2D GENE_ENCODES_PROTEIN KMT2D",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2099",
"text": "KMT2D PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "KMT2D",
"interaction_partner": "ESR1",
"affected_target": "adenomyosis",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.677032 |
co_coun_00197 | counterfactual | coding_variant | hard | 4 | If CDKN1A were knocked out, its physical interaction with CCND1 would be lost. Which disease association of CCND1 could therefore be indirectly affected? | CDKN1A GENE_ENCODES_PROTEIN CDKN1A -> CDKN1A PROTEIN_PHYSICALLY_INTERACTS_WITH CCND1 -> CCND1 GENE_ENCODES_PROTEIN CCND1 -> CCND1 GENE_ASSOCIATED_WITH_DISEASE anaplastic large cell lymphoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CDKN1A",
"source_node_type": "GENE",
"source_node_label": "CDKN1A",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "10... | anaplastic large cell lymphoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDKN1A",
"source_db": "UniProt",
"payload": {
"accession": "P38936",
"sequence": "MSEPAGDVRQNPCGSKACRRLFGPVDSEQLSRDCDALMAGCIQEARERWNFDFVTETPLEGDFAWERVRGLGLPKLYLPTGPRRGRDELGGGRRPGTSPALLQGTAEEDHVDLSLSCTLVPRSGEQAEGSPG... | [
{
"source_db": "bridge",
"source_id": "1026",
"text": "CDKN1A GENE_ENCODES_PROTEIN CDKN1A",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "595",
"text": "CDKN1A PROTEIN_PHYSICALLY_INTERACTS_WITH CCND1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "CDKN1A",
"interaction_partner": "CCND1",
"affected_target": "anaplastic large cell lymphoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.616107 |
co_coun_00198 | counterfactual | coding_variant | hard | 4 | If BIRC5 were knocked out, its physical interaction with CDK4 would be lost. Which disease association of CDK4 could therefore be indirectly affected? | BIRC5 GENE_ENCODES_PROTEIN BIRC5 -> BIRC5 PROTEIN_PHYSICALLY_INTERACTS_WITH CDK4 -> CDK4 GENE_ENCODES_PROTEIN CDK4 -> CDK4 GENE_ASSOCIATED_WITH_DISEASE Borderline Ovarian Mucinous Tumor | {
"steps": [
{
"hop": 1,
"source_node_id": "BIRC5",
"source_node_type": "GENE",
"source_node_label": "BIRC5",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "332"... | Borderline Ovarian Mucinous Tumor | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BIRC5",
"source_db": "UniProt",
"payload": {
"accession": "O15392",
"sequence": "MGAPTLPPAWQPFLKDHRISTFKNWPFLEGCACTPERMAEAGFIHCPTENEPDLAQCFFCFKELEGWEPDDDPIEEHKKHSSGCAFLSVKKQFEELTLGEFLKLDRERAKNKIAKETNNKKKEFEETAKKVRR... | [
{
"source_db": "bridge",
"source_id": "332",
"text": "BIRC5 GENE_ENCODES_PROTEIN BIRC5",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1019",
"text": "BIRC5 PROTEIN_PHYSICALLY_INTERACTS_WITH CDK4",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "BIRC5",
"interaction_partner": "CDK4",
"affected_target": "Borderline Ovarian Mucinous Tumor",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00199 | counterfactual | coding_variant | hard | 4 | If C9orf72 were knocked out, its physical interaction with CDKN2A would be lost. Which disease association of CDKN2A could therefore be indirectly affected? | C9orf72 GENE_ENCODES_PROTEIN C9orf72 -> C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN2A -> CDKN2A GENE_ENCODES_PROTEIN CDKN2A -> CDKN2A GENE_ASSOCIATED_WITH_DISEASE basaloid carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "C9orf72",
"source_node_type": "GENE",
"source_node_label": "C9orf72",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "... | basaloid carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "C9orf72",
"source_db": "UniProt",
"payload": {
"accession": "Q96LT7",
"sequence": "MSTLCPPPSPAVAKTEIALSGKSPLLAATFAYWDNILGPRVRHIWAPKTEQVLLSDGEITFLANHTLNGEILRNAESGAIDVKFFVLSEKGVIIVSLIFDGNWNGDRSTYGLSIILPQTELSFYLPLHRVC... | [
{
"source_db": "bridge",
"source_id": "203228",
"text": "C9orf72 GENE_ENCODES_PROTEIN C9orf72",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1029",
"text": "C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN2A",
"confidence": 0.9
},
{
"source_db": "bridge",
... | {
"knocked_out_gene": "C9orf72",
"interaction_partner": "CDKN2A",
"affected_target": "basaloid carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.672409 |
co_coun_00200 | counterfactual | coding_variant | hard | 4 | If ESR1 were knocked out, its physical interaction with PGR would be lost. Which disease association of PGR could therefore be indirectly affected? | ESR1 GENE_ENCODES_PROTEIN ESR1 -> ESR1 PROTEIN_PHYSICALLY_INTERACTS_WITH PGR -> PGR GENE_ENCODES_PROTEIN PGR -> PGR GENE_ASSOCIATED_WITH_DISEASE acne | {
"steps": [
{
"hop": 1,
"source_node_id": "ESR1",
"source_node_type": "GENE",
"source_node_label": "ESR1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2099",... | acne | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ESR1",
"source_db": "UniProt",
"payload": {
"accession": "P03372",
"sequence": "MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANAQVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLEN... | [
{
"source_db": "bridge",
"source_id": "2099",
"text": "ESR1 GENE_ENCODES_PROTEIN ESR1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5241",
"text": "ESR1 PROTEIN_PHYSICALLY_INTERACTS_WITH PGR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "ESR1",
"interaction_partner": "PGR",
"affected_target": "acne",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.812102 |
co_coun_00201 | counterfactual | coding_variant | medium | 3 | If ERG were knocked out, the ribonucleoprotein complex complex would lose one of its members, indirectly affecting ACTB, another member of the same complex. Which pathway of ACTB could therefore be indirectly affected? | ERG PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex -> ACTB PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex -> ACTB GENE_PARTICIPATES_IN_PATHWAY Regulation of MITF-M-dependent genes involved in pigmentation | {
"steps": [
{
"hop": 1,
"source_node_id": "ERG",
"source_node_type": "GENE",
"source_node_label": "ERG",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Comp... | Regulation of MITF-M-dependent genes involved in pigmentation | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ERG",
"source_db": "UniProt",
"payload": {
"accession": "P11308",
"sequence": "MASTIKEALSVVSEDQSLFECAYGTPHLAKTEMTASSSSDYGQTSKMSPRVPQQDWLSQPPARVTIKMECNPSQVNGSRNSPDECSVAKGGKMVGSPDTVGMNYGSYMEEKHMPPPNMTTNERRVIVPADPTLWS... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC393",
"text": "ERG PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "ACTB",
"text": "ACTB PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex",
"confidence": 1
},... | {
"knocked_out_gene": "ERG",
"disrupted_complex": "ribonucleoprotein complex",
"complex_partner": "ACTB",
"affected_target": "Regulation of MITF-M-dependent genes involved in pigmentation",
"target_kind": "pathway",
"mechanism": "complex"
} | 1 |
co_coun_00202 | counterfactual | coding_variant | hard | 4 | If CDKN2A were knocked out, its physical interaction with TP53 would be lost. Which disease association of TP53 could therefore be indirectly affected? | CDKN2A GENE_ENCODES_PROTEIN CDKN2A -> CDKN2A PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_ASSOCIATED_WITH_DISEASE chromophobe renal cell carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CDKN2A",
"source_node_type": "GENE",
"source_node_label": "CDKN2A",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "10... | chromophobe renal cell carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDKN2A",
"source_db": "UniProt",
"payload": {
"accession": "Q8N726",
"sequence": "MVRRFLVTLRIRRACGPPRVRVFVVHIPRLTGEWAAPGAPAAVALVLMLLRSQRLGQQPLPRRPGHDDGQRPSGGAAAAPRRGAQLRRPRHSHPTRARRCPGGLPGHAGGAAPGRGAAGRARCLGPSARGPG... | [
{
"source_db": "bridge",
"source_id": "1029",
"text": "CDKN2A GENE_ENCODES_PROTEIN CDKN2A",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "CDKN2A PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "CDKN2A",
"interaction_partner": "TP53",
"affected_target": "chromophobe renal cell carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.79156 |
co_coun_00203 | counterfactual | coding_variant | hard | 4 | If AXL were knocked out, its physical interaction with EGFR would be lost. Which pathway of EGFR could therefore be indirectly affected? | AXL GENE_ENCODES_PROTEIN AXL -> AXL PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_PARTICIPATES_IN_PATHWAY Signaling by ERBB2 KD Mutants | {
"steps": [
{
"hop": 1,
"source_node_id": "AXL",
"source_node_type": "GENE",
"source_node_label": "AXL",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "558",
... | Signaling by ERBB2 KD Mutants | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AXL",
"source_db": "UniProt",
"payload": {
"accession": "P30530",
"sequence": "MAWRCPRMGRVPLAWCLALCGWACMAPRGTQAEESPFVGNPGNITGARGLTGTLRCQLQVQGEPPEVHWLRDGQILELADSTQTQVPLGEDEQDDWIVVSQLRITSLQLSDTGQYQCLVFLGHQTFVSQPGYVGL... | [
{
"source_db": "bridge",
"source_id": "558",
"text": "AXL GENE_ENCODES_PROTEIN AXL",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "AXL PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "E... | {
"knocked_out_gene": "AXL",
"interaction_partner": "EGFR",
"affected_target": "Signaling by ERBB2 KD Mutants",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00204 | counterfactual | coding_variant | hard | 4 | If CREBBP were knocked out, its physical interaction with TP53 would be lost. Which disease association of TP53 could therefore be indirectly affected? | CREBBP GENE_ENCODES_PROTEIN CREBBP -> CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_ASSOCIATED_WITH_DISEASE thymic carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CREBBP",
"source_node_type": "GENE",
"source_node_label": "CREBBP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "13... | thymic carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CREBBP",
"source_db": "UniProt",
"payload": {
"accession": "Q92793",
"sequence": "MAENLLDGPPNPKRAKLSSPGFSANDSTDFGSLFDLENDLPDELIPNGGELGLLNSGNLVPDAASKHKQLSELLRGGSGSSINPGIGNVSASSPVQQGLGGQAQGQPNSANMASLSAMGKSPLSQGDSSAPS... | [
{
"source_db": "bridge",
"source_id": "1387",
"text": "CREBBP GENE_ENCODES_PROTEIN CREBBP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "CREBBP",
"interaction_partner": "TP53",
"affected_target": "thymic carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.716746 |
co_coun_00205 | counterfactual | coding_variant | hard | 4 | If EGFR were knocked out, its physical interaction with CTNNB1 would be lost. Which pathway of CTNNB1 could therefore be indirectly affected? | EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1 -> CTNNB1 GENE_ENCODES_PROTEIN CTNNB1 -> CTNNB1 GENE_PARTICIPATES_IN_PATHWAY Regulation of MITF-M-dependent genes involved in cell cycle and proliferation | {
"steps": [
{
"hop": 1,
"source_node_id": "EGFR",
"source_node_type": "GENE",
"source_node_label": "EGFR",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1956",... | Regulation of MITF-M-dependent genes involved in cell cycle and proliferation | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "EGFR",
"source_db": "UniProt",
"payload": {
"accession": "P00533",
"sequence": "MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKE... | [
{
"source_db": "bridge",
"source_id": "1956",
"text": "EGFR GENE_ENCODES_PROTEIN EGFR",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1499",
"text": "EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "EGFR",
"interaction_partner": "CTNNB1",
"affected_target": "Regulation of MITF-M-dependent genes involved in cell cycle and proliferation",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00206 | counterfactual | coding_variant | hard | 4 | If MYC were knocked out, its physical interaction with SPOP would be lost. Which disease association of SPOP could therefore be indirectly affected? | MYC GENE_ENCODES_PROTEIN MYC -> MYC PROTEIN_PHYSICALLY_INTERACTS_WITH SPOP -> SPOP GENE_ENCODES_PROTEIN SPOP -> SPOP GENE_ASSOCIATED_WITH_DISEASE lung inflammatory myofibroblastic tumor | {
"steps": [
{
"hop": 1,
"source_node_id": "MYC",
"source_node_type": "GENE",
"source_node_label": "MYC",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4609",
... | lung inflammatory myofibroblastic tumor | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MYC",
"source_db": "UniProt",
"payload": {
"accession": "P01106",
"sequence": "MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD... | [
{
"source_db": "bridge",
"source_id": "4609",
"text": "MYC GENE_ENCODES_PROTEIN MYC",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "8405",
"text": "MYC PROTEIN_PHYSICALLY_INTERACTS_WITH SPOP",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "... | {
"knocked_out_gene": "MYC",
"interaction_partner": "SPOP",
"affected_target": "lung inflammatory myofibroblastic tumor",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.605831 |
co_coun_00207 | counterfactual | coding_variant | hard | 4 | If FUS were knocked out, its physical interaction with VCP would be lost. Which disease association of VCP could therefore be indirectly affected? | FUS GENE_ENCODES_PROTEIN FUS -> FUS PROTEIN_PHYSICALLY_INTERACTS_WITH VCP -> VCP GENE_ENCODES_PROTEIN VCP -> VCP GENE_ASSOCIATED_WITH_DISEASE severe acute respiratory syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "FUS",
"source_node_type": "GENE",
"source_node_label": "FUS",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2521",
... | severe acute respiratory syndrome | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FUS",
"source_db": "UniProt",
"payload": {
"accession": "P35637",
"sequence": "MASNDYTQQATQSYGAYPTQPGQGYSQQSSQPYGQQSYSGYSQSTDTSGYGQSSYSSYGQSQNTGYGTQSTPQGYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGSSSQSSSYGQPQSGSYSQQPS... | [
{
"source_db": "bridge",
"source_id": "2521",
"text": "FUS GENE_ENCODES_PROTEIN FUS",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7415",
"text": "FUS PROTEIN_PHYSICALLY_INTERACTS_WITH VCP",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "V... | {
"knocked_out_gene": "FUS",
"interaction_partner": "VCP",
"affected_target": "severe acute respiratory syndrome",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.720458 |
co_coun_00208 | counterfactual | coding_variant | hard | 3 | If PALB2 were knocked out, the BRCA complex would lose one of its members, indirectly affecting BRCA1, another member of the same complex. Which disease association of BRCA1 could therefore be indirectly affected? | PALB2 PROTEIN_MEMBER_OF_COMPLEX BRCA -> BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCA -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE lung adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "PALB2",
"source_node_type": "GENE",
"source_node_label": "PALB2",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | lung adenocarcinoma | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PALB2",
"source_db": "UniProt",
"payload": {
"accession": "Q86YC2",
"sequence": "MDEPPGKPLSCEEKEKLKEKLAFLKREYSKTLARLQRAQRAEKIKHSIKKTVEEQDCLSQQDLSPQLKHSEPKNKICVYDKLHIKTHLDEETGEKTSITLDVGPESFNPGDGPGGLPIQRTDDTQEHFPHRVS... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC973",
"text": "PALB2 PROTEIN_MEMBER_OF_COMPLEX BRCA",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCA",
"confidence": 1
},
{
"source_db": "OpenTargets",
... | {
"knocked_out_gene": "PALB2",
"disrupted_complex": "BRCA",
"complex_partner": "BRCA1",
"affected_target": "lung adenocarcinoma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.657685 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.