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_00209 | counterfactual | coding_variant | hard | 3 | If CDK6 were knocked out, the BRCA1 / CCNA1 / CCNA2 / CCNB1... 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? | CDK6 PROTEIN_MEMBER_OF_COMPLEX BRCA1 / CCNA1 / CCNA2 / CCNB1... -> BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCA1 / CCNA1 / CCNA2 / CCNB1... -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE Gastrointestinal Neoplasms | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK6",
"source_node_type": "GENE",
"source_node_label": "CDK6",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Co... | Gastrointestinal Neoplasms | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK6",
"source_db": "UniProt",
"payload": {
"accession": "Q00534",
"sequence": "MEKDGLCRADQQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVQTGEEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTVSRTDRETKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLD... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC3729",
"text": "CDK6 PROTEIN_MEMBER_OF_COMPLEX BRCA1 / CCNA1 / CCNA2 / CCNB1...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCA1 / CCNA1 / CCNA2 / CCNB1...",
"c... | {
"knocked_out_gene": "CDK6",
"disrupted_complex": "BRCA1 / CCNA1 / CCNA2 / CCNB1...",
"complex_partner": "BRCA1",
"affected_target": "Gastrointestinal Neoplasms",
"target_kind": "disease",
"mechanism": "complex"
} | 0.669433 |
co_coun_00210 | counterfactual | coding_variant | hard | 4 | If CHEK2 were knocked out, its physical interaction with TP53 would be lost. Which disease association of TP53 could therefore be indirectly affected? | CHEK2 GENE_ENCODES_PROTEIN CHEK2 -> CHEK2 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_ASSOCIATED_WITH_DISEASE atypical endometrial hyperplasia | {
"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... | atypical endometrial hyperplasia | 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": "7157",
"text": "CHEK2 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "CHEK2",
"interaction_partner": "TP53",
"affected_target": "atypical endometrial hyperplasia",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.736345 |
co_coun_00211 | 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 prophylactic surgery | {
"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",... | prophylactic surgery | 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": "prophylactic surgery",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.811531 |
co_coun_00212 | counterfactual | coding_variant | hard | 4 | If BRCA1 were knocked out, its physical interaction with TP53 would be lost. Which disease association of TP53 could therefore be indirectly affected? | BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_ASSOCIATED_WITH_DISEASE salivary gland carcinoma | {
"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"... | salivary gland carcinoma | 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": "7157",
"text": "BRCA1 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "BRCA1",
"interaction_partner": "TP53",
"affected_target": "salivary gland carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.709682 |
co_coun_00213 | counterfactual | coding_variant | hard | 4 | If ABL1 were knocked out, its physical interaction with SQSTM1 would be lost. Which pathway of SQSTM1 could therefore be indirectly affected? | ABL1 GENE_ENCODES_PROTEIN ABL1 -> ABL1 PROTEIN_PHYSICALLY_INTERACTS_WITH SQSTM1 -> SQSTM1 GENE_ENCODES_PROTEIN SQSTM1 -> SQSTM1 GENE_PARTICIPATES_IN_PATHWAY Nuclear events mediated by NFE2L2 | {
"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",
... | Nuclear events mediated by NFE2L2 | 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": "8878",
"text": "ABL1 PROTEIN_PHYSICALLY_INTERACTS_WITH SQSTM1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "ABL1",
"interaction_partner": "SQSTM1",
"affected_target": "Nuclear events mediated by NFE2L2",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00214 | counterfactual | coding_variant | hard | 4 | If SPOP were knocked out, its physical interaction with NLRP3 would be lost. Which pathway of NLRP3 could therefore be indirectly affected? | SPOP GENE_ENCODES_PROTEIN SPOP -> SPOP PROTEIN_PHYSICALLY_INTERACTS_WITH NLRP3 -> NLRP3 GENE_ENCODES_PROTEIN NLRP3 -> NLRP3 GENE_PARTICIPATES_IN_PATHWAY Purinergic signaling in leishmaniasis infection | {
"steps": [
{
"hop": 1,
"source_node_id": "SPOP",
"source_node_type": "GENE",
"source_node_label": "SPOP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "8405",... | Purinergic signaling in leishmaniasis infection | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SPOP",
"source_db": "UniProt",
"payload": {
"accession": "O43791",
"sequence": "MSRVPSPPPPAEMSSGPVAESWCYTQIKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFK... | [
{
"source_db": "bridge",
"source_id": "8405",
"text": "SPOP GENE_ENCODES_PROTEIN SPOP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "114548",
"text": "SPOP PROTEIN_PHYSICALLY_INTERACTS_WITH NLRP3",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "SPOP",
"interaction_partner": "NLRP3",
"affected_target": "Purinergic signaling in leishmaniasis infection",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00215 | counterfactual | coding_variant | hard | 4 | If PMS2 were knocked out, its physical interaction with BRCA2 would be lost. Which disease association of BRCA2 could therefore be indirectly affected? | PMS2 GENE_ENCODES_PROTEIN PMS2 -> PMS2 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA2 -> BRCA2 GENE_ENCODES_PROTEIN BRCA2 -> BRCA2 GENE_ASSOCIATED_WITH_DISEASE BAP1-related tumor predisposition syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5395",... | BAP1-related tumor predisposition syndrome | 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": "bridge",
"source_id": "5395",
"text": "PMS2 GENE_ENCODES_PROTEIN PMS2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "675",
"text": "PMS2 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "PMS2",
"interaction_partner": "BRCA2",
"affected_target": "BAP1-related tumor predisposition syndrome",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.706273 |
co_coun_00216 | counterfactual | coding_variant | hard | 3 | If BRIP1 were knocked out, the BRCA1-B 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? | BRIP1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-B complex -> BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-B complex -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE fibrous meningioma | {
"steps": [
{
"hop": 1,
"source_node_id": "BRIP1",
"source_node_type": "GENE",
"source_node_label": "BRIP1",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | fibrous meningioma | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRIP1",
"source_db": "UniProt",
"payload": {
"accession": "Q9BX63",
"sequence": "MSSMWSEYTIGGVKIYFPYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLALLCSALAWQQSLSGKPADEGVSEKAEVQLSCCCACHSKDFTNNDMNQGTSRHFNYPSTPPSERNGTSSTCQDSPEKTT... | [
{
"source_db": "OmniPath",
"source_id": "SIGNOR:SIGNOR-C298",
"text": "BRIP1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-B complex",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-B complex",
"confidence": 1
},
{
"so... | {
"knocked_out_gene": "BRIP1",
"disrupted_complex": "BRCA1-B complex",
"complex_partner": "BRCA1",
"affected_target": "fibrous meningioma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.652013 |
co_coun_00217 | counterfactual | coding_variant | hard | 4 | If NLRP3 were knocked out, its physical interaction with SPOP would be lost. Which disease association of SPOP could therefore be indirectly affected? | NLRP3 GENE_ENCODES_PROTEIN NLRP3 -> NLRP3 PROTEIN_PHYSICALLY_INTERACTS_WITH SPOP -> SPOP GENE_ENCODES_PROTEIN SPOP -> SPOP GENE_ASSOCIATED_WITH_DISEASE basal cell carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "NLRP3",
"source_node_type": "GENE",
"source_node_label": "NLRP3",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1145... | basal cell carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NLRP3",
"source_db": "UniProt",
"payload": {
"accession": "Q96P20",
"sequence": "MKMASTRCKLARYLEDLEDVDLKKFKMHLEDYPPQKGCIPLPRGQTEKADHVDLATLMIDFNGEEKAWAMAVWIFAAINRRDLYEKAKRDEPKWGSDNARVSNPTVICQEDSIEEEWMGLLEYLSRISICKMK... | [
{
"source_db": "bridge",
"source_id": "114548",
"text": "NLRP3 GENE_ENCODES_PROTEIN NLRP3",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "8405",
"text": "NLRP3 PROTEIN_PHYSICALLY_INTERACTS_WITH SPOP",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"knocked_out_gene": "NLRP3",
"interaction_partner": "SPOP",
"affected_target": "basal cell carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.605831 |
co_coun_00218 | counterfactual | coding_variant | hard | 4 | If AURKB were knocked out, its physical interaction with BARD1 would be lost. Which disease association of BARD1 could therefore be indirectly affected? | AURKB GENE_ENCODES_PROTEIN AURKB -> AURKB PROTEIN_PHYSICALLY_INTERACTS_WITH BARD1 -> BARD1 GENE_ENCODES_PROTEIN BARD1 -> BARD1 GENE_ASSOCIATED_WITH_DISEASE hereditary cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "AURKB",
"source_node_type": "GENE",
"source_node_label": "AURKB",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "9212... | hereditary cancer | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AURKB",
"source_db": "UniProt",
"payload": {
"accession": "Q96GD4",
"sequence": "MAQKENSYPWPYGRQTAPSGLSTLPQRVLRKEPVTPSALVLMSRSNVQPTAAPGQKVMENSSGTPDILTRHFTIDDFEIGRPLGKGKFGNVYLAREKKSHFIVALKVLFKSQIEKEGVEHQLRREIEIQAHLH... | [
{
"source_db": "bridge",
"source_id": "9212",
"text": "AURKB GENE_ENCODES_PROTEIN AURKB",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "580",
"text": "AURKB PROTEIN_PHYSICALLY_INTERACTS_WITH BARD1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "AURKB",
"interaction_partner": "BARD1",
"affected_target": "hereditary cancer",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.597844 |
co_coun_00219 | counterfactual | coding_variant | hard | 4 | If BRCA2 were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | BRCA2 GENE_ENCODES_PROTEIN BRCA2 -> BRCA2 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE punctate palmoplantar keratoderma type 2 | {
"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"... | punctate palmoplantar keratoderma type 2 | null | [
"expression",
"intercell_role",
"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": "672",
"text": "BRCA2 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "BRCA2",
"interaction_partner": "BRCA1",
"affected_target": "punctate palmoplantar keratoderma type 2",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.705596 |
co_coun_00220 | counterfactual | coding_variant | hard | 4 | If CREBBP were knocked out, its physical interaction with FGFR1 would be lost. Which disease association of FGFR1 could therefore be indirectly affected? | CREBBP GENE_ENCODES_PROTEIN CREBBP -> CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH FGFR1 -> FGFR1 GENE_ENCODES_PROTEIN FGFR1 -> FGFR1 GENE_ASSOCIATED_WITH_DISEASE craniosynostosis | {
"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... | craniosynostosis | 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": "2260",
"text": "CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH FGFR1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sou... | {
"knocked_out_gene": "CREBBP",
"interaction_partner": "FGFR1",
"affected_target": "craniosynostosis",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.747908 |
co_coun_00221 | 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 schizophrenia | {
"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... | schizophrenia | 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": "schizophrenia",
"target_kind": "disease",
"mechanism": "complex"
} | 0.669433 |
co_coun_00222 | counterfactual | coding_variant | hard | 4 | If VCP were knocked out, its physical interaction with AR would be lost. Which disease association of AR could therefore be indirectly affected? | VCP GENE_ENCODES_PROTEIN VCP -> VCP PROTEIN_PHYSICALLY_INTERACTS_WITH AR -> AR GENE_ENCODES_PROTEIN AR -> AR GENE_ASSOCIATED_WITH_DISEASE thyroid gland carcinoma | {
"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",
... | thyroid gland carcinoma | 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": "367",
"text": "VCP PROTEIN_PHYSICALLY_INTERACTS_WITH AR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "AR"... | {
"knocked_out_gene": "VCP",
"interaction_partner": "AR",
"affected_target": "thyroid gland carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.680924 |
co_coun_00223 | counterfactual | coding_variant | hard | 4 | If AXIN2 were knocked out, its physical interaction with CTNNB1 would be lost. Which pathway of CTNNB1 could therefore be indirectly affected? | AXIN2 GENE_ENCODES_PROTEIN AXIN2 -> AXIN2 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": "AXIN2",
"source_node_type": "GENE",
"source_node_label": "AXIN2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "8313... | Formation of definitive endoderm | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AXIN2",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y2T1",
"sequence": "MSSAMLVTCLPDPSSSFREDAPRPPVPGEEGETPPCQPGVGKGQVTKPMPVSSNTRRNEDGLGEPEGRASPDSPLTRWTKSLHSLLGDQDGAYLFRTFLEREKCVDTLDFWFACNGFRQMNLKDTKTLRVAKA... | [
{
"source_db": "bridge",
"source_id": "8313",
"text": "AXIN2 GENE_ENCODES_PROTEIN AXIN2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1499",
"text": "AXIN2 PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"knocked_out_gene": "AXIN2",
"interaction_partner": "CTNNB1",
"affected_target": "Formation of definitive endoderm",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00224 | counterfactual | coding_variant | hard | 4 | If MAPT were knocked out, its physical interaction with ABL1 would be lost. Which disease association of ABL1 could therefore be indirectly affected? | MAPT GENE_ENCODES_PROTEIN MAPT -> MAPT PROTEIN_PHYSICALLY_INTERACTS_WITH ABL1 -> ABL1 GENE_ENCODES_PROTEIN ABL1 -> ABL1 GENE_ASSOCIATED_WITH_DISEASE uterine corpus adenosarcoma | {
"steps": [
{
"hop": 1,
"source_node_id": "MAPT",
"source_node_type": "GENE",
"source_node_label": "MAPT",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4137",... | uterine corpus adenosarcoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MAPT",
"source_db": "UniProt",
"payload": {
"accession": "P10636",
"sequence": "MAEPRQEFEVMEDHAGTYGLGDRKDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAKSTPTAEDVTAPLVDEGAPGKQAAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAGHVTQEPESGKVVQE... | [
{
"source_db": "bridge",
"source_id": "4137",
"text": "MAPT GENE_ENCODES_PROTEIN MAPT",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "25",
"text": "MAPT PROTEIN_PHYSICALLY_INTERACTS_WITH ABL1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "MAPT",
"interaction_partner": "ABL1",
"affected_target": "uterine corpus adenosarcoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00225 | 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 nodular malignant melanoma | {
"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... | nodular malignant melanoma | 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": "nodular malignant melanoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00226 | 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 malignant epithelial tumor of ovary | {
"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... | malignant epithelial tumor of ovary | 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": "malignant epithelial tumor of ovary",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.681952 |
co_coun_00227 | counterfactual | coding_variant | medium | 3 | If BRCA2 were knocked out, the BRCC ubiquitin ligase complex complex would lose one of its members, indirectly affecting BRCA1, another member of the same complex. Which pathway of BRCA1 could therefore be indirectly affected? | BRCA2 PROTEIN_MEMBER_OF_COMPLEX BRCC ubiquitin ligase complex -> BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCC ubiquitin ligase complex -> BRCA1 GENE_PARTICIPATES_IN_PATHWAY EGFR | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA2",
"source_node_type": "GENE",
"source_node_label": "BRCA2",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | EGFR | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA2",
"source_db": "UniProt",
"payload": {
"accession": "P51587",
"sequence": "MPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPYNSEPAEESEHKNNNYEPNLFKTPQRKPSYNQLASTPIIFKEQGLTLPLYQSPVKELDKFKLDLGRNVPNSRHKSLRTVKTKMDQADDVSCP... | [
{
"source_db": "OmniPath",
"source_id": "PDB:1jm7",
"text": "BRCA2 PROTEIN_MEMBER_OF_COMPLEX BRCC ubiquitin ligase complex",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCC ubiquitin ligase complex",
"confidence": ... | {
"knocked_out_gene": "BRCA2",
"disrupted_complex": "BRCC ubiquitin ligase complex",
"complex_partner": "BRCA1",
"affected_target": "EGFR",
"target_kind": "pathway",
"mechanism": "complex"
} | 0.947268 |
co_coun_00228 | counterfactual | coding_variant | hard | 4 | If ABL2 were knocked out, its physical interaction with ABL1 would be lost. Which pathway of ABL1 could therefore be indirectly affected? | ABL2 GENE_ENCODES_PROTEIN ABL2 -> ABL2 PROTEIN_PHYSICALLY_INTERACTS_WITH ABL1 -> ABL1 GENE_ENCODES_PROTEIN ABL1 -> ABL1 GENE_PARTICIPATES_IN_PATHWAY RHO GTPases Activate WASPs and WAVEs | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL2",
"source_node_type": "GENE",
"source_node_label": "ABL2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "27",
... | RHO GTPases Activate WASPs and WAVEs | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL2",
"source_db": "UniProt",
"payload": {
"accession": "P42684",
"sequence": "MGQQVGRVGEAPGLQQPQPRGIRGSSAARPSGRRRDPAGRTTETGFNIFTQHDHFASCVEDGFEGDKTGGSSPEALHRPYGCDVEPQALNEAIRWSSKENLLGATESDPNLFVALYDFVASGDNTLSITKGEKL... | [
{
"source_db": "bridge",
"source_id": "27",
"text": "ABL2 GENE_ENCODES_PROTEIN ABL2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "25",
"text": "ABL2 PROTEIN_PHYSICALLY_INTERACTS_WITH ABL1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "A... | {
"knocked_out_gene": "ABL2",
"interaction_partner": "ABL1",
"affected_target": "RHO GTPases Activate WASPs and WAVEs",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00229 | counterfactual | coding_variant | hard | 4 | If ALK were knocked out, its physical interaction with MAPK1 would be lost. Which pathway of MAPK1 could therefore be indirectly affected? | ALK GENE_ENCODES_PROTEIN ALK -> ALK PROTEIN_PHYSICALLY_INTERACTS_WITH MAPK1 -> MAPK1 GENE_ENCODES_PROTEIN MAPK1 -> MAPK1 GENE_PARTICIPATES_IN_PATHWAY RAF-independent MAPK1/3 activation | {
"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",
... | RAF-independent MAPK1/3 activation | 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": "5594",
"text": "ALK PROTEIN_PHYSICALLY_INTERACTS_WITH MAPK1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "... | {
"knocked_out_gene": "ALK",
"interaction_partner": "MAPK1",
"affected_target": "RAF-independent MAPK1/3 activation",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00230 | counterfactual | coding_variant | hard | 3 | If BRCA2 were knocked out, the BRCA1/BARD1 complex would lose one of its members, indirectly affecting MLH1, another member of the same complex. Which disease association of MLH1 could therefore be indirectly affected? | BRCA2 PROTEIN_MEMBER_OF_COMPLEX BRCA1/BARD1 -> MLH1 PROTEIN_MEMBER_OF_COMPLEX BRCA1/BARD1 -> MLH1 GENE_ASSOCIATED_WITH_DISEASE acute lymphoblastic leukemia | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA2",
"source_node_type": "GENE",
"source_node_label": "BRCA2",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | acute lymphoblastic leukemia | 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": "OmniPath",
"source_id": "Compleat:HC1079",
"text": "BRCA2 PROTEIN_MEMBER_OF_COMPLEX BRCA1/BARD1",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "MLH1",
"text": "MLH1 PROTEIN_MEMBER_OF_COMPLEX BRCA1/BARD1",
"confidence": 1
},
{
"source_db": "Op... | {
"knocked_out_gene": "BRCA2",
"disrupted_complex": "BRCA1/BARD1",
"complex_partner": "MLH1",
"affected_target": "acute lymphoblastic leukemia",
"target_kind": "disease",
"mechanism": "complex"
} | 0.573925 |
co_coun_00231 | counterfactual | coding_variant | hard | 4 | If SOX2 were knocked out, its physical interaction with TUBA4A would be lost. Which disease association of TUBA4A could therefore be indirectly affected? | SOX2 GENE_ENCODES_PROTEIN SOX2 -> SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH TUBA4A -> TUBA4A GENE_ENCODES_PROTEIN TUBA4A -> TUBA4A GENE_ASSOCIATED_WITH_DISEASE hypopharynx squamous cell 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",... | hypopharynx squamous cell 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": "7277",
"text": "SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH TUBA4A",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "SOX2",
"interaction_partner": "TUBA4A",
"affected_target": "hypopharynx squamous cell carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.709198 |
co_coun_00232 | counterfactual | coding_variant | hard | 4 | If FGFR1 were knocked out, its physical interaction with BAX would be lost. Which disease association of BAX could therefore be indirectly affected? | FGFR1 GENE_ENCODES_PROTEIN FGFR1 -> FGFR1 PROTEIN_PHYSICALLY_INTERACTS_WITH BAX -> BAX GENE_ENCODES_PROTEIN BAX -> BAX GENE_ASSOCIATED_WITH_DISEASE adnexal spiradenoma/cylindroma of a sweat gland | {
"steps": [
{
"hop": 1,
"source_node_id": "FGFR1",
"source_node_type": "GENE",
"source_node_label": "FGFR1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2260... | adnexal spiradenoma/cylindroma of a sweat gland | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FGFR1",
"source_db": "UniProt",
"payload": {
"accession": "P11362",
"sequence": "MWSWKCLLFWAVLVTATLCTARPSPTLPEQAQPWGAPVEVESFLVHPGDLLQLRCRLRDDVQSINWLRDGVQLAESNRTRITGEEVEVQDSVPADSGLYACVTSSPSGSDTTYFSVNVSDALPSSEDDDDDDD... | [
{
"source_db": "bridge",
"source_id": "2260",
"text": "FGFR1 GENE_ENCODES_PROTEIN FGFR1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "581",
"text": "FGFR1 PROTEIN_PHYSICALLY_INTERACTS_WITH BAX",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"knocked_out_gene": "FGFR1",
"interaction_partner": "BAX",
"affected_target": "adnexal spiradenoma/cylindroma of a sweat gland",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.605831 |
co_coun_00233 | counterfactual | coding_variant | hard | 4 | If TUBA4A were knocked out, its physical interaction with MAPT would be lost. Which disease association of MAPT could therefore be indirectly affected? | TUBA4A GENE_ENCODES_PROTEIN TUBA4A -> TUBA4A PROTEIN_PHYSICALLY_INTERACTS_WITH MAPT -> MAPT GENE_ENCODES_PROTEIN MAPT -> MAPT GENE_ASSOCIATED_WITH_DISEASE COVID-19 | {
"steps": [
{
"hop": 1,
"source_node_id": "TUBA4A",
"source_node_type": "GENE",
"source_node_label": "TUBA4A",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "72... | COVID-19 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TUBA4A",
"source_db": "UniProt",
"payload": {
"accession": "P68366",
"sequence": "MRECISVHVGQAGVQMGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFTTFFCETGAGKHVPRAVFVDLEPTVIDEIRNGPYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDPVLDRIRKLSDQCTGL... | [
{
"source_db": "bridge",
"source_id": "7277",
"text": "TUBA4A GENE_ENCODES_PROTEIN TUBA4A",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4137",
"text": "TUBA4A PROTEIN_PHYSICALLY_INTERACTS_WITH MAPT",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "TUBA4A",
"interaction_partner": "MAPT",
"affected_target": "COVID-19",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.691625 |
co_coun_00234 | counterfactual | coding_variant | hard | 4 | If VCP were knocked out, its physical interaction with APP would be lost. Which disease association of APP could therefore be indirectly affected? | VCP GENE_ENCODES_PROTEIN VCP -> VCP PROTEIN_PHYSICALLY_INTERACTS_WITH APP -> APP GENE_ENCODES_PROTEIN APP -> APP GENE_ASSOCIATED_WITH_DISEASE ABetaA21G amyloidosis | {
"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",
... | ABetaA21G amyloidosis | 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": "351",
"text": "VCP PROTEIN_PHYSICALLY_INTERACTS_WITH APP",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "AP... | {
"knocked_out_gene": "VCP",
"interaction_partner": "APP",
"affected_target": "ABetaA21G amyloidosis",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.826693 |
co_coun_00235 | counterfactual | coding_variant | hard | 4 | If CAMK4 were knocked out, its physical interaction with NOTCH1 would be lost. Which disease association of NOTCH1 could therefore be indirectly affected? | CAMK4 GENE_ENCODES_PROTEIN CAMK4 -> CAMK4 PROTEIN_PHYSICALLY_INTERACTS_WITH NOTCH1 -> NOTCH1 GENE_ENCODES_PROTEIN NOTCH1 -> NOTCH1 GENE_ASSOCIATED_WITH_DISEASE aortic valve stenosis | {
"steps": [
{
"hop": 1,
"source_node_id": "CAMK4",
"source_node_type": "GENE",
"source_node_label": "CAMK4",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "814"... | aortic valve stenosis | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CAMK4",
"source_db": "UniProt",
"payload": {
"accession": "Q16566",
"sequence": "MLKVTVPSCSASSCSSVTASAAPGTASLVPDYWIDGSNRDALSDFFEVESELGRGATSIVYRCKQKGTQKPYALKVLKKTVDKKIVRTEIGVLLRLSHPNIIKLKEIFETPTEISLVLELVTGGELFDRIVEK... | [
{
"source_db": "bridge",
"source_id": "814",
"text": "CAMK4 GENE_ENCODES_PROTEIN CAMK4",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4851",
"text": "CAMK4 PROTEIN_PHYSICALLY_INTERACTS_WITH NOTCH1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "CAMK4",
"interaction_partner": "NOTCH1",
"affected_target": "aortic valve stenosis",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.85204 |
co_coun_00236 | counterfactual | coding_variant | hard | 4 | If APOE were knocked out, its physical interaction with MAPT would be lost. Which disease association of MAPT could therefore be indirectly affected? | APOE GENE_ENCODES_PROTEIN APOE -> APOE PROTEIN_PHYSICALLY_INTERACTS_WITH MAPT -> MAPT GENE_ENCODES_PROTEIN MAPT -> MAPT GENE_ASSOCIATED_WITH_DISEASE portal hypertension | {
"steps": [
{
"hop": 1,
"source_node_id": "APOE",
"source_node_type": "GENE",
"source_node_label": "APOE",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "348",
... | portal hypertension | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APOE",
"source_db": "UniProt",
"payload": {
"accession": "P02649",
"sequence": "MKVLWAALLVTFLAGCQAKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVCGRLV... | [
{
"source_db": "bridge",
"source_id": "348",
"text": "APOE GENE_ENCODES_PROTEIN APOE",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4137",
"text": "APOE PROTEIN_PHYSICALLY_INTERACTS_WITH MAPT",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "APOE",
"interaction_partner": "MAPT",
"affected_target": "portal hypertension",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.642658 |
co_coun_00237 | counterfactual | coding_variant | hard | 4 | If CASP3 were knocked out, its physical interaction with TP53 would be lost. Which disease association of TP53 could therefore be indirectly affected? | CASP3 GENE_ENCODES_PROTEIN CASP3 -> CASP3 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_ASSOCIATED_WITH_DISEASE head and neck squamous cell carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CASP3",
"source_node_type": "GENE",
"source_node_label": "CASP3",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "836"... | head and neck squamous cell carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CASP3",
"source_db": "UniProt",
"payload": {
"accession": "P42574",
"sequence": "MENTENSVDSKSIKNLEPKIIHGSESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGP... | [
{
"source_db": "bridge",
"source_id": "836",
"text": "CASP3 GENE_ENCODES_PROTEIN CASP3",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "CASP3 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "CASP3",
"interaction_partner": "TP53",
"affected_target": "head and neck squamous cell carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.867565 |
co_coun_00238 | counterfactual | coding_variant | hard | 4 | If ETV4 were knocked out, its physical interaction with STK11 would be lost. Which disease association of STK11 could therefore be indirectly affected? | ETV4 GENE_ENCODES_PROTEIN ETV4 -> ETV4 PROTEIN_PHYSICALLY_INTERACTS_WITH STK11 -> STK11 GENE_ENCODES_PROTEIN STK11 -> STK11 GENE_ASSOCIATED_WITH_DISEASE hepatobiliary neoplasm | {
"steps": [
{
"hop": 1,
"source_node_id": "ETV4",
"source_node_type": "GENE",
"source_node_label": "ETV4",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2118",... | hepatobiliary neoplasm | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ETV4",
"source_db": "UniProt",
"payload": {
"accession": "P43268",
"sequence": "MERRMKAGYLDQQVPYTFSSKSPGNGSLREALIGPLGKLMDPGSLPPLDSEDLFQDLSHFQETWLAEAQVPDSDEQFVPDFHSENLAFHSPTTRIKKEPQSPRTDPALSCSRKPPLPYHHGEQCLYSSAYDPPR... | [
{
"source_db": "bridge",
"source_id": "2118",
"text": "ETV4 GENE_ENCODES_PROTEIN ETV4",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "6794",
"text": "ETV4 PROTEIN_PHYSICALLY_INTERACTS_WITH STK11",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"knocked_out_gene": "ETV4",
"interaction_partner": "STK11",
"affected_target": "hepatobiliary neoplasm",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00239 | counterfactual | coding_variant | hard | 4 | If CREBBP were knocked out, its physical interaction with FGFR1 would be lost. Which disease association of FGFR1 could therefore be indirectly affected? | CREBBP GENE_ENCODES_PROTEIN CREBBP -> CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH FGFR1 -> FGFR1 GENE_ENCODES_PROTEIN FGFR1 -> FGFR1 GENE_ASSOCIATED_WITH_DISEASE pulmonary fibrosis | {
"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... | pulmonary fibrosis | 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": "2260",
"text": "CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH FGFR1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sou... | {
"knocked_out_gene": "CREBBP",
"interaction_partner": "FGFR1",
"affected_target": "pulmonary fibrosis",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.791144 |
co_coun_00240 | counterfactual | coding_variant | hard | 4 | If ATM were knocked out, its physical interaction with CBL would be lost. Which disease association of CBL could therefore be indirectly affected? | ATM GENE_ENCODES_PROTEIN ATM -> ATM PROTEIN_PHYSICALLY_INTERACTS_WITH CBL -> CBL GENE_ENCODES_PROTEIN CBL -> CBL GENE_ASSOCIATED_WITH_DISEASE embryonal carcinoma of the central nervous system | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "472",
... | embryonal carcinoma of the central nervous system | 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": "bridge",
"source_id": "472",
"text": "ATM GENE_ENCODES_PROTEIN ATM",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "867",
"text": "ATM PROTEIN_PHYSICALLY_INTERACTS_WITH CBL",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "CBL... | {
"knocked_out_gene": "ATM",
"interaction_partner": "CBL",
"affected_target": "embryonal carcinoma of the central nervous system",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.605831 |
co_coun_00241 | counterfactual | coding_variant | hard | 4 | If OPTN were knocked out, its physical interaction with JAK2 would be lost. Which disease association of JAK2 could therefore be indirectly affected? | OPTN GENE_ENCODES_PROTEIN OPTN -> OPTN PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2 -> JAK2 GENE_ENCODES_PROTEIN JAK2 -> JAK2 GENE_ASSOCIATED_WITH_DISEASE superficial spreading melanoma | {
"steps": [
{
"hop": 1,
"source_node_id": "OPTN",
"source_node_type": "GENE",
"source_node_label": "OPTN",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "10133"... | superficial spreading melanoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "OPTN",
"source_db": "UniProt",
"payload": {
"accession": "Q96CV9",
"sequence": "MSHQPLSCLTEKEDSPSESTGNGPPHLAHPNLDTFTPEELLQQMKELLTENHQLKEAMKLNNQAMKGRFEELSAWTEKQKEERQFFEIQSKEAKERLMALSHENEKLKEELGKLKGKSERSSEDPTDDSRLPRA... | [
{
"source_db": "bridge",
"source_id": "10133",
"text": "OPTN GENE_ENCODES_PROTEIN OPTN",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "3717",
"text": "OPTN PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"knocked_out_gene": "OPTN",
"interaction_partner": "JAK2",
"affected_target": "superficial spreading melanoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00242 | counterfactual | coding_variant | hard | 3 | If ACTB were knocked out, the ACTB / BRCA1 / CENPA / H2AX... 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? | ACTB PROTEIN_MEMBER_OF_COMPLEX ACTB / BRCA1 / CENPA / H2AX... -> BRCA1 PROTEIN_MEMBER_OF_COMPLEX ACTB / BRCA1 / CENPA / H2AX... -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE Carcinoma, Spindle-Cell | {
"steps": [
{
"hop": 1,
"source_node_id": "ACTB",
"source_node_type": "GENE",
"source_node_label": "ACTB",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Co... | Carcinoma, Spindle-Cell | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACTB",
"source_db": "UniProt",
"payload": {
"accession": "P60709",
"sequence": "MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYV... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC6246",
"text": "ACTB PROTEIN_MEMBER_OF_COMPLEX ACTB / BRCA1 / CENPA / H2AX...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX ACTB / BRCA1 / CENPA / H2AX...",
"confi... | {
"knocked_out_gene": "ACTB",
"disrupted_complex": "ACTB / BRCA1 / CENPA / H2AX...",
"complex_partner": "BRCA1",
"affected_target": "Carcinoma, Spindle-Cell",
"target_kind": "disease",
"mechanism": "complex"
} | 0.669433 |
co_coun_00243 | counterfactual | coding_variant | hard | 4 | If CASP3 were knocked out, its physical interaction with TP53 would be lost. Which disease association of TP53 could therefore be indirectly affected? | CASP3 GENE_ENCODES_PROTEIN CASP3 -> CASP3 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_ASSOCIATED_WITH_DISEASE pancreatic neoplasm | {
"steps": [
{
"hop": 1,
"source_node_id": "CASP3",
"source_node_type": "GENE",
"source_node_label": "CASP3",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "836"... | pancreatic neoplasm | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CASP3",
"source_db": "UniProt",
"payload": {
"accession": "P42574",
"sequence": "MENTENSVDSKSIKNLEPKIIHGSESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGP... | [
{
"source_db": "bridge",
"source_id": "836",
"text": "CASP3 GENE_ENCODES_PROTEIN CASP3",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "CASP3 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "CASP3",
"interaction_partner": "TP53",
"affected_target": "pancreatic neoplasm",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.757632 |
co_coun_00244 | counterfactual | coding_variant | hard | 4 | If BRIP1 were knocked out, its physical interaction with MLH1 would be lost. Which disease association of MLH1 could therefore be indirectly affected? | BRIP1 GENE_ENCODES_PROTEIN BRIP1 -> BRIP1 PROTEIN_PHYSICALLY_INTERACTS_WITH MLH1 -> MLH1 GENE_ENCODES_PROTEIN MLH1 -> MLH1 GENE_ASSOCIATED_WITH_DISEASE brain astrocytoma | {
"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... | brain astrocytoma | 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": "4292",
"text": "BRIP1 PROTEIN_PHYSICALLY_INTERACTS_WITH MLH1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "BRIP1",
"interaction_partner": "MLH1",
"affected_target": "brain astrocytoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00245 | 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 lung carcinoma | {
"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"... | lung carcinoma | 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": "lung carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.685163 |
co_hall_00000 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | CDK1 GENE_ENCODES_PROTEIN CDK1 -> CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH WEE1 -> WEE1 GENE_ENCODES_PROTEIN WEE1 | {
"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",
... | A | [
"A. ENSP00000794310 interacts with NR2C1",
"B. CDK1 interacts with WEE1",
"C. BECN1 interacts with BRCA1",
"D. TIA1 interacts with RBM33"
] | [
"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": "7465",
"text": "CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH WEE1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"mode": "interaction",
"fabricated": "ENSP00000794310 interacts with NR2C1",
"real_options": [
"CDK1 interacts with WEE1",
"TIA1 interacts with RBM33",
"BECN1 interacts with BRCA1"
]
} | 0.9 |
co_hall_00001 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | PMS2 GENE_ENCODES_PROTEIN PMS2 -> PMS2 PROTEIN_PHYSICALLY_INTERACTS_WITH NSUN2 -> NSUN2 GENE_ENCODES_PROTEIN NSUN2 | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5395",... | D | [
"A. PMS2 interacts with NSUN2",
"B. ABCA7 interacts with PICALM",
"C. UBQLN2 interacts with PSMA3",
"D. YES1 interacts with DOCK1"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PMS2",
"source_db": "UniProt",
"payload": {
"accession": "P54278",
"sequence": "MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTR... | [
{
"source_db": "bridge",
"source_id": "5395",
"text": "PMS2 GENE_ENCODES_PROTEIN PMS2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "54888",
"text": "PMS2 PROTEIN_PHYSICALLY_INTERACTS_WITH NSUN2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"mode": "interaction",
"fabricated": "YES1 interacts with DOCK1",
"real_options": [
"PMS2 interacts with NSUN2",
"UBQLN2 interacts with PSMA3",
"ABCA7 interacts with PICALM"
]
} | 0.9 |
co_hall_00002 | hallucination_detection | coding_variant | easy | 1 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | PPP1R1B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PRKACB | {
"steps": [
{
"hop": 1,
"source_node_id": "PPP1R1B",
"source_node_type": "GENE",
"source_node_label": "PPP1R1B",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.963,
"edge_source_db": "STRING",
... | B | [
"A. RBBP5 interacts with SOX2",
"B. RIMS2 interacts with BIN3",
"C. TTI1 interacts with MTOR",
"D. PPP1R1B interacts with PRKACB"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PPP1R1B",
"source_db": "UniProt",
"payload": {
"accession": "Q9UD71",
"sequence": "MDPKDRKKIQFSVPAPPSQLDPRQVEMIRRRRPTPAMLFRLSEHSSPEEEASPHQRASGEGHHLKSKRPNPCAYTPPSLKAVQRIAESHLQSISNLNENQASEEEDELGELRELGYPREEDEEEEEDDEEE... | [
{
"source_db": "STRING",
"source_id": "PRKACB",
"text": "PPP1R1B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PRKACB",
"confidence": 0.963
}
] | {
"mode": "interaction",
"fabricated": "RIMS2 interacts with BIN3",
"real_options": [
"PPP1R1B interacts with PRKACB",
"RBBP5 interacts with SOX2",
"TTI1 interacts with MTOR"
]
} | 0.963 |
co_hall_00003 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | UBE2O GENE_ENCODES_PROTEIN UBE2O -> UBE2O PROTEIN_PHYSICALLY_INTERACTS_WITH BIN1 -> BIN1 GENE_ENCODES_PROTEIN BIN1 | {
"steps": [
{
"hop": 1,
"source_node_id": "UBE2O",
"source_node_type": "GENE",
"source_node_label": "UBE2O",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "6389... | D | [
"A. SMN1 interacts with SETX",
"B. UBE2O interacts with BIN1",
"C. CCND1 interacts with ITLN1",
"D. ENSP00000636289 interacts with MAP1LC3B"
] | [
"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": "63893",
"text": "UBE2O GENE_ENCODES_PROTEIN UBE2O",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "274",
"text": "UBE2O PROTEIN_PHYSICALLY_INTERACTS_WITH BIN1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"mode": "interaction",
"fabricated": "ENSP00000636289 interacts with MAP1LC3B",
"real_options": [
"UBE2O interacts with BIN1",
"SMN1 interacts with SETX",
"CCND1 interacts with ITLN1"
]
} | 0.9 |
co_hall_00004 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | IL4R GENE_ENCODES_PROTEIN IL4R -> IL4R PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2 -> JAK2 GENE_ENCODES_PROTEIN JAK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "IL4R",
"source_node_type": "GENE",
"source_node_label": "IL4R",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "3566",... | A | [
"A. ENSP00000525840 interacts with STAT3",
"B. ATM interacts with HLA-A",
"C. C9orf72 interacts with VPS33A",
"D. IL4R interacts with JAK2"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "JAK2",
"source_db": "UniProt",
"payload": {
"accession": "O60674",
"sequence": "MGMACLTMTEMEGTSTSSIYQNGDISGNANSMKQIDPVLQVYLYHSLGKSEADYLTFPSGEYVAEEICIAASKACGITPVYHNMFALMSETERIWYPPNHVFHIDESTRHNVLYRIRFYFPRWYCSGSNRAYRH... | [
{
"source_db": "bridge",
"source_id": "3566",
"text": "IL4R GENE_ENCODES_PROTEIN IL4R",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "3717",
"text": "IL4R PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"mode": "interaction",
"fabricated": "ENSP00000525840 interacts with STAT3",
"real_options": [
"IL4R interacts with JAK2",
"ATM interacts with HLA-A",
"C9orf72 interacts with VPS33A"
]
} | 0.9 |
co_hall_00005 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH RPS10 -> RPS10 GENE_ENCODES_PROTEIN RPS10 | {
"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",... | B | [
"A. SPOP interacts with SLC27A2",
"B. GSTP1 interacts with SLC30A9",
"C. WRN interacts with VCP",
"D. TP53 interacts with RPS10"
] | [
"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": "6204",
"text": "TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH RPS10",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"mode": "interaction",
"fabricated": "GSTP1 interacts with SLC30A9",
"real_options": [
"TP53 interacts with RPS10",
"WRN interacts with VCP",
"SPOP interacts with SLC27A2"
]
} | 0.9 |
co_hall_00006 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | CDC6 GENE_ENCODES_PROTEIN CDC6 -> CDC6 PROTEIN_PHYSICALLY_INTERACTS_WITH SQSTM1 -> SQSTM1 GENE_ENCODES_PROTEIN SQSTM1 | {
"steps": [
{
"hop": 1,
"source_node_id": "CDC6",
"source_node_type": "PROTEIN",
"source_node_label": "CDC6",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "990... | D | [
"A. EXO1 interacts with BRCA1",
"B. AKT1 interacts with EGLN1",
"C. CDC6 interacts with SQSTM1",
"D. MCM9 interacts with ENSP00000462995"
] | [
"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": "990",
"text": "CDC6 GENE_ENCODES_PROTEIN CDC6",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "8878",
"text": "CDC6 PROTEIN_PHYSICALLY_INTERACTS_WITH SQSTM1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"mode": "interaction",
"fabricated": "MCM9 interacts with ENSP00000462995",
"real_options": [
"CDC6 interacts with SQSTM1",
"AKT1 interacts with EGLN1",
"EXO1 interacts with BRCA1"
]
} | 0.9 |
co_hall_00007 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | CDKN2A GENE_ENCODES_PROTEIN CDKN2A -> CDKN2A PROTEIN_PHYSICALLY_INTERACTS_WITH CDK6 -> CDK6 GENE_ENCODES_PROTEIN CDK6 | {
"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... | B | [
"A. ESR1 interacts with MUC1",
"B. ENSP00000521963 interacts with UGT1A8",
"C. SQSTM1 interacts with CCND1",
"D. CDKN2A interacts with CDK6"
] | [
"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": "1021",
"text": "CDKN2A PROTEIN_PHYSICALLY_INTERACTS_WITH CDK6",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"mode": "interaction",
"fabricated": "ENSP00000521963 interacts with UGT1A8",
"real_options": [
"CDKN2A interacts with CDK6",
"SQSTM1 interacts with CCND1",
"ESR1 interacts with MUC1"
]
} | 0.9 |
co_hall_00008 | hallucination_detection | coding_variant | easy | 1 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | CDC25B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CHEK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "CDC25B",
"source_node_type": "GENE",
"source_node_label": "CDC25B",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.984,
"edge_source_db": "STRING",
... | A | [
"A. ENSP00000804524 interacts with FLOT2",
"B. BRIP1 interacts with RPA1",
"C. ASXL3 interacts with CDK1",
"D. CDC25B interacts with CHEK1"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDC25B",
"source_db": "UniProt",
"payload": {
"accession": "P30305",
"sequence": "MEVPQPEPAPGSALSPAGVCGGAQRPGHLPGLLLGSHGLLGSPVRAAASSPVTTLTQTMHDLAGLGSETPKSQVGTLLFRSRSRLTHLSLSRRASESSLSSESSESSDAGLCMDSPSPMDPHMAEQTFEQAI... | [
{
"source_db": "STRING",
"source_id": "CHEK1",
"text": "CDC25B PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CHEK1",
"confidence": 0.984
}
] | {
"mode": "interaction",
"fabricated": "ENSP00000804524 interacts with FLOT2",
"real_options": [
"CDC25B interacts with CHEK1",
"BRIP1 interacts with RPA1",
"ASXL3 interacts with CDK1"
]
} | 0.984 |
co_hall_00009 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH MEX3A -> MEX3A GENE_ENCODES_PROTEIN MEX3A | {
"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",... | C | [
"A. AR interacts with LINC00675",
"B. VCP interacts with EIF2S3",
"C. UBB_UBE2S interacts with MAGED1",
"D. TP53 interacts with MEX3A"
] | [
"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": "92312",
"text": "TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH MEX3A",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"mode": "interaction",
"fabricated": "UBB_UBE2S interacts with MAGED1",
"real_options": [
"TP53 interacts with MEX3A",
"VCP interacts with EIF2S3",
"AR interacts with LINC00675"
]
} | 0.9 |
co_hall_00010 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | CD2AP GENE_ENCODES_PROTEIN CD2AP -> CD2AP PROTEIN_PHYSICALLY_INTERACTS_WITH NR4A1 -> NR4A1 GENE_ENCODES_PROTEIN NR4A1 | {
"steps": [
{
"hop": 1,
"source_node_id": "CD2AP",
"source_node_type": "GENE",
"source_node_label": "CD2AP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2360... | C | [
"A. SOX2 interacts with LIMA1",
"B. CD2AP interacts with NR4A1",
"C. HK1 interacts with ENSP00000588661",
"D. FBXO22 interacts with PTEN"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD2AP",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y5K6",
"sequence": "MVDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKEIKRETEFKDDSLPIKRERHGNVASLVQRISTYGLPAGGIQPHPQTKNIKKKTKKRQCKVLFEYIPQNEDELELKVGD... | [
{
"source_db": "bridge",
"source_id": "23607",
"text": "CD2AP GENE_ENCODES_PROTEIN CD2AP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "3164",
"text": "CD2AP PROTEIN_PHYSICALLY_INTERACTS_WITH NR4A1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"mode": "interaction",
"fabricated": "HK1 interacts with ENSP00000588661",
"real_options": [
"CD2AP interacts with NR4A1",
"FBXO22 interacts with PTEN",
"SOX2 interacts with LIMA1"
]
} | 0.9 |
co_hall_00011 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | ZRANB1 GENE_ENCODES_PROTEIN ZRANB1 -> ZRANB1 PROTEIN_PHYSICALLY_INTERACTS_WITH ATM -> ATM GENE_ENCODES_PROTEIN ATM | {
"steps": [
{
"hop": 1,
"source_node_id": "ZRANB1",
"source_node_type": "GENE",
"source_node_label": "ZRANB1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "54... | D | [
"A. PFKP interacts with EGFR",
"B. BRCA2 interacts with RTEL1",
"C. ZRANB1 interacts with ATM",
"D. PRKDC interacts with ENSP00000627154"
] | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "bridge",
"source_id": "54764",
"text": "ZRANB1 GENE_ENCODES_PROTEIN ZRANB1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "472",
"text": "ZRANB1 PROTEIN_PHYSICALLY_INTERACTS_WITH ATM",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"mode": "interaction",
"fabricated": "PRKDC interacts with ENSP00000627154",
"real_options": [
"ZRANB1 interacts with ATM",
"PFKP interacts with EGFR",
"BRCA2 interacts with RTEL1"
]
} | 0.9 |
co_hall_00012 | hallucination_detection | coding_variant | easy | 1 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | AURKB PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDCA8 | {
"steps": [
{
"hop": 1,
"source_node_id": "AURKB",
"source_node_type": "GENE",
"source_node_label": "AURKB",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | A | [
"A. ME1 interacts with TEAD1",
"B. APOE interacts with TYRO3",
"C. AURKB interacts with CDCA8",
"D. MYC interacts with MRPL53"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AURKB",
"source_db": "UniProt",
"payload": {
"accession": "Q96GD4",
"sequence": "MAQKENSYPWPYGRQTAPSGLSTLPQRVLRKEPVTPSALVLMSRSNVQPTAAPGQKVMENSSGTPDILTRHFTIDDFEIGRPLGKGKFGNVYLAREKKSHFIVALKVLFKSQIEKEGVEHQLRREIEIQAHLH... | [
{
"source_db": "STRING",
"source_id": "CDCA8",
"text": "AURKB PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDCA8",
"confidence": 0.999
}
] | {
"mode": "interaction",
"fabricated": "ME1 interacts with TEAD1",
"real_options": [
"AURKB interacts with CDCA8",
"MYC interacts with MRPL53",
"APOE interacts with TYRO3"
]
} | 0.999 |
co_hall_00013 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | PTMA GENE_ENCODES_PROTEIN PTMA -> PTMA PROTEIN_PHYSICALLY_INTERACTS_WITH CDK1 -> CDK1 GENE_ENCODES_PROTEIN CDK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "PTMA",
"source_node_type": "GENE",
"source_node_label": "PTMA",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5757",... | B | [
"A. PTMA interacts with CDK1",
"B. NPTX1 interacts with PTCH1",
"C. REST interacts with SIN3B",
"D. MYC interacts with CEP57"
] | [
"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": "5757",
"text": "PTMA GENE_ENCODES_PROTEIN PTMA",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "983",
"text": "PTMA PROTEIN_PHYSICALLY_INTERACTS_WITH CDK1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"mode": "interaction",
"fabricated": "NPTX1 interacts with PTCH1",
"real_options": [
"PTMA interacts with CDK1",
"REST interacts with SIN3B",
"MYC interacts with CEP57"
]
} | 0.9 |
co_hall_00014 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | MYC GENE_ENCODES_PROTEIN MYC -> MYC PROTEIN_PHYSICALLY_INTERACTS_WITH HECTD3 -> HECTD3 GENE_ENCODES_PROTEIN HECTD3 | {
"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",
... | B | [
"A. CREBBP interacts with PSME3",
"B. ASNS interacts with TCOF1",
"C. ACKR3 interacts with CXCR4",
"D. MYC interacts with HECTD3"
] | [
"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": "79654",
"text": "MYC PROTEIN_PHYSICALLY_INTERACTS_WITH HECTD3",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"mode": "interaction",
"fabricated": "ASNS interacts with TCOF1",
"real_options": [
"MYC interacts with HECTD3",
"ACKR3 interacts with CXCR4",
"CREBBP interacts with PSME3"
]
} | 0.9 |
co_hall_00015 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | SOX2 GENE_ENCODES_PROTEIN SOX2 -> SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH PMVK -> PMVK GENE_ENCODES_PROTEIN PMVK | {
"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",... | A | [
"A. ENSP00000451166 interacts with ENSP00000626225",
"B. MEGF10 interacts with ACTB",
"C. SOX2 interacts with PMVK",
"D. BRCA1 interacts with TALDO1"
] | [
"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": "10654",
"text": "SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH PMVK",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"mode": "interaction",
"fabricated": "ENSP00000451166 interacts with ENSP00000626225",
"real_options": [
"SOX2 interacts with PMVK",
"MEGF10 interacts with ACTB",
"BRCA1 interacts with TALDO1"
]
} | 0.9 |
co_hall_00016 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | SNCA GENE_ENCODES_PROTEIN SNCA -> SNCA PROTEIN_PHYSICALLY_INTERACTS_WITH KIF5B -> KIF5B GENE_ENCODES_PROTEIN KIF5B | {
"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",... | D | [
"A. AURKB interacts with PKM",
"B. AR interacts with YAP1",
"C. SNCA interacts with KIF5B",
"D. BST1 interacts with MICAL2"
] | [
"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": "3799",
"text": "SNCA PROTEIN_PHYSICALLY_INTERACTS_WITH KIF5B",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"mode": "interaction",
"fabricated": "BST1 interacts with MICAL2",
"real_options": [
"SNCA interacts with KIF5B",
"AR interacts with YAP1",
"AURKB interacts with PKM"
]
} | 0.9 |
co_hall_00017 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | ANKRA2 GENE_ENCODES_PROTEIN ANKRA2 -> ANKRA2 PROTEIN_PHYSICALLY_INTERACTS_WITH CDK4 -> CDK4 GENE_ENCODES_PROTEIN CDK4 | {
"steps": [
{
"hop": 1,
"source_node_id": "ANKRA2",
"source_node_type": "GENE",
"source_node_label": "ANKRA2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "57... | B | [
"A. ATXN1 interacts with SNCA",
"B. ENSP00000365310 interacts with ENSP00000506212",
"C. C9orf72 interacts with CDC23",
"D. ANKRA2 interacts with CDK4"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK4",
"source_db": "UniProt",
"payload": {
"accession": "P11802",
"sequence": "MATSRYEPVAEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGGGGGGGLPISTVREVALLRRLEAFEHPNVVRLMDVCATSRTDREIKVTLVFEHVDQDLRTYLDKAPPPGLPAETIKDLMRQFLRGLDFLHAN... | [
{
"source_db": "bridge",
"source_id": "57763",
"text": "ANKRA2 GENE_ENCODES_PROTEIN ANKRA2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1019",
"text": "ANKRA2 PROTEIN_PHYSICALLY_INTERACTS_WITH CDK4",
"confidence": 0.9
},
{
"source_db": "bridge",
"sou... | {
"mode": "interaction",
"fabricated": "ENSP00000365310 interacts with ENSP00000506212",
"real_options": [
"ANKRA2 interacts with CDK4",
"ATXN1 interacts with SNCA",
"C9orf72 interacts with CDC23"
]
} | 0.9 |
co_hall_00018 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | C9orf72 GENE_ENCODES_PROTEIN C9orf72 -> C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH ILVBL -> ILVBL GENE_ENCODES_PROTEIN ILVBL | {
"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": "... | B | [
"A. TWIST1 interacts with SPOP",
"B. ENSP00000265734 interacts with SLC35D1",
"C. RAD51 interacts with ABL1",
"D. C9orf72 interacts with ILVBL"
] | [
"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": "10994",
"text": "C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH ILVBL",
"confidence": 0.9
},
{
"source_db": "bridge",
... | {
"mode": "interaction",
"fabricated": "ENSP00000265734 interacts with SLC35D1",
"real_options": [
"C9orf72 interacts with ILVBL",
"RAD51 interacts with ABL1",
"TWIST1 interacts with SPOP"
]
} | 0.9 |
co_hall_00019 | hallucination_detection | coding_variant | easy | 1 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | FBXO7 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PINK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "FBXO7",
"source_node_type": "GENE",
"source_node_label": "FBXO7",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.995,
"edge_source_db": "STRING",
... | D | [
"A. PFN1 interacts with GPHN",
"B. SNX2 interacts with LEPR",
"C. FBXO7 interacts with PINK1",
"D. ENSP00000693561 interacts with KRT2"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FBXO7",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y3I1",
"sequence": "MRLRVRLLKRTWPLEVPETEPTLGHLRSHLRQSLLCTWGYSSNTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPAPNIPSSTDSEHSSLQNNEQPSLATSSNQTSMQDEQPSDSFQGQAAQSGV... | [
{
"source_db": "STRING",
"source_id": "PINK1",
"text": "FBXO7 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PINK1",
"confidence": 0.995
}
] | {
"mode": "interaction",
"fabricated": "ENSP00000693561 interacts with KRT2",
"real_options": [
"FBXO7 interacts with PINK1",
"SNX2 interacts with LEPR",
"PFN1 interacts with GPHN"
]
} | 0.995 |
co_hall_00020 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | MYC GENE_ENCODES_PROTEIN MYC -> MYC PROTEIN_PHYSICALLY_INTERACTS_WITH CCNH -> CCNH GENE_ENCODES_PROTEIN CCNH | {
"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",
... | C | [
"A. AKAP11 interacts with PRKAR1A",
"B. MYC interacts with CCNH",
"C. RAD9A interacts with RBBP7",
"D. C9orf72 interacts with PABPC1"
] | [
"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": "902",
"text": "MYC PROTEIN_PHYSICALLY_INTERACTS_WITH CCNH",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "C... | {
"mode": "interaction",
"fabricated": "RAD9A interacts with RBBP7",
"real_options": [
"MYC interacts with CCNH",
"C9orf72 interacts with PABPC1",
"AKAP11 interacts with PRKAR1A"
]
} | 0.9 |
co_hall_00021 | hallucination_detection | coding_variant | easy | 1 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | DDX41 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH NKAP | {
"steps": [
{
"hop": 1,
"source_node_id": "DDX41",
"source_node_type": "GENE",
"source_node_label": "DDX41",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.847,
"edge_source_db": "STRING",
... | A | [
"A. KIAA1429 interacts with ZBTB17",
"B. DDX41 interacts with NKAP",
"C. LMO4 interacts with ESR1",
"D. FBXO7 interacts with PARK7"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "DDX41",
"source_db": "UniProt",
"payload": {
"accession": "Q9UJV9",
"sequence": "MEESEPERKRARTDEVPAGGSRSEAEDEDDEDYVPYVPLRQRRQLLLQKLLQRRRKGAAEEEQQDSGSEPRGDEDDIPLGPQSNVSLLDQHQHLKEKAEARKESAKEKQLKEEEKILESVAEGRALMSVKEMA... | [
{
"source_db": "STRING",
"source_id": "NKAP",
"text": "DDX41 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH NKAP",
"confidence": 0.847
}
] | {
"mode": "interaction",
"fabricated": "KIAA1429 interacts with ZBTB17",
"real_options": [
"DDX41 interacts with NKAP",
"FBXO7 interacts with PARK7",
"LMO4 interacts with ESR1"
]
} | 0.847 |
co_hall_00022 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | KRAS GENE_ENCODES_PROTEIN KRAS -> KRAS PROTEIN_PHYSICALLY_INTERACTS_WITH MAPKAP1 -> MAPKAP1 GENE_ENCODES_PROTEIN MAPKAP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "KRAS",
"source_node_type": "GENE",
"source_node_label": "KRAS",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "3845",... | B | [
"A. VCP interacts with UQCRC1",
"B. SDCBP interacts with UBA52_UBE2E3",
"C. AKT1 interacts with KANK1",
"D. KRAS interacts with MAPKAP1"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KRAS",
"source_db": "UniProt",
"payload": {
"accession": "P01116",
"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLA... | [
{
"source_db": "bridge",
"source_id": "3845",
"text": "KRAS GENE_ENCODES_PROTEIN KRAS",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "79109",
"text": "KRAS PROTEIN_PHYSICALLY_INTERACTS_WITH MAPKAP1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"mode": "interaction",
"fabricated": "SDCBP interacts with UBA52_UBE2E3",
"real_options": [
"KRAS interacts with MAPKAP1",
"VCP interacts with UQCRC1",
"AKT1 interacts with KANK1"
]
} | 0.9 |
co_hall_00023 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | CD44 GENE_ENCODES_PROTEIN CD44 -> CD44 PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR | {
"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",
... | C | [
"A. AURKB interacts with AURKA",
"B. CD44 interacts with EGFR",
"C. ENSP00000788323 interacts with DDX42",
"D. MLH1 interacts with CREBBP"
] | [
"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": "1956",
"text": "CD44 PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"mode": "interaction",
"fabricated": "ENSP00000788323 interacts with DDX42",
"real_options": [
"CD44 interacts with EGFR",
"AURKB interacts with AURKA",
"MLH1 interacts with CREBBP"
]
} | 0.9 |
co_hall_00024 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | MLH1 GENE_ENCODES_PROTEIN MLH1 -> MLH1 PROTEIN_PHYSICALLY_INTERACTS_WITH ATM -> ATM GENE_ENCODES_PROTEIN ATM | {
"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",... | D | [
"A. TP53 interacts with SLC38A10",
"B. MLH1 interacts with ATM",
"C. BCOR interacts with RNF2",
"D. PPP5C interacts with NKX1-1"
] | [
"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": "472",
"text": "MLH1 PROTEIN_PHYSICALLY_INTERACTS_WITH ATM",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"mode": "interaction",
"fabricated": "PPP5C interacts with NKX1-1",
"real_options": [
"MLH1 interacts with ATM",
"TP53 interacts with SLC38A10",
"BCOR interacts with RNF2"
]
} | 0.9 |
co_hall_00025 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | ABL1 GENE_ENCODES_PROTEIN ABL1 -> ABL1 PROTEIN_PHYSICALLY_INTERACTS_WITH HSPD1 -> HSPD1 GENE_ENCODES_PROTEIN HSPD1 | {
"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",
... | D | [
"A. ABL1 interacts with HSPD1",
"B. CASP3 interacts with SP1",
"C. SIRPA interacts with AKT1",
"D. HELZ interacts with ENSP00000490388"
] | [
"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": "3329",
"text": "ABL1 PROTEIN_PHYSICALLY_INTERACTS_WITH HSPD1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"mode": "interaction",
"fabricated": "HELZ interacts with ENSP00000490388",
"real_options": [
"ABL1 interacts with HSPD1",
"CASP3 interacts with SP1",
"SIRPA interacts with AKT1"
]
} | 0.9 |
co_hall_00026 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | GRWD1 GENE_ENCODES_PROTEIN GRWD1 -> GRWD1 PROTEIN_PHYSICALLY_INTERACTS_WITH KMT2D -> KMT2D GENE_ENCODES_PROTEIN KMT2D | {
"steps": [
{
"hop": 1,
"source_node_id": "GRWD1",
"source_node_type": "GENE",
"source_node_label": "GRWD1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "8374... | C | [
"A. GRWD1 interacts with KMT2D",
"B. KCTD11 interacts with CTNNB1",
"C. SMARCA2 interacts with ETV3",
"D. CDK4 interacts with CCND3"
] | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2D",
"source_db": "UniProt",
"payload": {
"accession": "O14686",
"sequence": "MDSQKLAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSSGSPRLQETPQDCSGGPVRRCALCNCGEPSLHGQRELRRFELPFDWPRCPVVSPGGSPGPNEAVLPSEDLSQIGFPEGLTPAHLGEPG... | [
{
"source_db": "bridge",
"source_id": "83743",
"text": "GRWD1 GENE_ENCODES_PROTEIN GRWD1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "8085",
"text": "GRWD1 PROTEIN_PHYSICALLY_INTERACTS_WITH KMT2D",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"mode": "interaction",
"fabricated": "SMARCA2 interacts with ETV3",
"real_options": [
"GRWD1 interacts with KMT2D",
"CDK4 interacts with CCND3",
"KCTD11 interacts with CTNNB1"
]
} | 0.9 |
co_hall_00027 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | SNCA GENE_ENCODES_PROTEIN SNCA -> SNCA PROTEIN_PHYSICALLY_INTERACTS_WITH PLIN1 -> PLIN1 GENE_ENCODES_PROTEIN PLIN1 | {
"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",... | C | [
"A. AURKB interacts with NSL1",
"B. SNCA interacts with PLIN1",
"C. CRABP2 interacts with RPS27A_UBE2V1",
"D. BUB1B interacts with CDC20"
] | [
"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": "5346",
"text": "SNCA PROTEIN_PHYSICALLY_INTERACTS_WITH PLIN1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"mode": "interaction",
"fabricated": "CRABP2 interacts with RPS27A_UBE2V1",
"real_options": [
"SNCA interacts with PLIN1",
"BUB1B interacts with CDC20",
"AURKB interacts with NSL1"
]
} | 0.9 |
co_hall_00028 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | LRRK2 GENE_ENCODES_PROTEIN LRRK2 -> LRRK2 PROTEIN_PHYSICALLY_INTERACTS_WITH RHOA -> RHOA GENE_ENCODES_PROTEIN RHOA | {
"steps": [
{
"hop": 1,
"source_node_id": "LRRK2",
"source_node_type": "GENE",
"source_node_label": "LRRK2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1208... | C | [
"A. FBXL2 interacts with AURKB",
"B. LRRK2 interacts with RHOA",
"C. ENSP00000633340 interacts with PPP1R9B",
"D. PTEN interacts with SMURF1"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "LRRK2",
"source_db": "UniProt",
"payload": {
"accession": "Q5S007",
"sequence": "MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNIHVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILKMLTVHNASVNLSV... | [
{
"source_db": "bridge",
"source_id": "120892",
"text": "LRRK2 GENE_ENCODES_PROTEIN LRRK2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "387",
"text": "LRRK2 PROTEIN_PHYSICALLY_INTERACTS_WITH RHOA",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"mode": "interaction",
"fabricated": "ENSP00000633340 interacts with PPP1R9B",
"real_options": [
"LRRK2 interacts with RHOA",
"FBXL2 interacts with AURKB",
"PTEN interacts with SMURF1"
]
} | 0.9 |
co_hall_00029 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | C9orf72 GENE_ENCODES_PROTEIN C9orf72 -> C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH PPIH -> PPIH GENE_ENCODES_PROTEIN PPIH | {
"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": "... | B | [
"A. MTOR interacts with KEAP1",
"B. HAT1 interacts with SCN3B",
"C. RXRA interacts with NR1I2",
"D. C9orf72 interacts with PPIH"
] | [
"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": "10465",
"text": "C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH PPIH",
"confidence": 0.9
},
{
"source_db": "bridge",
... | {
"mode": "interaction",
"fabricated": "HAT1 interacts with SCN3B",
"real_options": [
"C9orf72 interacts with PPIH",
"RXRA interacts with NR1I2",
"MTOR interacts with KEAP1"
]
} | 0.9 |
co_hall_00030 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | CEBPD GENE_ENCODES_PROTEIN CEBPD -> CEBPD PROTEIN_PHYSICALLY_INTERACTS_WITH CREBBP -> CREBBP GENE_ENCODES_PROTEIN CREBBP | {
"steps": [
{
"hop": 1,
"source_node_id": "CEBPD",
"source_node_type": "GENE",
"source_node_label": "CEBPD",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1052... | B | [
"A. CEBPD interacts with CREBBP",
"B. ENSP00000526474 interacts with CT55",
"C. FYN interacts with CBL",
"D. TP53 interacts with SYT5"
] | [
"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": "1052",
"text": "CEBPD GENE_ENCODES_PROTEIN CEBPD",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1387",
"text": "CEBPD PROTEIN_PHYSICALLY_INTERACTS_WITH CREBBP",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"mode": "interaction",
"fabricated": "ENSP00000526474 interacts with CT55",
"real_options": [
"CEBPD interacts with CREBBP",
"TP53 interacts with SYT5",
"FYN interacts with CBL"
]
} | 0.9 |
co_hall_00031 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | VCP GENE_ENCODES_PROTEIN VCP -> VCP PROTEIN_PHYSICALLY_INTERACTS_WITH TUBB3 -> TUBB3 GENE_ENCODES_PROTEIN TUBB3 | {
"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",
... | B | [
"A. MLH1 interacts with VAMP8",
"B. ENSP00000602632 interacts with DFFA",
"C. CDKN2A interacts with PML",
"D. VCP interacts with TUBB3"
] | [
"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": "10381",
"text": "VCP PROTEIN_PHYSICALLY_INTERACTS_WITH TUBB3",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"mode": "interaction",
"fabricated": "ENSP00000602632 interacts with DFFA",
"real_options": [
"VCP interacts with TUBB3",
"MLH1 interacts with VAMP8",
"CDKN2A interacts with PML"
]
} | 0.9 |
co_hall_00032 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | CDH1 GENE_ENCODES_PROTEIN CDH1 -> CDH1 PROTEIN_PHYSICALLY_INTERACTS_WITH CREBBP -> CREBBP GENE_ENCODES_PROTEIN CREBBP | {
"steps": [
{
"hop": 1,
"source_node_id": "CDH1",
"source_node_type": "GENE",
"source_node_label": "CDH1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "999",
... | B | [
"A. LRRC37A interacts with SNCA",
"B. IL17F interacts with ENSP00000607716",
"C. CDH1 interacts with CREBBP",
"D. SPRTN interacts with VCP"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDH1",
"source_db": "UniProt",
"payload": {
"accession": "P12830",
"sequence": "MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGHHHRPPPHQASVSG... | [
{
"source_db": "bridge",
"source_id": "999",
"text": "CDH1 GENE_ENCODES_PROTEIN CDH1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1387",
"text": "CDH1 PROTEIN_PHYSICALLY_INTERACTS_WITH CREBBP",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"mode": "interaction",
"fabricated": "IL17F interacts with ENSP00000607716",
"real_options": [
"CDH1 interacts with CREBBP",
"LRRC37A interacts with SNCA",
"SPRTN interacts with VCP"
]
} | 0.9 |
co_hall_00033 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | TBK1 GENE_ENCODES_PROTEIN TBK1 -> TBK1 PROTEIN_PHYSICALLY_INTERACTS_WITH MSR1 -> MSR1 GENE_ENCODES_PROTEIN MSR1 | {
"steps": [
{
"hop": 1,
"source_node_id": "TBK1",
"source_node_type": "GENE",
"source_node_label": "TBK1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "29110"... | A | [
"A. MAPK3 interacts with ACADM",
"B. TBK1 interacts with MSR1",
"C. TP53 interacts with UBE4B",
"D. TUBB interacts with MYC"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TBK1",
"source_db": "UniProt",
"payload": {
"accession": "Q9UHD2",
"sequence": "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHR... | [
{
"source_db": "bridge",
"source_id": "29110",
"text": "TBK1 GENE_ENCODES_PROTEIN TBK1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4481",
"text": "TBK1 PROTEIN_PHYSICALLY_INTERACTS_WITH MSR1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"mode": "interaction",
"fabricated": "MAPK3 interacts with ACADM",
"real_options": [
"TBK1 interacts with MSR1",
"TUBB interacts with MYC",
"TP53 interacts with UBE4B"
]
} | 0.9 |
co_hall_00034 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | APP GENE_ENCODES_PROTEIN APP -> APP PROTEIN_PHYSICALLY_INTERACTS_WITH AP1M2 -> AP1M2 GENE_ENCODES_PROTEIN AP1M2 | {
"steps": [
{
"hop": 1,
"source_node_id": "APP",
"source_node_type": "GENE",
"source_node_label": "APP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "351",
... | C | [
"A. APP interacts with AP1M2",
"B. UBQLN2 interacts with TMUB2",
"C. UBC_UBE2D4 interacts with MYH10",
"D. INPPL1 interacts with MET"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APP",
"source_db": "UniProt",
"payload": {
"accession": "P05067",
"sequence": "MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKF... | [
{
"source_db": "bridge",
"source_id": "351",
"text": "APP GENE_ENCODES_PROTEIN APP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "10053",
"text": "APP PROTEIN_PHYSICALLY_INTERACTS_WITH AP1M2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"mode": "interaction",
"fabricated": "UBC_UBE2D4 interacts with MYH10",
"real_options": [
"APP interacts with AP1M2",
"UBQLN2 interacts with TMUB2",
"INPPL1 interacts with MET"
]
} | 0.9 |
co_hall_00035 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | ANP32A GENE_ENCODES_PROTEIN ANP32A -> ANP32A PROTEIN_PHYSICALLY_INTERACTS_WITH PGR -> PGR GENE_ENCODES_PROTEIN PGR | {
"steps": [
{
"hop": 1,
"source_node_id": "ANP32A",
"source_node_type": "GENE",
"source_node_label": "ANP32A",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "81... | B | [
"A. CEBPB interacts with CREBBP",
"B. PPP1R7 interacts with CEBPB",
"C. ANP32A interacts with PGR",
"D. RB1 interacts with POLD1"
] | [
"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": "8125",
"text": "ANP32A GENE_ENCODES_PROTEIN ANP32A",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5241",
"text": "ANP32A PROTEIN_PHYSICALLY_INTERACTS_WITH PGR",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"mode": "interaction",
"fabricated": "PPP1R7 interacts with CEBPB",
"real_options": [
"ANP32A interacts with PGR",
"CEBPB interacts with CREBBP",
"RB1 interacts with POLD1"
]
} | 0.9 |
co_hall_00036 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | BCL2L1 GENE_ENCODES_PROTEIN BCL2L1 -> BCL2L1 PROTEIN_PHYSICALLY_INTERACTS_WITH BCL2 -> BCL2 GENE_ENCODES_PROTEIN BCL2 | {
"steps": [
{
"hop": 1,
"source_node_id": "BCL2L1",
"source_node_type": "PROTEIN",
"source_node_label": "BCL2L1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": ... | A | [
"A. ENSP00000407720 interacts with ENSP00000393628",
"B. CDKN2A interacts with HIF1A",
"C. BCL2L1 interacts with BCL2",
"D. SOX2 interacts with YLPM1"
] | [
"expression",
"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": "598",
"text": "BCL2L1 GENE_ENCODES_PROTEIN BCL2L1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "596",
"text": "BCL2L1 PROTEIN_PHYSICALLY_INTERACTS_WITH BCL2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"mode": "interaction",
"fabricated": "ENSP00000407720 interacts with ENSP00000393628",
"real_options": [
"BCL2L1 interacts with BCL2",
"CDKN2A interacts with HIF1A",
"SOX2 interacts with YLPM1"
]
} | 0.9 |
co_hall_00037 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | CD44 GENE_ENCODES_PROTEIN CD44 -> CD44 PROTEIN_PHYSICALLY_INTERACTS_WITH EHD1 -> EHD1 GENE_ENCODES_PROTEIN EHD1 | {
"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",
... | D | [
"A. CD274 interacts with VPRBP",
"B. EPHA2 interacts with NF1",
"C. CD44 interacts with EHD1",
"D. WASH1 interacts with ENSP00000677263"
] | [
"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": "10938",
"text": "CD44 PROTEIN_PHYSICALLY_INTERACTS_WITH EHD1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"mode": "interaction",
"fabricated": "WASH1 interacts with ENSP00000677263",
"real_options": [
"CD44 interacts with EHD1",
"CD274 interacts with VPRBP",
"EPHA2 interacts with NF1"
]
} | 0.9 |
co_hall_00038 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH TPT1 -> TPT1 GENE_ENCODES_PROTEIN TPT1 | {
"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",... | C | [
"A. TP53 interacts with TPT1",
"B. DNMT3A interacts with MIR124-3",
"C. SNAI2 interacts with CDC42",
"D. DCLK3 interacts with ADM"
] | [
"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": "7178",
"text": "TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH TPT1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"mode": "interaction",
"fabricated": "SNAI2 interacts with CDC42",
"real_options": [
"TP53 interacts with TPT1",
"DNMT3A interacts with MIR124-3",
"DCLK3 interacts with ADM"
]
} | 0.9 |
co_hall_00039 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | HMGA1 GENE_ENCODES_PROTEIN HMGA1 -> HMGA1 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "HMGA1",
"source_node_type": "GENE",
"source_node_label": "HMGA1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "3159... | C | [
"A. C9orf72 interacts with USMG5",
"B. HMGA1 interacts with TP53",
"C. CCT8 interacts with ENSP00000615817",
"D. APP interacts with LGALS3BP"
] | [
"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": "3159",
"text": "HMGA1 GENE_ENCODES_PROTEIN HMGA1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "HMGA1 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"mode": "interaction",
"fabricated": "CCT8 interacts with ENSP00000615817",
"real_options": [
"HMGA1 interacts with TP53",
"C9orf72 interacts with USMG5",
"APP interacts with LGALS3BP"
]
} | 0.9 |
co_hall_00040 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH IPO7 -> IPO7 GENE_ENCODES_PROTEIN IPO7 | {
"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",... | D | [
"A. EGFR interacts with IPO7",
"B. ASXL1 interacts with TUFM",
"C. TP53 interacts with AATF",
"D. ENSP00000576339 interacts with PIK3CB"
] | [
"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": "10527",
"text": "EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH IPO7",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"mode": "interaction",
"fabricated": "ENSP00000576339 interacts with PIK3CB",
"real_options": [
"EGFR interacts with IPO7",
"TP53 interacts with AATF",
"ASXL1 interacts with TUFM"
]
} | 0.9 |
co_hall_00041 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | SPOP GENE_ENCODES_PROTEIN SPOP -> SPOP PROTEIN_PHYSICALLY_INTERACTS_WITH ERF -> ERF GENE_ENCODES_PROTEIN ERF | {
"steps": [
{
"hop": 1,
"source_node_id": "SPOP",
"source_node_type": "GENE",
"source_node_label": "SPOP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "8405",... | D | [
"A. MAPK1 interacts with HNF4A",
"B. SPOP interacts with ERF",
"C. ATM interacts with FEN1",
"D. ENSP00000465673 interacts with BIRC6"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SPOP",
"source_db": "UniProt",
"payload": {
"accession": "O43791",
"sequence": "MSRVPSPPPPAEMSSGPVAESWCYTQIKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFK... | [
{
"source_db": "bridge",
"source_id": "8405",
"text": "SPOP GENE_ENCODES_PROTEIN SPOP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2077",
"text": "SPOP PROTEIN_PHYSICALLY_INTERACTS_WITH ERF",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"mode": "interaction",
"fabricated": "ENSP00000465673 interacts with BIRC6",
"real_options": [
"SPOP interacts with ERF",
"ATM interacts with FEN1",
"MAPK1 interacts with HNF4A"
]
} | 0.9 |
co_hall_00042 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH ATIC -> ATIC GENE_ENCODES_PROTEIN ATIC | {
"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",... | D | [
"A. EGFR interacts with ATIC",
"B. PSEN1 interacts with DHCR24",
"C. RXRA interacts with TRIP4",
"D. POLR2A interacts with FOXF1"
] | [
"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": "471",
"text": "EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH ATIC",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"mode": "interaction",
"fabricated": "POLR2A interacts with FOXF1",
"real_options": [
"EGFR interacts with ATIC",
"PSEN1 interacts with DHCR24",
"RXRA interacts with TRIP4"
]
} | 0.9 |
co_hall_00043 | hallucination_detection | coding_variant | easy | 1 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | AOPEP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AGT | {
"steps": [
{
"hop": 1,
"source_node_id": "AOPEP",
"source_node_type": "GENE",
"source_node_label": "AOPEP",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.769,
"edge_source_db": "STRING",
... | A | [
"A. CT47A9 interacts with Transitional endoplasmic reticulum ATPase",
"B. ESR1 interacts with MED24",
"C. AOPEP interacts with AGT",
"D. PSEN1 interacts with APH1A"
] | [
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AOPEP",
"source_db": "UniProt",
"payload": {
"accession": "Q8N6M6",
"sequence": "MDIQLDPARDDLPLMANTSHILVKHYVLDLDVDFESQVIEGTIVLFLEDGNRFKKQNSSIEEACQSESNKACKFGMPEPCHIPVTNARTFSSEMEYNDFAICSKGEKDTSDKDGNHDNQEHASGISSSKYCCD... | [
{
"source_db": "STRING",
"source_id": "AGT",
"text": "AOPEP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AGT",
"confidence": 0.769
}
] | {
"mode": "interaction",
"fabricated": "CT47A9 interacts with Transitional endoplasmic reticulum ATPase",
"real_options": [
"AOPEP interacts with AGT",
"ESR1 interacts with MED24",
"PSEN1 interacts with APH1A"
]
} | 0.769 |
co_hall_00044 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH CDC25C -> CDC25C GENE_ENCODES_PROTEIN CDC25C | {
"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",... | A | [
"A. ROCK1 interacts with ARID3B",
"B. MLH1 interacts with GABARAP",
"C. EGFR interacts with CDC25C",
"D. CTNNB1 interacts with SQSTM1"
] | [
"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": "995",
"text": "EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH CDC25C",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"mode": "interaction",
"fabricated": "ROCK1 interacts with ARID3B",
"real_options": [
"EGFR interacts with CDC25C",
"MLH1 interacts with GABARAP",
"CTNNB1 interacts with SQSTM1"
]
} | 0.9 |
co_hall_00045 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | RPS27A GENE_ENCODES_PROTEIN RPS27A -> RPS27A PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "RPS27A",
"source_node_type": "PROTEIN",
"source_node_label": "RPS27A",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": ... | D | [
"A. APP interacts with APBA2",
"B. ESR1 interacts with SMC4",
"C. RPS27A interacts with TP53",
"D. EIF2B1 interacts with ENSP00000535312"
] | [
"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": "6233",
"text": "RPS27A GENE_ENCODES_PROTEIN RPS27A",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "RPS27A PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"mode": "interaction",
"fabricated": "EIF2B1 interacts with ENSP00000535312",
"real_options": [
"RPS27A interacts with TP53",
"APP interacts with APBA2",
"ESR1 interacts with SMC4"
]
} | 0.9 |
co_hall_00046 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | MLH1 GENE_ENCODES_PROTEIN MLH1 -> MLH1 PROTEIN_PHYSICALLY_INTERACTS_WITH HDAC6 -> HDAC6 GENE_ENCODES_PROTEIN HDAC6 | {
"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",... | A | [
"A. ENSP00000453002 interacts with CDC20",
"B. MLH1 interacts with HDAC6",
"C. VCP interacts with GAPDH",
"D. C9orf72 interacts with USP11"
] | [
"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": "10013",
"text": "MLH1 PROTEIN_PHYSICALLY_INTERACTS_WITH HDAC6",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"mode": "interaction",
"fabricated": "ENSP00000453002 interacts with CDC20",
"real_options": [
"MLH1 interacts with HDAC6",
"VCP interacts with GAPDH",
"C9orf72 interacts with USP11"
]
} | 0.9 |
co_hall_00047 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | C9orf72 GENE_ENCODES_PROTEIN C9orf72 -> C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH CKMT1A -> CKMT1A GENE_ENCODES_PROTEIN CKMT1A | {
"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": "... | A | [
"A. ENSP00000368032 interacts with ENSP00000730617",
"B. SFRP4 interacts with WNT5A",
"C. C9orf72 interacts with CKMT1A",
"D. EGFR interacts with RANGAP1"
] | [
"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": "548596",
"text": "C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH CKMT1A",
"confidence": 0.9
},
{
"source_db": "bridge",
... | {
"mode": "interaction",
"fabricated": "ENSP00000368032 interacts with ENSP00000730617",
"real_options": [
"C9orf72 interacts with CKMT1A",
"SFRP4 interacts with WNT5A",
"EGFR interacts with RANGAP1"
]
} | 0.9 |
co_hall_00048 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | SUCLG2 GENE_ENCODES_PROTEIN SUCLG2 -> SUCLG2 PROTEIN_PHYSICALLY_INTERACTS_WITH KMT2D -> KMT2D GENE_ENCODES_PROTEIN KMT2D | {
"steps": [
{
"hop": 1,
"source_node_id": "SUCLG2",
"source_node_type": "GENE",
"source_node_label": "SUCLG2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "88... | A | [
"A. ENSP00000444286 interacts with SUPT6H",
"B. SUCLG2 interacts with KMT2D",
"C. TP53 interacts with EP400",
"D. MYC interacts with HNRNPU"
] | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2D",
"source_db": "UniProt",
"payload": {
"accession": "O14686",
"sequence": "MDSQKLAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSSGSPRLQETPQDCSGGPVRRCALCNCGEPSLHGQRELRRFELPFDWPRCPVVSPGGSPGPNEAVLPSEDLSQIGFPEGLTPAHLGEPG... | [
{
"source_db": "bridge",
"source_id": "8801",
"text": "SUCLG2 GENE_ENCODES_PROTEIN SUCLG2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "8085",
"text": "SUCLG2 PROTEIN_PHYSICALLY_INTERACTS_WITH KMT2D",
"confidence": 0.9
},
{
"source_db": "bridge",
"sou... | {
"mode": "interaction",
"fabricated": "ENSP00000444286 interacts with SUPT6H",
"real_options": [
"SUCLG2 interacts with KMT2D",
"TP53 interacts with EP400",
"MYC interacts with HNRNPU"
]
} | 0.9 |
co_hall_00049 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | SFPQ GENE_ENCODES_PROTEIN SFPQ -> SFPQ PROTEIN_PHYSICALLY_INTERACTS_WITH RAD51D -> RAD51D GENE_ENCODES_PROTEIN RAD51D | {
"steps": [
{
"hop": 1,
"source_node_id": "SFPQ",
"source_node_type": "PROTEIN",
"source_node_label": "SFPQ",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "642... | B | [
"A. POLR2A interacts with CDKN1A",
"B. RPS27A_UBE2G2 interacts with ENSP00000466887",
"C. EGFR interacts with NEDD4L",
"D. SFPQ interacts with RAD51D"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RAD51D",
"source_db": "UniProt",
"payload": {
"accession": "O75771",
"sequence": "MGVLRVGLCPGLTEEMIQLLRSHRIKTVVDLVSADLEEVAQKCGLSYKALVALRRVLLAQFSAFPVNGADLYEELKTSTAILSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCMAANVAHGLQQNV... | [
{
"source_db": "bridge",
"source_id": "6421",
"text": "SFPQ GENE_ENCODES_PROTEIN SFPQ",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5892",
"text": "SFPQ PROTEIN_PHYSICALLY_INTERACTS_WITH RAD51D",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"mode": "interaction",
"fabricated": "RPS27A_UBE2G2 interacts with ENSP00000466887",
"real_options": [
"SFPQ interacts with RAD51D",
"POLR2A interacts with CDKN1A",
"EGFR interacts with NEDD4L"
]
} | 0.9 |
co_hall_00050 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | PROP1 GENE_ENCODES_PROTEIN PROP1 -> PROP1 PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1 -> CTNNB1 GENE_ENCODES_PROTEIN CTNNB1 | {
"steps": [
{
"hop": 1,
"source_node_id": "PROP1",
"source_node_type": "GENE",
"source_node_label": "PROP1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5626... | C | [
"A. SPRTN interacts with MLH1",
"B. PROP1 interacts with CTNNB1",
"C. CHAF1A interacts with SNRK",
"D. BAX interacts with CRYAA"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CTNNB1",
"source_db": "UniProt",
"payload": {
"accession": "P35222",
"sequence": "MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSLSGKGNPEEEDVDTSQVLYEWEQGFSQSFTQEQVADIDGQYAMTRAQRVRAAMFPETLDEGMQIPSTQFDAAHPTNVQRLAEPSQML... | [
{
"source_db": "bridge",
"source_id": "5626",
"text": "PROP1 GENE_ENCODES_PROTEIN PROP1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1499",
"text": "PROP1 PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"mode": "interaction",
"fabricated": "CHAF1A interacts with SNRK",
"real_options": [
"PROP1 interacts with CTNNB1",
"SPRTN interacts with MLH1",
"BAX interacts with CRYAA"
]
} | 0.9 |
co_hall_00051 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | MTOR GENE_ENCODES_PROTEIN MTOR -> MTOR PROTEIN_PHYSICALLY_INTERACTS_WITH RHEB -> RHEB GENE_ENCODES_PROTEIN RHEB | {
"steps": [
{
"hop": 1,
"source_node_id": "MTOR",
"source_node_type": "GENE",
"source_node_label": "MTOR",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2475",... | C | [
"A. CTNNB1 interacts with TNKS",
"B. MTOR interacts with RHEB",
"C. RTEL1 interacts with ENSP00000546110",
"D. VCP interacts with CCT3"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MTOR",
"source_db": "UniProt",
"payload": {
"accession": "P42345",
"sequence": "MLGTGPAAATTAATTSSNVSVLQQFASGLKSRNEETRAKAAKELQHYVTMELREMSQEESTRFYDQLNHHIFELVSSSDANERKGGILAIASLIGVEGGNATRIGRFANYLRNLLPSNDPVVMEMASKAIGRLA... | [
{
"source_db": "bridge",
"source_id": "2475",
"text": "MTOR GENE_ENCODES_PROTEIN MTOR",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "6009",
"text": "MTOR PROTEIN_PHYSICALLY_INTERACTS_WITH RHEB",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"mode": "interaction",
"fabricated": "RTEL1 interacts with ENSP00000546110",
"real_options": [
"MTOR interacts with RHEB",
"CTNNB1 interacts with TNKS",
"VCP interacts with CCT3"
]
} | 0.9 |
co_hall_00052 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | GTF2H1 GENE_ENCODES_PROTEIN GTF2H1 -> GTF2H1 PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1 -> ESR1 GENE_ENCODES_PROTEIN ESR1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GTF2H1",
"source_node_type": "PROTEIN",
"source_node_label": "GTF2H1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": ... | A | [
"A. ENSP00000788558 interacts with ENSP00000537619",
"B. AR interacts with KLK3",
"C. TBK1 interacts with DPCD",
"D. GTF2H1 interacts with ESR1"
] | [
"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": "2965",
"text": "GTF2H1 GENE_ENCODES_PROTEIN GTF2H1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2099",
"text": "GTF2H1 PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"mode": "interaction",
"fabricated": "ENSP00000788558 interacts with ENSP00000537619",
"real_options": [
"GTF2H1 interacts with ESR1",
"AR interacts with KLK3",
"TBK1 interacts with DPCD"
]
} | 0.9 |
co_hall_00053 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | AXIN1 GENE_ENCODES_PROTEIN AXIN1 -> AXIN1 PROTEIN_PHYSICALLY_INTERACTS_WITH SQSTM1 -> SQSTM1 GENE_ENCODES_PROTEIN SQSTM1 | {
"steps": [
{
"hop": 1,
"source_node_id": "AXIN1",
"source_node_type": "PROTEIN",
"source_node_label": "AXIN1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "8... | D | [
"A. ABL1 interacts with STUB1",
"B. FKBP5 interacts with MAPT",
"C. AXIN1 interacts with SQSTM1",
"D. DDX1 interacts with ENSP00000344456"
] | [
"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": "8312",
"text": "AXIN1 GENE_ENCODES_PROTEIN AXIN1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "8878",
"text": "AXIN1 PROTEIN_PHYSICALLY_INTERACTS_WITH SQSTM1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"mode": "interaction",
"fabricated": "DDX1 interacts with ENSP00000344456",
"real_options": [
"AXIN1 interacts with SQSTM1",
"ABL1 interacts with STUB1",
"FKBP5 interacts with MAPT"
]
} | 0.9 |
co_hall_00054 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | DNMT3A GENE_ENCODES_PROTEIN DNMT3A -> DNMT3A PROTEIN_PHYSICALLY_INTERACTS_WITH HDAC1 -> HDAC1 GENE_ENCODES_PROTEIN HDAC1 | {
"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... | C | [
"A. DNMT3A interacts with HDAC1",
"B. RNF115 interacts with EGFR",
"C. TNPO1 interacts with NCBP1",
"D. ESR1 interacts with POU5F1"
] | [
"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": "3065",
"text": "DNMT3A PROTEIN_PHYSICALLY_INTERACTS_WITH HDAC1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sou... | {
"mode": "interaction",
"fabricated": "TNPO1 interacts with NCBP1",
"real_options": [
"DNMT3A interacts with HDAC1",
"RNF115 interacts with EGFR",
"ESR1 interacts with POU5F1"
]
} | 0.9 |
co_hall_00055 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | TARDBP GENE_ENCODES_PROTEIN TARDBP -> TARDBP PROTEIN_PHYSICALLY_INTERACTS_WITH VDAC1 -> VDAC1 GENE_ENCODES_PROTEIN VDAC1 | {
"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... | C | [
"A. UBE2I interacts with CD2AP",
"B. TARDBP interacts with VDAC1",
"C. ENSP00000493610 interacts with ADCY4",
"D. CSF1R interacts with EPHA7"
] | [
"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": "7416",
"text": "TARDBP PROTEIN_PHYSICALLY_INTERACTS_WITH VDAC1",
"confidence": 0.9
},
{
"source_db": "bridge",
"so... | {
"mode": "interaction",
"fabricated": "ENSP00000493610 interacts with ADCY4",
"real_options": [
"TARDBP interacts with VDAC1",
"CSF1R interacts with EPHA7",
"UBE2I interacts with CD2AP"
]
} | 0.9 |
co_hall_00056 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | SOX2 GENE_ENCODES_PROTEIN SOX2 -> SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH MEX3C -> MEX3C GENE_ENCODES_PROTEIN MEX3C | {
"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",... | B | [
"A. SOX2 interacts with MEX3C",
"B. ND4 interacts with SLC1A2",
"C. TP53 interacts with MDM4",
"D. NCOA1 interacts with VCP"
] | [
"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": "51320",
"text": "SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH MEX3C",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"mode": "interaction",
"fabricated": "ND4 interacts with SLC1A2",
"real_options": [
"SOX2 interacts with MEX3C",
"TP53 interacts with MDM4",
"NCOA1 interacts with VCP"
]
} | 0.9 |
co_hall_00057 | hallucination_detection | coding_variant | easy | 1 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | CDH1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH IQGAP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "CDH1",
"source_node_type": "GENE",
"source_node_label": "CDH1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.997,
"edge_source_db": "STRING",
"t... | A | [
"A. HIP1R interacts with ZDHHC5",
"B. CHMP2B interacts with VPS4B",
"C. CDH1 interacts with IQGAP1",
"D. AURKA interacts with MAPRE1"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDH1",
"source_db": "UniProt",
"payload": {
"accession": "P12830",
"sequence": "MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGHHHRPPPHQASVSG... | [
{
"source_db": "STRING",
"source_id": "IQGAP1",
"text": "CDH1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH IQGAP1",
"confidence": 0.997
}
] | {
"mode": "interaction",
"fabricated": "HIP1R interacts with ZDHHC5",
"real_options": [
"CDH1 interacts with IQGAP1",
"CHMP2B interacts with VPS4B",
"AURKA interacts with MAPRE1"
]
} | 0.997 |
co_hall_00058 | hallucination_detection | coding_variant | easy | 1 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | FIG4 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH MTMR1 | {
"steps": [
{
"hop": 1,
"source_node_id": "FIG4",
"source_node_type": "GENE",
"source_node_label": "FIG4",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.943,
"edge_source_db": "STRING",
"t... | C | [
"A. CDH1 interacts with CREBBP",
"B. FIG4 interacts with MTMR1",
"C. ORM1 interacts with ENSP00000402577",
"D. EGFR interacts with FKBP8"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FIG4",
"source_db": "UniProt",
"payload": {
"accession": "Q92562",
"sequence": "MPTAAAPIISSVQKLVLYETRARYFLVGSNNAETKYRVLKIDRTEPKDLVIIDDRHVYTQQEVRELLGRLDLGNRTKMGQKGSSGLFRAVSAFGVVGFVRFLEGYYIVLITKRRKMADIGGHAIYKVEDTNMIY... | [
{
"source_db": "STRING",
"source_id": "MTMR1",
"text": "FIG4 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH MTMR1",
"confidence": 0.943
}
] | {
"mode": "interaction",
"fabricated": "ORM1 interacts with ENSP00000402577",
"real_options": [
"FIG4 interacts with MTMR1",
"CDH1 interacts with CREBBP",
"EGFR interacts with FKBP8"
]
} | 0.943 |
co_hall_00059 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | PPP1CC GENE_ENCODES_PROTEIN PPP1CC -> PPP1CC PROTEIN_PHYSICALLY_INTERACTS_WITH ACTB -> ACTB GENE_ENCODES_PROTEIN ACTB | {
"steps": [
{
"hop": 1,
"source_node_id": "PPP1CC",
"source_node_type": "PROTEIN",
"source_node_label": "PPP1CC",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": ... | A | [
"A. PPL interacts with ABCC6",
"B. EHD1 interacts with CD44",
"C. C9orf72 interacts with ASNS",
"D. PPP1CC interacts with ACTB"
] | [
"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": "5501",
"text": "PPP1CC GENE_ENCODES_PROTEIN PPP1CC",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "60",
"text": "PPP1CC PROTEIN_PHYSICALLY_INTERACTS_WITH ACTB",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"mode": "interaction",
"fabricated": "PPL interacts with ABCC6",
"real_options": [
"PPP1CC interacts with ACTB",
"C9orf72 interacts with ASNS",
"EHD1 interacts with CD44"
]
} | 0.9 |
co_hall_00060 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | CDK1 GENE_ENCODES_PROTEIN CDK1 -> CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH ID2 -> ID2 GENE_ENCODES_PROTEIN ID2 | {
"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",
... | A | [
"A. ENSP00000783691 interacts with NELFCD",
"B. ACTB interacts with ACTG1",
"C. UBQLN2 interacts with CNOT4",
"D. CDK1 interacts with ID2"
] | [
"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": "3398",
"text": "CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH ID2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"mode": "interaction",
"fabricated": "ENSP00000783691 interacts with NELFCD",
"real_options": [
"CDK1 interacts with ID2",
"ACTB interacts with ACTG1",
"UBQLN2 interacts with CNOT4"
]
} | 0.9 |
co_hall_00061 | hallucination_detection | coding_variant | easy | 1 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | PARK7 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PRKN | {
"steps": [
{
"hop": 1,
"source_node_id": "PARK7",
"source_node_type": "GENE",
"source_node_label": "PARK7",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | A | [
"A. ENSP00000539318 interacts with STXBP1",
"B. MLH1 interacts with IGKC",
"C. AKAP11 interacts with PRKAR2A",
"D. PARK7 interacts with PRKN"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PARK7",
"source_db": "UniProt",
"payload": {
"accession": "Q99497",
"sequence": "MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGGNLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGFGSKVTTHPLAKDKM... | [
{
"source_db": "STRING",
"source_id": "PRKN",
"text": "PARK7 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PRKN",
"confidence": 0.999
}
] | {
"mode": "interaction",
"fabricated": "ENSP00000539318 interacts with STXBP1",
"real_options": [
"PARK7 interacts with PRKN",
"AKAP11 interacts with PRKAR2A",
"MLH1 interacts with IGKC"
]
} | 0.999 |
co_hall_00062 | hallucination_detection | coding_variant | medium | 3 | One of the following protein interactions is NOT supported by any entry in BioGRID or STRING. Which one is fabricated? | AIMP2 GENE_ENCODES_PROTEIN AIMP2 -> AIMP2 PROTEIN_PHYSICALLY_INTERACTS_WITH ACE -> ACE GENE_ENCODES_PROTEIN ACE | {
"steps": [
{
"hop": 1,
"source_node_id": "AIMP2",
"source_node_type": "GENE",
"source_node_label": "AIMP2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "7965... | B | [
"A. GRB2 interacts with PTEN",
"B. ENSP00000451347 interacts with FBXO44",
"C. UBQLN2 interacts with PSMA1",
"D. AIMP2 interacts with ACE"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACE",
"source_db": "UniProt",
"payload": {
"accession": "P12821",
"sequence": "MGAASGRRGPGLLLPLPLLLLLPPQPALALDPGLQPGNFSADEAGAQLFAQSYNSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAKELYEPIWQNFTDPQLRRIIGAVRTLGSANLPLA... | [
{
"source_db": "bridge",
"source_id": "7965",
"text": "AIMP2 GENE_ENCODES_PROTEIN AIMP2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1636",
"text": "AIMP2 PROTEIN_PHYSICALLY_INTERACTS_WITH ACE",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"mode": "interaction",
"fabricated": "ENSP00000451347 interacts with FBXO44",
"real_options": [
"AIMP2 interacts with ACE",
"UBQLN2 interacts with PSMA1",
"GRB2 interacts with PTEN"
]
} | 0.9 |
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