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pd-discovery-benchmark-dashboard

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parkinsons-disease
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pd-discovery-benchmark-dashboard / data /pd_discovery_benchmark_knowledge_graph.graphml
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Add PD discovery benchmark dashboard resource
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<?xml version='1.0' encoding='utf-8'?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd"><key id="d4" for="edge" attr.name="potency_nM" attr.type="double"/>
<key id="d3" for="edge" attr.name="relation" attr.type="string"/>
<key id="d2" for="node" attr.name="chembl_id" attr.type="string"/>
<key id="d1" for="node" attr.name="score" attr.type="double"/>
<key id="d0" for="node" attr.name="kind" attr.type="string"/>
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</node>
<node id="alpha-synuclein aggregation and propagation">
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<node id="SNCA triplication/A53T iPSC dopaminergic neurons or alpha-synuclein PFF model">
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<node id="pS129 alpha-synuclein, aggregate load, synaptic/neurite phenotypes">
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<node id="GLP1R">
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<node id="metabolic and GLP-1 receptor signalling">
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<node id="dopaminergic neuron stress model with metabolic/inflammatory co-culture">
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<node id="neuronal survival, inflammatory cytokines, mitochondrial respiration">
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<node id="LRRK2">
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<node id="LRRK2 kinase and lysosomal stress">
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<node id="LRRK2 G2019S or R1441C iPSC-derived dopaminergic neurons">
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<node id="phospho-Rab10/Rab12, lysosomal morphology, neurite survival">
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<node id="GBA1 lysosome/autophagy">
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<node id="GBA1-mutant iPSC dopaminergic neurons and macrophage/microglia-like cells">
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</node>
<node id="glucocerebrosidase activity, lysosomal pH, alpha-synuclein burden">
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<node id="MAPK1">
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</node>
<node id="MAP kinase activation">
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</node>
<node id="stress-response assay in neurons and microglia">
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<node id="phospho-ERK, inflammatory/stress response, toxicity counterscreen">
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<node id="NOD2">
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<node id="NOD1/2 inflammatory signalling">
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<node id="iPSC-derived microglia or monocyte-derived macrophages">
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<node id="NOD ligand response, cytokines, inflammasome-related markers">
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</node>
<node id="IL17A">
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<node id="IL-17 inflammatory signalling">
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</node>
<node id="microglia/astrocyte inflammatory co-culture">
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</node>
<node id="IL-17 response genes, cytokine release, neuronal stress markers">
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</node>
<node id="TLR2">
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<node id="innate immune signalling">
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<node id="iPSC-derived microglia and neuron-microglia co-culture">
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<node id="TNF/IL6/IL1B release, NF-kB activation, neuronal toxicity">
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</node>
<node id="NTRK1">
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</node>
<node id="NTRK/neurotrophin signalling">
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</node>
<node id="dopaminergic neuron survival/trophic support model">
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</node>
<node id="neurite length, survival, phospho-ERK/AKT">
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</node>
<node id="SLC6A3">
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</node>
<node id="dopaminergic synapse">
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</node>
<node id="iPSC dopaminergic neuron maturation/readout assay">
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</node>
<node id="DAT expression/function, dopamine uptake, neuron identity QC">
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</node>
<node id="PINK1">
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</node>
<node id="mitochondrial quality control">
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</node>
<node id="PINK1 knockout iPSC dopaminergic neurons">
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</node>
<node id="mitophagy reporter, mitochondrial membrane potential, ATP/ROS">
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<node id="LAMP2">
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<node id="lysosome/autophagy">
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</node>
<node id="iPSC dopaminergic neurons with lysosomal stress">
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<node id="LC3/p62 flux, lysosomal pH, autophagosome clearance">
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</node>
<node id="MYD88">
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<node id="iPSC-derived microglia inflammatory challenge">
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<node id="NF-kB reporter, cytokine release, rescue of co-culture toxicity">
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<node id="NDUFS3">
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<node id="mitochondrial oxidative phosphorylation">
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</node>
<node id="iPSC dopaminergic neuron mitochondrial stress model">
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<node id="Seahorse OCR, complex I activity, ATP/ROS">
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<node id="PRKN">
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<node id="PRKN knockout iPSC dopaminergic neurons">
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<edge source="SNCA" target="CHEMBL2063797">
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<edge source="SNCA" target="CHEMBL3593901">
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<edge source="SNCA" target="CHEMBL3593923">
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<edge source="SNCA" target="CHEMBL3593931">
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<edge source="SNCA" target="CHEMBL3593910">
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<edge source="SNCA" target="CHEMBL2063798">
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<edge source="SNCA triplication/A53T iPSC dopaminergic neurons or alpha-synuclein PFF model" target="pS129 alpha-synuclein, aggregate load, synaptic/neurite phenotypes">
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<edge source="GLP1R" target="CHEMBL250091">
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<edge source="dopaminergic neuron stress model with metabolic/inflammatory co-culture" target="neuronal survival, inflammatory cytokines, mitochondrial respiration">
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<edge source="NOD2" target="NOD1/2 inflammatory signalling">
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<edge source="PRKN" target="PRKN knockout iPSC dopaminergic neurons">
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</graph></graphml>