Table 5 Prioritization of genes related to heart defects based on KF data.

HGNC ID	Common Neighbors Score	Jaccard’s Index	Gene symbol	Evidence for heart defect linkage
HGNC:4173	13	0.005488	GATA4	PMID: 24000169
HGNC:905	10	0.004554	AXL
HGNC:7881	9	0.003447	NOTCH1	PMID: 36583388
HGNC:7976	9	0.003089	NR2F2	PMID: 24702954
HGNC:10449	8	0.003457	RREB1	PMID: 33929320
HGNC:961	8	0.003288	BAZ1B
HGNC:7882	8	0.003031	NOTCH2	PMID: 22340493
HGNC:4916	8	0.002690	HIRA	PMID: 27518902
HGNC:29216	7	0.003794	ARHGAP31	PMID: 27760138
HGNC:10898	7	0.003568	SKIV2L	PMID: 23302111
HGNC:1390	7	0.003552	CACNA1C	PMID: 36277185
HGNC:7660	7	0.003011	NCF1	MGI:97283
HGNC:12796	7	0.002315	WT1	PMID: 17853480
HGNC:1097	7	0.002137	BRAF	PMID: 23312968
HGNC:11105	6	0.003043	SMARCC2	PMID: 35241061
HGNC:4084	6	0.002879	GABRD
HGNC:3767	6	0.002591	FLT4	PMID: 36496429
HGNC:14881	6	0.002140	ZEB2	PMID: 29263819

Results of link prediction in Petagraph using a Common Neighbors algorithm. We identified genes with predicted damaging de novo variants from children in the Kids First cohort phs001138.v4 with tetralogy of Fallot (ToF). The Common Neighbors score prioritizes likely relationships between Petagraph nodes for each gene and the node for Human Phenotype Ontology ID HP:0001636 (ToF), thus helping prioritize gene-to-phenotype relationships based on evidence from genomics data and annotation. GATA4, NOTCH1, NOTCH2, FLT4 are all previously known ToF-related variants, while other genes with PMIDs show evidence to links to other heart defects in humans or mice. Evidence for heart defect linkage was based on manual searches in PubMed for evidence linking these genes to heart defects. These results show how researchers can explore known and proposed relationships between genes, diseases, or disorders from utilizing Petagraph omics dataset connectivity with information in CF omics datasets and supporting annotation datasets. Jaccard's Index was calculated as the ratio of Common Neighbors and Total Neighbors, all calculated on Petagraph using the Neo4j GDS library. MGI: Mouse Genome Informatics ID. PMID: PubMed Identifier.

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