Table 2.

Pathway Analysis for Proteomics and Genomic Datasets

Dataset	Pathway Identifier	Pathway Category	Pathway Name	Entities P
Mass spectrometry (Proteomics)	R-HSA-5661231	Cellular responses to stimuli	Metallothioneins bind metals.	2.21E-13
	R-HSA-195399	Signal transduction	VEGF binds to VEGFR leading to receptor dimerization.	6.91E-04
	R-HSA-6806834	Signal transduction	Signaling by MET	0.001351944
	R-HSA-9673768	Disease associated	Signaling by membrane-tethered fusions of PDGFRA or PDGFRB	0.006833935
	R-HSA-9706369	Immune system response	Negative regulation of FLT3	0.01175446
	R-HSA-5619115	Disease associated	Disorders of transmembrane transporters	0.016165492
	R-HSA-8941333	Gene expression transduction	RUNX2 regulates genes involved in differentiation of myeloid cells.	0.031066791
Whole-genome sequencing (Genomics)	R-HSA-5083627	Disease associated	Defective LARGE causes MDDGA6 and MDDGB6.	0.003533237
	R-HSA-6794361	Neuronal system	Neurexins and neuroligins	0.005939488
	R-HSA-5173105	Metabolism of proteins	O-linked glycosylation	0.007319633
	R-HSA-6794362	Neuronal system	Protein–protein interactions at synapses	0.014511731
	R-HSA-8856688	Vesicle-mediated transport	Golgi-to-ER retrograde transport	0.019718755
	R-HSA-428359	Metabolism of RNA	Insulin-like growth factor-2 mRNA binding proteins (IGF2BPs/IMPs/VICKZs) bind RNA.	0.020155209
	R-HSA-8941333	Gene expression transduction	RUNX2 regulates genes involved in differentiation of myeloid cells.	0.021022733
	R-HSA-5626467	Signal transduction	RHO GTPases activate IQGAPs.	0.038221149
	R-HSA-1300645	Reproduction	Acrosome reaction and sperm: oocyte membrane binding	0.039073511
	R-HSA-3134963	Immune system response	DEx/H-box helicases activate type I IFN and inflammatory cytokine production.	0.040776089

Pathway analysis of candidate proteins in the mass spectrometry proteomics and WGS genomics datasets. Pathway analysis was performed utilizing the REACTOME database. The “project to human” and “includes interactors” features were included as part of the parameters. Pathways were curated based on a P < 0.05. VEGF, vascular endothelial growth factor; VEGFR, vascular endothelial growth factor receptor; MET, hepatocyte growth factor receptor; PDGFRA, platelet-derived growth factor receptor alpha; PDGFRB, platelet-derived growth factor receptor beta; FLT3, FMS-like tyrosine kinase-3; RUNX2, runt-related transcription factor 2; MDDGA6/MDDGB6, congenital muscular dystrophy-dystroglycanopathy with brain and eye anomalies (type A6/B6); ER, endoplasmic reticulum; IGF2BPs/IMPs/VICKZs, insulin-like growth factor 2 mRNA-binding proteins; IQGAPs, IQ motif-containing GTPase-activating proteins; IFN, interferon