Co-expression network of neural-differentiation genes shows specific pattern in schizophrenia

BMC Medical Genomics

Table 1 Signaling cellular pathways over-represented among the 228 gene set

Pathway	Statistical test	Genes
MAPK signalling pathway	C = 268;O = 13;E = 1.38;R = 9.42; p = 1.47e09;adjP = 1.50E-07	PDGFA, ATF4, AKT1, CACNA1C,
		DUSP6, CACNA1E, CACNA1H, NLK,
		CHUK, MAP3K5, NTF3, FOS, PPM1V
Pathways in cancer	C = 326;O = 13;E = 1.68;R = 7.75; p = 1.80e08;adjP = 7.74E-07	PDGFA, RARA, AKT1, ITGA2, E2F3,
		FH, SMO, CHUK, FZD5, FOS, BID,
		SPI1, HDAC2
Metabolic pathways	C = 1130;O = 21;E = 5.82;R = 3.61; p = 4.84e07;adjP = 1.39E-05	IMPA1, TRDMT1, HSD17B8, DPM1,
		MGAT4B, CPOX, FH, SPHK1, DCT,
		GAL3ST1, PNMT, PIK3C2A, ASNS, PC, MTHFS, PPAP2B, CDO1, HAAO,
		ATP6V1C1, ALDH1A1, AGL

Criteria: at least 10 genes represented in the pathway and adjpvalue ≤0.05 (hypergeometric t test with p value adjusted by multiple test adjustment, Benjamini and Hochberg [69])
C number of reference genes in the category number of genes in the gene set and O in the observed category, E expected number in the category, R ratio of enrichment, p p value from hypergeometric test, adjP value adjusted by the multiple test adjustment (adjP)

ISSN: 1755-8794