Investigating perturbed pathway modules from gene expression data via structural equation models

BMC Bioinformatics

Table 4 Perturbed pathways obtained by SPIA on MS data

Name pathway	pSize	NDE	pNDE	tA	pPERT	pGFdr	Status
B cell receptor signaling pathway	73	8	0.000	6.822	0.372	0.000	Activated
Fc gamma R-mediated phagocytosis	89	4	0.015	-13.66	0.006	0.036	Inhibited
Salmonella infection	71	5	0.001	-4.901	0.174	0.041	Inhibited

pSize = number of genes in the pathway; NDE = number of DEGs in the pathway; pNDE = p-value of the enrichment; tA = total perturbation; pPERT = p-value of the perturbation; Status = direction of the perturbation.

ISSN: 1471-2105