A statistical network pre-processing method to improve relevance and significance of gene lists in microarray gene expression studies

Table 11 The 6 enriched pathways using the list of relevant up regulated DEGs obtained from the Alzheimer GSE16759 data set

PathwayName	Pvalue	FDRC	BonfC	\(\|lg_{2}(P_{value})\|\)	\(\|lg_{2}(FDR(P_{value})\|\)	\(\|lg_{2}Bonf(P_{value})\|\)
1) PERK regulates gene expression	4.81E−05	0.02	0.02	14.34	5.42	5.42
2) Signaling pathways	1.10E−04	0.03	0.05	13.15	5.23	4.23
3) Unfolded protein response (UPR)	3.33E−04	0.05	0.16	11.55	4.21	2.63
4) Neurophilin interactions with VEGF and VEGFR	0.0011	0.14	0.56	9.77	2.85	0.85
5) ATF6 (ATF6-alpha) activates chaperone genes	0.0028	0.28	1.00	8.45	1.85	0.00
6) ATF6 (ATF6-alpha) activates chaperones	0.0034	0.28	1.00	8.19	1.85	0.00

The FDRC indicates the corrected p value using FDR statistical corrector. The BonfC represents the corrected p value using Bonferroni statistical corrector. Finally, the last three columns contain the \(|lg_{2}(\cdot )|\) of each p value, for ease comparison

ISSN: 1471-2105