LS permutation | KS permutation | Efron-Tibshirani's GSA test | ||
---|---|---|---|---|
Pathway description | Number of genes | p Value | p Value | p Value |
Biocarta pathway | ||||
HIV-I Nef: negative effector of Fas and TNF | 35 | *0.00001 | 0.00626 | 0.025 (+) |
Keratinocyte differentiation | 25 | *0.00014 | 0.01083 | 0.235 (+) |
Chaperones modulate interferon Signalling pathway | 11 | *0.00095 | 0.04736 | 0.17 (+) |
NF-κB signalling pathway | 11 | *0.00123 | 0.06918 | 0.115 (−) |
Toll-like receptor pathway | 12 | *0.00139 | 0.11089 | 0.185 (−) |
TNFR2 signalling pathway | 12 | *0.00165 | 0.16091 | 0.305 (+) |
Acetylation and deacetylation of RelA in the nucleus | 10 | *0.00323 | 0.04009 | 0.245 (−) |
CD40L signalling pathway | 9 | *0.00359 | 0.2707 | 0.265 (+) |
Regulation of transcriptional activity by PML | 9 | *0.00451 | 0.01201 | 0.375 (−) |
Double-stranded RNA-induced gene expression | 8 | *0.00471 | 0.32605 | 0.25 (+) |
IL 3 signalling pathway | 10 | 0.00545 | *0.00368 | 0.275 (−) |
Role of ERBB2 in signal transduction and oncology | 11 | 0.01509 | *0.00022 | 0.49 (+) |
Transcriptional activation of dbpb from mRNA | 6 | 0.02236 | *0.00221 | 0.41 (+) |
NFAT and hypertrophy of the heart | 24 | 0.02685 | *0.00179 | 0.29 (−) |
Fc epsilon receptor I signalling in mast cells | 18 | 0.03265 | *0.0046 | 0.385 (−) |
Multistep regulation of transcription by Pitx2 | 6 | 0.05738 | *0.0038 | 0.49 (+) |
Growth hormone signalling pathway | 12 | 0.06599 | *0.00362 | 0.255 (+) |
Oxidative stress-induced gene Expression Via Nrf2 | 8 | 0.11679 | 0.74512 | *<0.005 (−) |
Protein kinase A at the centrosome | 7 | 0.90048 | 0.6826 | *<0.005 (−) |
A total of 19 of 202 investigated gene sets among the Biocarta pathways passed the 0.005 significance threshold of the LS/KS permutation test or Efron-Tibshirani's GSA maxmean test.
*Denotes significant p value.
ACS, acute coronary syndrome; GSA, gene set analysis; NFAT, nuclear factor of activated T-cells; NF-κB, nuclear factor-κB; PML, promyelocytic leukemia; TNF, tumor necrosis factor.