LS permutation | KS permutation | Efron-Tibshirani's GSA test | ||
---|---|---|---|---|
Pathway description | Number of genes | p Value | p Value | p Value |
Biocarta | ||||
T-cell receptor signalling pathway | 26 | *0.00001 | *0.00001 | 0.25 (+) |
Fc epsilon receptor I signalling in mast cells | 18 | *0.00005 | *0.00097 | 0.105 (+) |
Lck and Fyn tyrosine kinases in the initiation of TCR Activation | 9 | *0.00006 | *0.00168 | 0.37 (−) |
BCR signalling pathway | 15 | *0.00009 | *0.00325 | 0.42 (+) |
The co-stimulated signal during T-cell activation | 11 | *0.00019 | 0.0119 | 0.26 (−) |
Nerve growth factor pathway | 11 | *0.00027 | 0.04891 | 0.29 (+) |
Phosphoinositides and their downstream targets | 11 | *0.00048 | 0.02979 | 0.36 (+) |
Activation of Csk by cAMP-dependent protein kinase inhibits signalling through the T-cell receptor | 14 | *0.00049 | 0.01546 | 0.435 (+) |
Granzyme A-mediated apoptosis pathway | 7 | *0.00052 | *0.0002 | 0.435 (+) |
Role of Tob in T-cell activation | 10 | *0.00223 | *0.00365 | 0.495 (+) |
Ras-independent pathway in NK cell-mediated Cytotoxicity | 12 | *0.00227 | *0.00075 | 0.345 (−) |
HIV-induced T-cell apoptosis | 5 | *0.00305 | 0.01715 | 0.495 (+) |
Mechanism of gene regulation by peroxisome Proliferators via PPARα | 28 | *0.00379 | 0.10998 | 0.105 (+) |
Links between Pyk2 and MAP kinases | 14 | *0.00415 | 0.03066 | 0.385 (+) |
Angiotensin II-mediated activation of the JNK pathway via Pyk2-dependent Signalling | 10 | *0.00454 | 0.0191 | 0.21 (−) |
KEGG | ||||
T-cell receptor signalling pathway | 57 | *0.00001 | *0.00036 | 0.125 (+) |
Primary immunodeficiency | 20 | *0.00001 | *0.00177 | 0.375 (+) |
Natural killer cell-mediated cytotoxicity | 54 | *0.00003 | *0.00086 | 0.12 (+) |
Chemokine signalling pathway | 78 | *0.00081 | 0.01394 | 0.06 (−) |
Fc epsilon RI signalling pathway | 32 | *0.00219 | 0.03961 | 0.025 (−) |
B-cell receptor signalling pathway | 38 | *0.00262 | 0.03951 | 0.515 (+) |
Pyrimidine metabolism | 45 | *0.00416 | 0.06912 | 0.185 (−) |
Pentose phosphate pathway | 14 | *0.00471 | 0.16112 | 0.48 (+) |
Amino sugar and nucleotide sugar metabolism | 20 | 0.00903 | *0.00303 | 0.285 (−) |
Glyoxylate and dicarboxylate metabolism | 7 | 0.05672 | *0.00454 | 0.175 (−) |
Ribosome | 77 | 0.3271 | *0.00405 | 0.29 (+) |
A total of 15 of 202 and 11 of 203 investigated gene sets among the Biocarta and KEGG pathways, respectively, passed the 0.005 significance threshold of the LS/KS permutation test or Efron-Tibshirani's GSA maxmean test.
*Denotes significant p value.
BCR, B-cell receptor; NFE, non-fatal coronary event; NK, natural killer; TCR, T-cell receptor.