Description of the problem:
Number of classes: 2
Column of the Experiment Descriptors sheet that defines class variable: OBNSC vs heNSC
Number of genes that passed filtering criteria: 47231
Type of Gene Sets: Kegg Pathway
Number of total investigated Gene Sets: 171
Type of univariate test used: Two-sample T-test
Random variance model was not used because distribution assumptions of this model were not satisfied.
Tests used to find significant gene sets are: LS/KS permutation test, Efron-Tibshirani's GSA maxmean test
The threshold of determining significant gene sets is 0.005
LS/KS permutation test finds gene sets which have more genes differentially expressed among the phenotype classes than expected by chance.
Efron-Tibshirani's test uses 'maxmean' statistics to identify gene sets differentially expressed.
Summary of Results:
75 out of 171 investigated gene sets passed the 0.005 significance threshold
LS/KS permutation test found 72 significant gene sets.
Efron-Tibshirani's maxmean test found 17 significant gene sets (under 200 permutations).
Table - Table of Gene Sets:
75
gene sets sorted by LS permutation p-value (significant p-values are in red)
To access the list of genes within each gene set, click the hyperlinked number of genes for each gene set.
Kegg Pathway | Pathway description | Number of | Heatmap link | LS permutation | KS permutation | Efron-Tibshirani's GSA test 1 | hsa00010 | Glycolysis / Gluconeogenesis | 121 | heatmap | 0.00001 | 0.09652 | 0.115 (+)
| 2 | hsa00020 | Citrate cycle (TCA cycle) | 49 | heatmap | 0.00001 | 0.00164 | < 0.005 (-)
| 3 | hsa00062 | Fatty acid elongation in mitochondria | 13 | heatmap | 0.00001 | 0.00005 | < 0.005 (+)
| 4 | hsa00100 | Biosynthesis of steroids | 25 | heatmap | 0.00001 | 0.00073 | 0.02 (+)
| 5 | hsa00190 | Oxidative phosphorylation | 159 | heatmap | 0.00001 | 0.00001 | < 0.005 (+)
| 6 | hsa00193 | ATP synthesis | 66 | heatmap | 0.00001 | 0.00001 | < 0.005 (+)
| 7 | hsa00230 | Purine metabolism | 258 | heatmap | 0.00001 | 0.00046 | 0.25 (+)
| 8 | hsa00240 | Pyrimidine metabolism | 142 | heatmap | 0.00001 | 0.00001 | 0.25 (+)
| 9 | hsa00280 | Valine, leucine and isoleucine degradation | 67 | heatmap | 0.00001 | 0.00039 | 0.17 (+)
| 10 | hsa00380 | Tryptophan metabolism | 138 | heatmap | 0.00001 | 0.00223 | 0.235 (+)
| 11 | hsa00640 | Propanoate metabolism | 62 | heatmap | 0.00001 | 0.01057 | 0.06 (+)
| 12 | hsa00650 | Butanoate metabolism | 63 | heatmap | 0.00001 | 0.00217 | 0.12 (+)
| 13 | hsa00790 | Folate biosynthesis | 53 | heatmap | 0.00001 | 0.00043 | 0.275 (+)
| 14 | hsa00900 | Terpenoid biosynthesis | 9 | heatmap | 0.00001 | 0.0004 | < 0.005 (+)
| 15 | hsa00970 | Aminoacyl-tRNA biosynthesis | 40 | heatmap | 0.00001 | 0.00001 | 0.23 (+)
| 16 | hsa03010 | Ribosome | 150 | heatmap | 0.00001 | 0.00001 | < 0.005 (+)
| 17 | hsa03050 | Proteasome | 49 | heatmap | 0.00001 | 0.00001 | < 0.005 (+)
| 18 | hsa04110 | Cell cycle | 200 | heatmap | 0.00001 | 0.00001 | 0.16 (+)
| 19 | hsa04130 | SNARE interactions in vesicular transport | 55 | heatmap | 0.00001 | 0.00186 | 0.25 (+)
| 20 | hsa04510 | Focal adhesion | 359 | heatmap | 0.00001 | 0.0024 | < 0.005 (-)
| 21 | hsa04520 | Adherens junction | 154 | heatmap | 0.00001 | 0.00092 | < 0.005 (-)
| 22 | hsa04720 | Long-term potentiation | 111 | heatmap | 0.00001 | 0.0007 | < 0.005 (-)
| 23 | hsa04810 | Regulation of actin cytoskeleton | 357 | heatmap | 0.00001 | 0.03696 | 0.155 (+)
| 24 | hsa05120 | Epithelial cell signaling in Helicobacter pylori infection | 118 | heatmap | 0.00001 | 0.02608 | 0.09 (-)
| 25 | hsa05210 | Colorectal cancer | 148 | heatmap | 0.00001 | 0.00002 | 0.035 (-)
| 26 | hsa05060 | Prion disease | 24 | heatmap | 0.00002 | 0.00048 | < 0.005 (+)
| 27 | hsa04310 | Wnt signaling pathway | 269 | heatmap | 0.00002 | 0.001 | 0.045 (-)
| 28 | hsa00310 | Lysine degradation | 90 | heatmap | 0.00003 | 0.00393 | 0.235 (+)
| 29 | hsa00620 | Pyruvate metabolism | 83 | heatmap | 0.00003 | 0.02507 | 0.07 (+)
| 30 | hsa04910 | Insulin signaling pathway | 236 | heatmap | 0.00003 | 0.03914 | 0.195 (-)
| 31 | hsa00626 | Nitrobenzene degradation | 23 | heatmap | 0.00004 | 0.00009 | 0.165 (+)
| 32 | hsa00440 | Aminophosphonate metabolism | 29 | heatmap | 0.00004 | 0.001 | 0.165 (+)
| 33 | hsa03020 | RNA polymerase | 37 | heatmap | 0.00005 | 0.00787 | 0.205 (+)
| 34 | hsa00030 | Pentose phosphate pathway | 41 | heatmap | 0.00006 | 0.06757 | 0.045 (+)
| 35 | hsa00071 | Fatty acid metabolism | 81 | heatmap | 0.00007 | 0.08007 | 0.035 (+)
| 36 | hsa00330 | Arginine and proline metabolism | 85 | heatmap | 0.00007 | 0.09745 | 0.125 (+)
| 37 | hsa04120 | Ubiquitin mediated proteolysis | 92 | heatmap | 0.00007 | 0.00053 | 0.41 (+)
| 38 | hsa00251 | Glutamate metabolism | 46 | heatmap | 0.00008 | 0.07319 | 0.185 (+)
| 39 | hsa04360 | Axon guidance | 229 | heatmap | 0.00008 | 0.08966 | 0.14 (-)
| 40 | hsa05010 | Alzheimer@ | 47 | heatmap | 0.00009 | 0.05598 | 0.255 (+)
| 41 | hsa00511 | N-Glycan degradation | 19 | heatmap | 0.0001 | 0.00014 | 0.345 (+)
| 42 | hsa00530 | Aminosugars metabolism | 45 | heatmap | 0.0001 | 0.03275 | 0.155 (-)
| 43 | hsa01510 | Neurodegenerative Disorders | 77 | heatmap | 0.00014 | 0.07706 | 0.135 (+)
| 44 | hsa00340 | Histidine metabolism | 66 | heatmap | 0.00015 | 0.00364 | 0.25 (+)
| 45 | hsa03022 | Basal transcription factors | 53 | heatmap | 0.00027 | 0.06649 | < 0.005 (-)
| 46 | hsa05020 | Parkinson@ | 27 | heatmap | 0.00027 | 0.00594 | 0.145 (+)
| 47 | hsa01032 | Glycan structures - degradation | 46 | heatmap | 0.00045 | 0.00102 | 0.29 (+)
| 48 | hsa04150 | mTOR signaling pathway | 95 | heatmap | 0.00047 | 0.27327 | 0.13 (-)
| 49 | hsa04540 | Gap junction | 153 | heatmap | 0.00059 | 0.01674 | 0.145 (-)
| 50 | hsa04530 | Tight junction | 225 | heatmap | 0.0006 | 0.07017 | 0.16 (-)
| 51 | hsa00051 | Fructose and mannose metabolism | 70 | heatmap | 0.00091 | 0.12761 | 0.3 (+)
| 52 | hsa00930 | Caprolactam degradation | 30 | heatmap | 0.00094 | 0.09204 | 0.09 (+)
| 53 | hsa04010 | MAPK signaling pathway | 498 | heatmap | 0.00112 | 0.6331 | 0.16 (-)
| 54 | hsa04710 | Circadian rhythm | 27 | heatmap | 0.00131 | 0.01468 | 0.06 (-)
| 55 | hsa03060 | Protein export | 16 | heatmap | 0.0014 | 0.00025 | 0.175 (+)
| 56 | hsa00400 | Phenylalanine, tyrosine and tryptophan biosynthesis | 14 | heatmap | 0.00145 | 0.08306 | 0.075 (+)
| 57 | hsa00450 | Selenoamino acid metabolism | 53 | heatmap | 0.00146 | 0.01416 | 0.245 (+)
| 58 | hsa00290 | Valine, leucine and isoleucine biosynthesis | 16 | heatmap | 0.00151 | 0.00605 | 0.24 (+)
| 59 | hsa00410 | beta-Alanine metabolism | 40 | heatmap | 0.00168 | 0.0113 | 0.12 (+)
| 60 | hsa00561 | Glycerolipid metabolism | 102 | heatmap | 0.00212 | 0.16484 | 0.165 (+)
| 61 | hsa00903 | Limonene and pinene degradation | 41 | heatmap | 0.00233 | 0.04428 | 0.225 (+)
| 62 | hsa00532 | Chondroitin sulfate biosynthesis | 24 | heatmap | 0.00234 | 0.0007 | 0.31 (+)
| 63 | hsa04670 | Leukocyte transendothelial migration | 203 | heatmap | 0.00249 | 0.62332 | 0.145 (-)
| 64 | hsa00710 | Carbon fixation | 41 | heatmap | 0.00269 | 0.14482 | 0.125 (+)
| 65 | hsa04330 | Notch signaling pathway | 81 | heatmap | 0.0027 | 0.04124 | 0.47 (+)
| 66 | hsa00670 | One carbon pool by folate | 25 | heatmap | 0.00274 | 0.14825 | 0.215 (+)
| 67 | hsa00600 | Sphingolipid metabolism | 65 | heatmap | 0.00286 | 0.02053 | 0.355 (+)
| 68 | hsa04612 | Antigen processing and presentation | 141 | heatmap | 0.00333 | 0.17877 | < 0.005 (+)
| 69 | hsa00362 | Benzoate degradation via hydroxylation | 6 | heatmap | 0.00371 | 0.01957 | 0.13 (+)
| 70 | hsa00510 | N-Glycan biosynthesis | 62 | heatmap | 0.004 | 0.13349 | 0.35 (+)
| 71 | hsa00904 | Diterpenoid biosynthesis | 5 | heatmap | 0.0102 | 0.0024 | < 0.005 (-)
| 72 | hsa00052 | Galactose metabolism | 62 | heatmap | 0.01908 | 0.00444 | 0.385 (+)
| 73 | hsa00780 | Biotin metabolism | 14 | heatmap | 0.05232 | 0.01355 | < 0.005 (-)
| 74 | hsa05030 | Amyotrophic lateral sclerosis (ALS) | 32 | heatmap | 0.10658 | 0.43079 | < 0.005 (-)
| 75 | hsa00623 | 2,4-Dichlorobenzoate degradation | 6 | heatmap | 0.1751 | 0.28288 | < 0.005 (+)
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Links to the genes within gene sets:
Gene Sets 1 - 75