Gene Set Enrichment Analysis
The method compares the distribution of the t-test statistic values per gene within a pathway with the distribution of the same statistic in the remaining genes using two z-score tests. These two tests are based on two different null hypothesis obtained through a permutation on samples and on genes. In the following table the significantly enriched pathways (NEk q-value and NTk q-value <= 0.05) are reported. Otherwise the top 50 pathways are shown.
| Pathway | Set Size | Percent Up | NTk Stat | NTk q-value | NTk Rank | NEk Stat | NEk q-value | NEk Rank |
|---|---|---|---|---|---|---|---|---|
| Signaling by Interleukins | 83.0 | 68.67 | -4.63 | 0.0 | 6.0 | -2.33 | 1.0 | 7.0 |
| Chemokine receptors bind chemokines | 30.0 | 93.33 | -6.25 | 0.0 | 1.0 | -2.17 | 1.0 | 12.5 |
| Interleukin-1 processing | 7.0 | 85.71 | -4.03 | 0.0 | 17.0 | -3.09 | 0.814 | 1.5 |
| Interferon alpha/beta signaling | 41.0 | 80.49 | -5.18 | 0.0 | 3.0 | -2.01 | 1.0 | 21.0 |
| Toll Receptor Cascades | 90.0 | 71.11 | -4.5 | 0.0 | 8.0 | -2.03 | 1.0 | 20.0 |
| Costimulation by the CD28 family | 39.0 | 69.23 | -4.05 | 0.0 | 16.0 | -2.07 | 1.0 | 16.5 |
| Regulation of pyruvate dehydrogenase (PDH) complex | 10.0 | 10.0 | 3.23 | 0.0 | 34.0 | 3.09 | 0.814 | 1.5 |
| PD-1 signaling | 13.0 | 84.62 | -4.46 | 0.0 | 10.0 | -1.96 | 1.0 | 27.0 |
| TRAF6 mediated NF-kB activation | 20.0 | 75.0 | -3.28 | 0.0 | 33.0 | -2.37 | 1.0 | 6.0 |
| Interferon Signaling | 99.0 | 65.66 | -4.34 | 0.0 | 12.0 | -1.91 | 1.0 | 30.5 |
| Interleukin-3, 5 and GM-CSF signaling | 35.0 | 77.14 | -3.51 | 0.0 | 32.0 | -2.2 | 1.0 | 11.0 |
| Antigen Activates B Cell Receptor Leading to Generation of Second Messengers | 21.0 | 95.24 | -3.68 | 0.0 | 29.0 | -2.12 | 1.0 | 15.0 |
| Phosphorylation of CD3 and TCR zeta chains | 11.0 | 90.91 | -4.46 | 0.0 | 9.0 | -1.87 | 1.0 | 35.5 |
| Death Receptor Signalling | 10.0 | 90.0 | -3.22 | 0.0 | 35.0 | -2.23 | 1.0 | 10.0 |
| Extrinsic Pathway for Apoptosis | 10.0 | 90.0 | -3.22 | 0.0 | 35.0 | -2.23 | 1.0 | 10.0 |
| Activated TLR4 signalling | 76.0 | 69.74 | -3.98 | 0.0 | 20.0 | -1.94 | 1.0 | 28.0 |
| Trafficking and processing of endosomal TLR | 6.0 | 100.0 | -3.09 | 0.023 | 39.0 | -2.17 | 1.0 | 12.5 |
| Cytosolic sensors of pathogen-associated DNA | 21.0 | 76.19 | -3.09 | 0.023 | 39.0 | -2.05 | 1.0 | 18.5 |
| Toll Like Receptor 4 (TLR4) Cascade | 80.0 | 68.75 | -3.71 | 0.0 | 28.0 | -1.88 | 1.0 | 33.0 |
| RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways | 47.0 | 63.83 | -3.09 | 0.023 | 39.0 | -2.0 | 1.0 | 22.5 |
| Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | 33.0 | 84.85 | -4.78 | 0.0 | 4.0 | -1.7 | 1.0 | 59.0 |
| Apoptosis | 101.0 | 69.31 | -2.88 | 0.038 | 48.0 | -2.05 | 1.0 | 18.5 |
| Regulation of Insulin Secretion by Fatty Acids Bound to GPR40 (FFAR1) | 7.0 | 100.0 | -2.65 | 0.062 | 63.0 | -2.58 | 1.0 | 4.0 |
| Regulation of Insulin Secretion by Free Fatty Acids | 7.0 | 100.0 | -2.65 | 0.062 | 63.0 | -2.58 | 1.0 | 4.0 |
| RIP-mediated NFkB activation via DAI | 18.0 | 77.78 | -2.65 | 0.062 | 63.0 | -2.29 | 1.0 | 8.5 |
| MyD88:Mal cascade initiated on plasma membrane | 69.0 | 68.12 | -3.09 | 0.023 | 39.0 | -1.87 | 1.0 | 35.5 |
| Toll Like Receptor 2 (TLR2) Cascade | 69.0 | 68.12 | -3.09 | 0.023 | 39.0 | -1.87 | 1.0 | 35.5 |
| Toll Like Receptor TLR1:TLR2 Cascade | 69.0 | 68.12 | -3.09 | 0.023 | 39.0 | -1.87 | 1.0 | 35.5 |
| Toll Like Receptor TLR6:TLR2 Cascade | 69.0 | 68.12 | -3.09 | 0.023 | 39.0 | -1.87 | 1.0 | 35.5 |
| Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon | 9.0 | 77.78 | -2.65 | 0.062 | 63.0 | -2.14 | 1.0 | 14.0 |
| Translocation of ZAP-70 to Immunological synapse | 9.0 | 88.89 | -3.72 | 0.0 | 27.0 | -1.74 | 1.0 | 53.5 |
| DAI mediated induction of type I IFNs | 20.0 | 75.0 | -2.75 | 0.053 | 55.5 | -1.98 | 1.0 | 25.0 |
| MyD88-independent cascade | 65.0 | 67.69 | -3.09 | 0.023 | 39.0 | -1.8 | 1.0 | 45.0 |
| Toll Like Receptor 3 (TLR3) Cascade | 65.0 | 67.69 | -3.09 | 0.023 | 39.0 | -1.8 | 1.0 | 45.0 |
| TCR signaling | 42.0 | 57.14 | -2.88 | 0.038 | 48.0 | -1.84 | 1.0 | 39.5 |
| Toll Like Receptor 9 (TLR9) Cascade | 68.0 | 66.18 | -2.88 | 0.038 | 48.0 | -1.84 | 1.0 | 39.5 |
| TRAF3-dependent IRF activation pathway | 11.0 | 72.73 | -2.75 | 0.053 | 55.5 | -1.88 | 1.0 | 33.0 |
| Generation of second messenger molecules | 20.0 | 65.0 | -2.88 | 0.038 | 48.0 | -1.79 | 1.0 | 47.5 |
| Interleukin-6 signaling | 7.0 | 85.71 | -2.37 | 0.109 | 82.0 | -2.07 | 1.0 | 16.5 |
| NFkB and MAP kinases activation mediated by TLR4 signaling repertoire | 60.0 | 66.67 | -2.75 | 0.053 | 55.5 | -1.76 | 1.0 | 50.5 |
| TRAIL signaling | 5.0 | 80.0 | -2.29 | 0.12 | 93.0 | -2.0 | 1.0 | 22.5 |
| Interleukin-2 signaling | 34.0 | 73.53 | -2.51 | 0.082 | 73.0 | -1.81 | 1.0 | 43.0 |
| Signal regulatory protein (SIRP) family interactions | 8.0 | 87.5 | -2.29 | 0.12 | 93.0 | -1.98 | 1.0 | 25.0 |
| Activation of BH3-only proteins | 9.0 | 77.78 | -2.07 | 0.167 | 113.0 | -2.41 | 1.0 | 5.0 |
| Interleukin-7 signaling | 8.0 | 87.5 | -2.05 | 0.17 | 116.0 | -2.65 | 1.0 | 3.0 |
| Interleukin receptor SHC signaling | 21.0 | 80.95 | -2.51 | 0.082 | 73.0 | -1.79 | 1.0 | 47.5 |
| Activation of Matrix Metalloproteinases | 18.0 | 77.78 | -2.58 | 0.072 | 69.0 | -1.74 | 1.0 | 53.5 |
| Degradation of the extracellular matrix | 18.0 | 77.78 | -2.58 | 0.072 | 69.0 | -1.74 | 1.0 | 53.5 |
| Intrinsic Pathway for Apoptosis | 20.0 | 75.0 | -2.05 | 0.17 | 116.0 | -2.29 | 1.0 | 8.5 |
| Negative regulators of RIG-I/MDA5 signaling | 20.0 | 65.0 | -2.46 | 0.095 | 75.0 | -1.76 | 1.0 | 50.5 |
- Set Size = the number of genes in the pathway.
- Percent up= Percentage of up-regulated genes.
- NTk Stat = the value of the Ntk statistic (see above for more details).
- NTk q-value = the adjusted p-value of the NTk statistic.
- NTk rank = the ranking of the pathways according to the Ntk statistic.
- NEK Stat = the value of the NEk statistic (see above for more details).
- NEK q-value = the adjusted p-value of the NEk statistic.
- NEK Rank = the ranking of the pathways according to the Ntk statistic.
