Table 3.
Changed gene sets in the gastrocnemius versus quadriceps.
| N | ES | NES | FDR | |
|---|---|---|---|---|
| up-regulated cellular processes | ||||
| Striated muscle contraction1 | 41 | 0.68 | 2.37 | 0.000 |
| Ribosome2 | 20 | 0.71 | 2.05 | 0.005 |
| down-regulated cellular processes | ||||
| Tissues, muscle, fat, bone and connective 21 | 47 | -0.57 | -2.14 | 0.003 |
| Cell cycle1 | 85 | -0.52 | -2.14 | 0.003 |
| CTCF first multivalent nuclear factor3 | 17 | -0.71 | -2.07 | 0.006 |
| Valine, leucine and isoleucine degradation2 | 40 | -0.59 | -2.16 | 0.006 |
| Cell cycle G1 to S control reactome2 | 69 | -0.49 | -2.01 | 0.013 |
| Antigen processing and presentation2 | 51 | -0.52 | -2.01 | 0.014 |
| Mets affect on macrophage differentiation3 | 16 | -0.69 | -1.97 | 0.014 |
| Amino acid metabolism1 | 46 | -0.52 | -1.95 | 0.016 |
| Porphyrin and Chlorophyll metabolism2 | 19 | -0.64 | -1.88 | 0.033 |
| DNA replication reactome1 | 40 | -0.51 | -1.86 | 0.038 |
GSEA was applied to identify up-regulated and down-regulated processes in the gastrocnemius as compared with the quadriceps in LFD mice. Presented are regulated processes with a false discovery rate (FDR) < 0.05. An FDR was calculated to adjust for multiple hypothesis testing. Sources of the gene sets: 1GenMAPP, 2KEGG, 3Biocarta. N, number of genes; ES, enrichment score for the gene set, that reflects the degree to which a gene set is overrepresented at the top or bottom of the ranked list; FDR, NES, normalized enrichment score, that is, the normalized ES to account for the size of the set.