Table 3.
A, B and C. Enrichment analysis of proteins uniquely segregating with caveolae in untreated cells. The 251 proteins uniquely segregating with caveolae in untreated cells where selected as the target group for the GOrilla enrichment analysis. The control dataset plus the GTM dataset were chosen as background group. GO terms with a FDR q-value p < or = 10− 5 were considered in the table. The complete list of significantly enriched GO terms to p < 0.05 is presented as additional file [See Additional file 3]. The enrichment showed significance for terms in the categories “Biological process”, “Cellular component” and “Molecular function”. The enriched terms showed the suppressed activities and functions in the cells once GTM is administered.
| A Biological process | |||
| GO term | Description | FDR q-value | Enrichment (N, B, n, b) |
| GO:0090304 | nucleic acid metabolic process | 2.59E-10 | 1.96 (2597,537,249,101) |
| GO:0016070 | RNA metabolic process | 3.1E-10 | 2.06 (2597,455,249,90) |
| GO:0006139 | nucleobase-containing compound metabolic process | 1.86E-5 | 1.61 (2597,673,249,104) |
| GO:0046483 | heterocycle metabolic process | 4.34E-5 | 1.57 (2597,704,249,106) |
| GO:0006725 | cellular aromatic compound metabolic process | 6.41E-5 | 1.56 (2597,694,249,104) |
| GO:0006351 | transcription, DNA-templated | 7.04E-5 | 2.23 (2597,210,249,45) |
| GO:0097659 | nucleic acid-templated transcription | 6.03E-5 | 2.23 (2597,210,249,45) |
| GO:0010468 | regulation of gene expression | 7.14E-5 | 1.66 (2597,539,249,86) |
| GO:0032774 | RNA biosynthetic process | 8.61E-5 | 2.19 (2597,214,249,45) |
| GO:0006396 | RNA processing | 9.71E-5 | 2.13 (2597,230,249,47) |
| B Cellular component | |||
| GO term | Description | FDR q-value | Enrichment (N, B, n, b) |
| GO:0044428 | nuclear part | 1.15E-6 | 1.54 (2597,855,249,126) |
| GO:0005634 | nucleus | 4.66E-6 | 1.38 (2597,1160,249,154) |
| C Molecular function | |||
| GO term | Description | FDR q-value | Enrichment (N, B, n, b) |
| GO:0003676 | nucleic acid binding | 5.68E-10 | 1.70 (2597,779,249,127) |
| GO:0003677 | DNA binding | 1.58E-7 | 2.36 (2597,243,249,55) |
| GO:0000975 | regulatory region DNA binding | 8.02E-7 | 3.56 (2597,79,249,27) |
| GO:0044212 | transcription regulatory region DNA binding | 6.01E-7 | 3.56 (2597,79,249,27) |
| GO:0001067 | regulatory region nucleic acid binding | 9.13E-7 | 3.48 (2597,81,249,27) |
| GO:0043565 | sequence-specific DNA binding | 1.34E-5 | 3.09 (2597,91,249,27) |
| GO:1990837 | sequence-specific double-stranded DNA binding | 4.73E-5 | 3.48 (2597,63,249,21) |