Table 1.
A and B. Enriched terms for the ontologies “Biological process” and “Cellular component” in gentamicin treated cells. Proteins that appeared in two out of three mass spectrometry repeats were considered for the analysis. Proteins segregating with caveolae in the GTM treated cells dataset where selected as the target for the GOrilla enrichment analysis. The control dataset plus the GTM dataset were chosen as background group in the analysis. All terms with FDR q-value below 0.05 are listed in Tables 1A and B. (A) The GO category “Cellular Process” showed significant enrichment for processes associated with transport and localization, and associated to metabolic, bioenergetic and biosynthetic processes. (B) The GO category “Cellular component” showed significant enrichment for terms participating in three main groups, one comprising terms referring to cell cytoplasm and organelles, the other comprising terms referring to extracellular components and vesicles, and a third group comprising terms referring to cell membrane and membrane/protein interactions.
| A GO biological process | |||
| GO term | Description | FDR q-value | Enrichment (N, B, n, b) |
| GO:0044710 | single-organism metabolic process | 3.50E-06 | 1.07 (2597,532,2348,515) |
| GO:0044281 | small molecule metabolic process | 1.65E-05 | 1.09 (2597,323,2348,317) |
| GO:0045184 | establishment of protein localization | 9.64E-03 | 1.06 (2597,376,2348,362) |
| GO:0006810 | transport | 8.07E-03 | 1.05 (2597,709,2348,670) |
| GO:0015031 | protein transport | 1.23E-02 | 1.07 (2597,351,2348,338) |
| GO:0008104 | protein localization | 1.62E-02 | 1.06 (2597,431,2348,412) |
| GO:0055114 | oxidation-reduction process | 1.71E-02 | 1.08 (2597,214,2348,209) |
| GO:0051179 | localization | 1.85E-02 | 1.04 (2597,793,2348,745) |
| GO:0042592 | homeostatic process | 1.71E-02 | 1.08 (2597,193,2348,189) |
| GO:0043436 | oxoacid metabolic process | 1.85E-02 | 1.09 (2597,172,2348,169) |
| GO:0019752 | carboxylic acid metabolic process | 1.68E-02 | 1.09 (2597,172,2348,169) |
| GO:0006082 | organic acid metabolic process | 2.16E-02 | 1.08 (2597,187,2348,183) |
| GO:0051234 | establishment of localization | 2.27E-02 | 1.04 (2597,733,2348,689) |
| GO:0044711 | single-organism biosynthetic process | 2.62E-02 | 1.08 (2597,183,2348,179) |
| B GO Cellular component | |||
| GO term | Description | FDR q-value | Enrichment (N, B, n, b) |
| GO:0044444 | cytoplasmic part | 1.91E-08 | 1.03 (2597,1603,2348,1499) |
| GO:0031982 | vesicle | 6.31E-07 | 1.05 (2597,1045,2348,988) |
| GO:0043230 | extracellular organelle | 7.51E-07 | 1.05 (2597,942,2348,893) |
| GO:1903561 | extracellular vesicle | 5.63E-07 | 1.05 (2597,942,2348,893) |
| GO:0070062 | extracellular exosome | 4.86E-07 | 1.05 (2597,941,2348,892) |
| GO:0031988 | membrane-bounded vesicle | 4.37E-07 | 1.05 (2597,1000,2348,946) |
| GO:0044421 | extracellular region part | 3.38E-06 | 1.04 (2597,982,2348,927) |
| GO:0098796 | membrane protein complex | 1.24E-05 | 1.09 (2597,272,2348,267) |
| GO:0044425 | membrane part | 1.25E-04 | 1.05 (2597,781,2348,738) |
| GO:0016020 | membrane | 4.63E-04 | 1.03 (2597,1470,2348,1363) |
| GO:0044432 | endoplasmic reticulum part | 2.25E-03 | 1.09 (2597,153,2348,151) |
| GO:0005829 | cytosol | 1.14E-02 | 1.05 (2597,397,2348,378) |
| GO:0031090 | organelle membrane | 2.65E-02 | 1.05 (2597,435,2348,412) |
| GO:0005783 | endoplasmic reticulum | 2.77E-02 | 1.06 (2597,312,2348,298) |
| GO:0005739 | mitochondrion | 2.82E-02 | 1.04 (2597,508,2348,479) |
| GO:0098588 | bounding membrane of organelle | 4.45E-02 | 1.06(2597,231,2348,222) |