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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.

From: In vitro gentamicin exposure alters caveolae protein profile in cochlear spiral ligament pericytes

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)