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.

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)

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)