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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.

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

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)