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Table 3 Gene clusters from WGCNA analysis and GO terms analysis of genes within the top three clusters

From: Changes to the identity of EndoC-βH1 beta cells may be mediated by stress-induced depletion of HNRNPD

(A) WGCNA

Eigengene module

LogFC

p

Adj p

B

ME light sky blue2

− 0.46265489

0.012

0.436

− 4.00

ME orange red 4

− 0.461540016

0.013

0.436

− 4.010

ME salmon 1

− 0.428245371

0.020

0.436

− 4.11

ME indian red 1

0.418718931

0.023

0.436

− 4.14

ME alice blue

0.414679702

0.025

0.436

− 4.5

ME pink 3

0.408739235

0.027

0.436

− 4.16

ME wheat 3

− 0.395082849

0.032

0.436

− 4.20

ME sky blue 2

0.384220441

0.037

0.436

− 4.23

ME indian red 2

− 0.380769172

0.039

0.436

− 4.24

ME medium purple

− 0.380324742

0.039

0.436

-4.24

ME blue 2

− 0.377223329

0.041

0.436

-4.25

B

GO biological process complete

Fold enrichment

Raw p value

FDR

Protein modification by small protein removal (GO:0070646)

20.27

4.42 × 10–10

3.51 × 10–6

Protein deubiquitination (GO:0016579)

21.51

2.66 × 10–10

4.22 × 10–6

Modification-dependent macromolecule catabolic process (GO:0043632)

10.83

9.03 × 10–8

2.86 × 10–4

Modification-dependent protein catabolic process (GO:0019941)

11.05

7.63 × 10–8

3.03 × 10–4

Ubiquitin-dependent protein catabolic process (GO:0006511)

11.2

6.84 × 10–8

3.62 × 10–4

Proteolysis involved in cellular protein catabolic process (GO:0051603)

9.98

1.79 × 10–7

4.73 × 10–4

Cellular protein catabolic process (GO:0044257)

9.46

2.79 × 10–7

6.33 × 10–4

Protein catabolic process (GO:0030163)

8.72

5.51 × 10–7

0.001

Macromolecule catabolic process (GO:0009057)

6.32

2.05 × 10–6

0.004

Cellular macromolecule catabolic process (GO:0044265)

6.52

5.88 × 10–6

0.009

Protein modification by small protein conjugation or removal (GO:0070647)

5.83

1.44 × 10–5

0.021

MiRNA 2ʹ-O-methylation (GO:0061715)

> 100

0.003

 

Immune system process (GO:000276)

3.15

0.004

 

Negative regulation of pre-miRNA processing (GO:2000632)

> 100

0.005

 

Regulation of pre-miRNA processing (GO:2000631)

> 100

0.005

 

Entry of viral genome into host nucleus through nuclear pore complex via importin (GO:0075506)

> 100

0.005

 

‘De novo’ co-translational protein folding (GO:0051083)

> 100

0.005

 

Intramembranous ossification (GO:0001957)

> 100

0.005

 

Direct ossification (GO:0036072)

> 100

0.005

 

Osteoclast fusion (GO:0072675)

> 100

0.005

 
  1. (A) WGCNA: The table illustrates the 11 gene modules identified by WGCNA and reaching statistical significance after multiple testing that demonstrate correlated differential expression in somatostatin-positive cells. The table gives the average module logged fold change (logFC), the logged odds ratio that the module is differentially expressed (B) and the nominal p value (p) and the FDR-adjusted p value (Adj p). (B) GO analysis: The table gives the Gene Ontology (GO) biological processes pathway, the fold enrichment of differentially-regulated genes within that pathway and the p value for significance for biological processes pathways that contain significantly more differentially regulated gene modules in somatostatin-positive cells than would be expected by chance. Only GO processes from the ‘light sky blue 2’ gene module made FDR corrected p values, genes from modules ‘Orange Red 4’ and ‘Salmon 1’ were nominally significant
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Cell & Bioscience

ISSN: 2045-3701

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