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Table 2 Gene ontology (GO) functional annotation clustering

From: Whole-transcriptome gene expression profiling in an epidermolysis bullosa simplex Dowling-Meara model keratinocyte cell line uncovered novel, potential therapeutic targets and affected pathways

Cluster

GO#

Term

Annotated

Significant

Expected

p value

(1)—16 clusters

 1

GO:0050680

Negative regulation of epithelial cell proliferation

42

5

0.4881

0.0001

 2

GO:0001658

Branching involved in ureteric bud morphogenesis

41

4

0.4765

0.0013

 3

GO:0009954

Proximal/distal pattern formation

21

3

0.2440

0.0018

 4

GO:0034341

Response to interferon-gamma

19

3

0.2208

0.0013

 5

GO:0034613

Cellular protein localization

36

4

0.4183

0.0008

 6

GO:0090103

Cochlea morphogenesis

20

3

0.2324

0.0015

 7

GO:0032526

Response to retinoic acid

51

4

0.5927

0.0029

 8

GO:0006024

Glycosaminoglycan biosynthetic process

30

3

0.3486

0.0050

 9

GO:0006635

Fatty acid beta-oxidation

28

3

0.3254

0.0041

 10

GO:0010811

Positive regulation of cell-substrate adhesion

29

3

0.3370

0.0045

 11

GO:0030513

Positive regulation of BMP signaling pathway

31

3

0.3602

0.0055

 13

GO:0048704

Embryonic skeletal system morphogenesis

38

3

0.4416

0.0097

 14

GO:0090090

Negative regulation of canonical Wnt receptor signaling pathway

71

4

0.8251

0.0093

 15

GO:0030326

Embryonic limb morphogenesis

39

3

0.4532

0.0104

 16

GO:0009411

Response to UV

41

3

0.4765

0.0119

(2)—2 clusters

 17

GO:0004725

Protein tyrosine phosphatase activity

84

5

1.0065

0.0033

 18

GO:0015293

Symporter activity

43

4

0.5152

0.0017

(3)—1 clusterr

 19

GO:0005883

Neurofilament

9

3

0.1026

0.0001

  1. Differentially regulated genes in EBS-DM KEB7 versus wild-type NEB1 cells were assigned GO terms and classified into clusters, which were further classified as biological processes (1), molecular functions (2) and cellular components (3). Statistical significance of each term was calculated by a one-sided hypergeometric test; a cluster with an adjusted p-value <0.05 was considered significant. Per cluster, a minimum of 3 genes (up- or down-regulated) is significant, equating to nearly 10 % of all annotated genes per enriched term