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Table 4 Ontology analysis of cohesin target genes

From: The effect of Nipped-B-like (Nipbl) haploinsufficiency on genome-wide cohesin binding and target gene expression: modeling Cornelia de Lange syndrome

Biological process

P value

Enrichment

Gene number

Expected number

Genes

Altered gene expression in Nipbl+/− MEFs associated with cohesin binding to the promoters

 Development

2.96E−04

2.38

18

7.55

Avpr1a, Dner, Fgf7, Thbd, Hoxa5,Hoxb5, Cebpa, Cebpb, Rcan2, Lama2, Ebf1, Klf4, Hunk, Tgfb3, Irx5, Odz4, Ptpre, Lpp

 Metabolism

2.90E−03

1.50

33

22

Dner, Acvr2a, Hoxa5, Hoxb5, Trib2, Satb1, Cebpa, Cebpb, Gstm2, Amacr, Cd55, Dhrs3, Grk5, Ell2, Serpinb1a, Cyp1b1, Chst1, Hsd3b7, Aldh1a7, Npr3, Man2a1, Klf4, Hunk, Prkd1,Prdx5, Ercc1, Irx5, Odz4, Sox11, Ptpre, Ccrn4l, Rgnef, Bcl11b

 Cell communication

2.96E−03

1.82

21

11.53

Dner, Acvr2a, Trib2, Cd55, Grk5, Hunk, Odz4, Ptpre, Rgnef, Avpr1a, Fgf7, Thbd, Fam43a, Rcan2, Socs3, Lama2, Cxcr7, Tpcn1, Rerg, Tgfb3, Lpp

 Immune system

6.44E−03

2.06

14

6.81

Dner, Cd55, Hunk, Ptpre, Thbd, Lama2, Cxcr7, Cebpa, Cebpb, Gstm2, Klf4, Prdx5, Fcgrt, Cd302

Altered gene expression in Nipbl+/− MEFs associated with cohesin binding to the gene regions

 Immune system

6.60E−06

2.34

30

12.83

Klf4, Dner, Thbd, Cd55, Lama2, Cd302, Cxcr7, Hunk, Cebpa, Cebpb, Gstm2, Fcgrt, Prdx5, Fmod, Crlf1, Prelp, Svep1, Plac8, Heph, Swap70, Mxra8, Sdc2, Colec12, Pcolce2, Flt4, Gbp1, Hck, Dusp14, Cd109, Ptpre

 Cell adhesion

1.33E−05

3.05

19

6.22

Dner, Cd55, Lama2, Fmod, Prelp, Svep1, Plac8, Heph, Mxra8, Sdc2, Colec12, Pcolce2, Flt4, Hck, Ptpre, Rerg, Vcan, Odz4, Rgnef

 Cell communication

1.65E−05

1.89

41

21.72

Dner, Cd55, Lama2, Fmod, Prelp, Svep1, Heph, Sdc2, Colec12, Pcolce2, Flt4, Hck, Ptpre, Rerg, Vcan, Odz4, Rgnef, Thbd, Cxcr7, Hunk, Crlf1, Dusp14, Cd109, Rcan2, Socs3, Fam43a, Trib2, Grk5, Tpcn1, Avpr1a, Fgf7, Acvr2a, Figf, Myh3, Tob1, Acvrl1, Moxd1, Tgfb3, Lpp, Wnt4

 Development

4.81E−05

2.11

30

14.22

Dner, Lama2, Fmod, Prelp, Heph, Sdc2, Colec12, Pcolce2, Flt4, Ebf1, Hck, Ptpre, Vcan, Odz4, Thbd, Hunk, Crlf1, Rcan2, Socs3, Avpr1a, Fgf7, Figf, Myh3, Tgfb3, Lpp, Klf4, Cebpa, Cebpb, Hoxa5, Hoxb5, Irx5

 Metabolism

1.91E−03

1.38

57

41.44

Dner, Heph, Pcolce2, Flt4, Hck, Ptpre, Odz4, Hunk, Klf4, Cebpa, Cebpb, Hoxa5, Hoxb5, Irx5, Cd55, Svep1, Rgnef, Dusp14, Cd109, Trib2, Grk5, Acvr2a, Acvrl1, Moxd1, Prdx5, Swap70, Satb1, Amacr, Dhrs3, Ell2, Npr3, Man2a1, Prkd1, Cyp1b1, Serpinb1a, Chst1, Hsd3b7, Aldh1a7, H6pd, Serpine2, Cyp7b1, P4ha2, Larp6, Mrps11, Aox1, Hdac5, Cpxm1, Eno2, Sox11, Prkcdbp, Ccrn4l, Ercc1, Pqlc3, Bcl11b

  1. Biological processes enriched in cohesin target genes with cohesin binding at either promoters or gene regions. “Gene number” is the number of cohesin target genes that belong to a specific category; “Expected number” is the expected gene numbers that belong to a specific category at random
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Clinical Epigenetics

ISSN: 1868-7083

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