Skip to main content

Advertisement

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