Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod349

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod349 Module size 38 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 80755 AARSD1 alanyl-tRNA synthetase domain containing 1 114781 BTBD9 BTB domain containing 9 81928 CABLES2 Cdk5 and Abl enzyme substrate 2 147372 CCBE1 collagen and calcium binding EGF domains 1 150684 COMMD1 copper metabolism domain containing 1 170622 COMMD6 COMM domain containing 6 79585 CORO7 coronin 7 8904 CPNE1 copine 1 221184 CPNE2 copine 2 1446 CSN1S1 casein alpha s1 1734 DIO2 iodothyronine deiodinase 2 23291 FBXW11 F-box and WD repeat domain containing 11 84163 GTF2IRD2 GTF2I repeat domain containing 2 89890 KBTBD6 kelch repeat and BTB domain containing 6 84078 KBTBD7 kelch repeat and BTB domain containing 7 147040 KCTD11 potassium channel tetramerization domain containing 11 3851 KRT4 keratin 4 93487 MAPK1IP1L mitogen-activated protein kinase 1 interacting protein 1 like 4291 MLF1 myeloid leukemia factor 1 23138 N4BP3 NEDD4 binding protein 3 140825 NEURL2 neuralized E3 ubiquitin protein ligase 2 84461 NEURL4 neuralized E3 ubiquitin protein ligase 4 78990 OTUB2 OTU deubiquitinase, ubiquitin aldehyde binding 2 192111 PGAM5 PGAM family member 5, mitochondrial serine/threonine protein phosphatase 54458 PRR13 proline rich 13 129831 RBM45 RNA binding motif protein 45 51151 SLC45A2 solute carrier family 45 member 2 22950 SLC4A1AP solute carrier family 4 member 1 adaptor protein 79921 TCEAL4 transcription elongation factor A like 4 7062 TCHH trichohyalin 10342 TFG TRK-fused gene 64222 TOR3A torsin family 3 member A 9321 TRIP11 thyroid hormone receptor interactor 11 81628 TSC22D4 TSC22 domain family member 4 23032 USP33 ubiquitin specific peptidase 33 29062 WDR91 WD repeat domain 91 49856 WRAP73 WD repeat containing, antisense to TP73 9189 ZBED1 zinc finger BED-type containing 1

Functional annotation

Modules were tested for enrichment in functional and pathway annotations using two complementary approaches:
1. To select a small number of specific / non-redundant annotations for each module, a regression-based approach was used;
2. To obtain the complete set of enriched annotations, an extension of Fisher’s exact test that takes annotation bias into account was employed (Wallenius’ non-central hypergeometric distribution).

Most specific annotations for this module

Coeff.1 P-value.2 Source.3 Term.4 Class.5 2.79e-02 5.75e-03 Reactome Regulation of thyroid hormone activity Metabolism

¹Regression coefficient

²Fisher’s exact test nominal P-value

³Annotation source (Reactome, GO biological process (BP), molecular function (MF) and cellular component (CC))

⁴GO category or Reactome pathway

⁵High-level branch of annotation tree

Gene membership

All enriched annotations

Gene Ontology

P-value1 FDR2 Term 5.27e-05 1.12e-02 ubiquitin ligase complex 9.21e-05 1.83e-02 cullin-RING ubiquitin ligase complex 2.80e-04 6.95e-02 phenol-containing compound metabolic process 4.42e-04 1.01e-01 protein K63-linked deubiquitination 5.13e-04 8.59e-02 NF-kappaB binding 5.58e-04 1.22e-01 protein K48-linked deubiquitination 9.12e-04 1.83e-01 protein ubiquitination 1.09e-03 1.57e-01 centrosome 1.36e-03 2.54e-01 cellular response to calcium ion 1.72e-03 3.07e-01 protein modification by small protein conjugation 1.82e-03 3.21e-01 Golgi vesicle transport 2.37e-03 3.90e-01 negative regulation of NF-kappaB transcription factor activity 2.38e-03 3.92e-01 regulation of I-kappaB kinase/NF-kappaB signaling 3.67e-03 4.73e-01 sucrose:proton symporter activity 3.82e-03 4.46e-01 transferase complex 3.90e-03 5.71e-01 negative regulation of neuroblast proliferation 3.90e-03 5.71e-01 negative regulation of stem cell proliferation 3.90e-03 5.71e-01 negative regulation of activation-induced cell death of T cells 3.90e-03 5.71e-01 regulation of activation-induced cell death of T cells 4.09e-03 4.70e-01 microtubule organizing center

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 5.18e-03 4.70e-01 ACTIVATION OF NF KAPPAB IN B CELLS 6.92e-03 5.95e-01 DOWNSTREAM SIGNALING EVENTS OF B CELL RECEPTOR BCR 7.29e-03 5.65e-01 ACTIVATION OF NF KAPPAB IN B CELLS 8.12e-03 6.80e-01 AMINE DERIVED HORMONES 8.26e-03 6.28e-01 DOWNSTREAM SIGNALING EVENTS OF B CELL RECEPTOR BCR 1.21e-02 9.26e-01 SIGNALING BY THE B CELL RECEPTOR BCR 1.46e-02 9.94e-01 AMINE DERIVED HORMONES 2.11e-02 1.00e+00 SIGNALING BY THE B CELL RECEPTOR BCR

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.54e-04 3e-01 abnormal skin pigmentation 1.21e-03 1e+00 diluted coat color 1.87e-03 1e+00 heart right ventricle outflow tract stenosis 1.87e-03 1e+00 small lung saccule 1.87e-03 1e+00 decreased fetal derived definitive erythrocyte cell number 5.61e-03 1e+00 absent eye pigmentation 5.61e-03 1e+00 esophageal epithelium hyperplasia 5.61e-03 1e+00 unidirectional circling 5.61e-03 1e+00 abnormal type I pneumocyte morphology 5.62e-03 1e+00 irregular coat pigmentation 7.47e-03 1e+00 abnormal esophageal epithelium morphology 7.47e-03 1e+00 failure of bone ossification 7.48e-03 1e+00 abnormal stomach epithelium morphology 7.48e-03 1e+00 small thoracic cage 7.48e-03 1e+00 abnormal pulmonary alveolus epithelial cell morphology 7.50e-03 1e+00 thick ventricular wall 9.33e-03 1e+00 abnormal pinna hair pigmentation 9.33e-03 1e+00 abnormal thermosensation 1.12e-02 1e+00 decreased eye pigmentation 1.12e-02 1e+00 abnormal mesenchyme morphology

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)