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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod29

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod29 Module size 33 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 124808 CCDC43 coiled-coil domain containing 43 8507 ENC1 ectodermal-neural cortex 1 8139 GAN gigaxonin 11146 GLMN glomulin, FKBP associated protein 64399 HHIP hedgehog interacting protein 84439 HHIPL1 HHIP like 1 79802 HHIPL2 HHIP like 2 3652 IPP intracisternal A particle-promoted polypeptide 10625 IVNS1ABP influenza virus NS1A binding protein 10324 KBTBD10 kelch like family member 41 83892 KCTD10 potassium channel tetramerization domain containing 10 253980 KCTD13 potassium channel tetramerization domain containing 13 9817 KEAP1 kelch like ECH associated protein 1 57542 KLHDC5 kelch like family member 42 55220 KLHDC8A kelch domain containing 8A 200942 KLHDC8B kelch domain containing 8B 55175 KLHL11 kelch like family member 11 90293 KLHL13 kelch like family member 13 339451 KLHL17 kelch like family member 17 11275 KLHL2 kelch like family member 2 27252 KLHL20 kelch like family member 20 9903 KLHL21 kelch like family member 21 84861 KLHL22 kelch like family member 22 64410 KLHL25 kelch like family member 25 54813 KLHL28 kelch like family member 28 26249 KLHL3 kelch like family member 3 123103 KLHL33 kelch like family member 33 55975 KLHL7 kelch like family member 7 57563 KLHL8 kelch like family member 8 55958 KLHL9 kelch like family member 9 8405 SPOP speckle type BTB/POZ protein 339745 SPOPL speckle type BTB/POZ protein like 7126 TNFAIP1 TNF alpha induced protein 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 3.88e-01 4.88e-48 GO Cul3-RING ubiquitin ligase complex cellular_component 2.87e-02 4.53e-03 GO hedgehog family protein binding molecular_function

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 0.00e+00 0.00e+00 protein modification by small protein conjugation 0.00e+00 0.00e+00 protein ubiquitination 0.00e+00 0.00e+00 cellular protein catabolic process 0.00e+00 0.00e+00 proteolysis involved in cellular protein catabolic process 0.00e+00 0.00e+00 protein catabolic process 0.00e+00 0.00e+00 cullin-RING ubiquitin ligase complex 0.00e+00 0.00e+00 transferase complex 0.00e+00 0.00e+00 ubiquitin ligase complex 0.00e+00 0.00e+00 Cul3-RING ubiquitin ligase complex 0.00e+00 0.00e+00 ubiquitin-protein transferase activity 0.00e+00 0.00e+00 ubiquitin-like protein transferase activity 3.88e-11 3.36e-08 ubiquitin-dependent protein catabolic process 4.12e-11 3.55e-08 modification-dependent protein catabolic process 3.32e-10 2.62e-07 proteasomal protein catabolic process 4.51e-09 3.07e-06 protein ubiquitination involved in ubiquitin-dependent protein catabolic process 9.55e-08 3.68e-05 oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor 1.87e-07 1.01e-04 proteasome-mediated ubiquitin-dependent protein catabolic process 1.14e-06 3.58e-04 quinone binding 5.51e-06 2.26e-03 proteasomal ubiquitin-independent protein catabolic process 4.18e-05 9.63e-03 actin binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.18e-08 8.76e-06 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 4.36e-08 1.18e-05 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 7.09e-06 1.09e-03 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 7.70e-06 1.18e-03 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.42e-04 7e-01 abnormal stomach glandular epithelium morphology 3.75e-03 1e+00 increased pancreatic beta cell mass 5.62e-03 1e+00 disorganized pancreatic islets 7.47e-03 1e+00 abnormal stomach non-glandular epithelium morphology 7.48e-03 1e+00 pleural effusion 7.48e-03 1e+00 abnormal radius morphology 7.49e-03 1e+00 muscle spasm 7.51e-03 1e+00 retinal neovascularization 1.05e-02 1e+00 hemorrhage 1.12e-02 1e+00 increased cardiomyocyte apoptosis 1.12e-02 1e+00 primary atelectasis 1.12e-02 1e+00 abnormal pulmonary alveolar duct morphology 1.20e-02 1e+00 decreased grip strength 1.24e-02 1e+00 salt-sensitive hypertension 1.30e-02 1e+00 ascites 1.31e-02 1e+00 abnormal head mesenchyme morphology 1.31e-02 1e+00 fused carpal bones 1.49e-02 1e+00 increased circulating amylase level 1.49e-02 1e+00 abnormal esophageal epithelium morphology 1.49e-02 1e+00 small stomach

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

²FDR corrected p-value (Benjamini-Hochberg)