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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod267

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod267 Module size 29 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 57698 KIAA1598 shootin 1 5954 RCN1 reticulocalbin 1 79024 SMIM2 small integral membrane protein 2 374768 SPEM1 spermatid maturation 1 140809 SRXN1 sulfiredoxin 1 10534 SSSCA1 Sjogren syndrome/scleroderma autoantigen 1 6817 SULT1A1 sulfotransferase family 1A member 1 80213 TM2D3 TM2 domain containing 3 55374 TMCO6 transmembrane and coiled-coil domains 6 55529 TMEM55A phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2 90809 TMEM55B phosphatidylinositol-4,5-bisphosphate 4-phosphatase 1 7265 TTC1 tetratricopeptide repeat domain 1 283237 TTC9C tetratricopeptide repeat domain 9C 23170 TTLL12 tubulin tyrosine ligase like 12 10277 UBE4B ubiquitination factor E4B 84993 UBL7 ubiquitin like 7 29979 UBQLN1 ubiquilin 1 29978 UBQLN2 ubiquilin 2 56893 UBQLN4 ubiquilin 4 23304 UBR2 ubiquitin protein ligase E3 component n-recognin 2 23352 UBR4 ubiquitin protein ligase E3 component n-recognin 4 51035 UBXN1 UBX domain protein 1 7347 UCHL3 ubiquitin C-terminal hydrolase L3 445268 UFC1 ubiquitin-fold modifier conjugating enzyme 1 51569 UFM1 ubiquitin fold modifier 1 85451 UNK unkempt family zinc finger 9736 USP34 ubiquitin specific peptidase 34 8239 USP9X ubiquitin specific peptidase 9 X-linked 9406 ZRANB2 zinc finger RANBP2-type containing 2

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 1.49e-01 1.71e-05 GO protein ufmylation biological_process 1.57e-02 4.17e-06 GO polyubiquitin modification-dependent 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 5.95e-09 3.98e-06 ubiquitin-dependent protein catabolic process 7.50e-09 4.95e-06 modification-dependent protein catabolic process 2.34e-08 1.45e-05 proteolysis involved in cellular protein catabolic process 3.18e-08 1.93e-05 cellular protein catabolic process 6.58e-08 3.83e-05 protein catabolic process 1.69e-06 5.15e-04 ubiquitin binding 3.23e-06 1.39e-03 regulation of proteasomal ubiquitin-dependent protein catabolic process 4.02e-06 1.14e-03 ubiquitin-like protein binding 5.85e-06 1.60e-03 phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity 7.81e-06 3.10e-03 regulation of proteasomal protein catabolic process 1.01e-05 2.63e-03 polyubiquitin binding 1.23e-05 4.66e-03 response to endoplasmic reticulum stress 1.63e-05 5.99e-03 regulation of ERAD pathway 2.54e-05 6.13e-03 phosphatidylinositol phosphate 4-phosphatase activity 2.97e-05 1.02e-02 proteasome-mediated ubiquitin-dependent protein catabolic process 3.44e-05 1.16e-02 proteasomal protein catabolic process 3.88e-05 1.29e-02 positive regulation of ER-associated ubiquitin-dependent protein catabolic process 6.74e-05 2.08e-02 ER-associated ubiquitin-dependent protein catabolic process 6.83e-05 2.10e-02 protein modification by small protein conjugation 8.67e-05 1.83e-02 phosphatidylinositol bisphosphate phosphatase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.64e-03 3.51e-01 RECYCLING PATHWAY OF L1 7.25e-03 6.18e-01 DOWNREGULATION OF SMAD2 3 SMAD4 TRANSCRIPTIONAL ACTIVITY 7.25e-03 6.18e-01 CYTOSOLIC SULFONATION OF SMALL MOLECULES 7.53e-03 5.81e-01 RECYCLING PATHWAY OF L1 1.00e-02 7.32e-01 DOWNREGULATION OF SMAD2 3 SMAD4 TRANSCRIPTIONAL ACTIVITY 1.08e-02 8.46e-01 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 1.09e-02 8.53e-01 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER 1.12e-02 8.71e-01 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 1.45e-02 1.00e+00 SIGNALING BY TGF BETA RECEPTOR COMPLEX 1.50e-02 1.00e+00 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 1.57e-02 1.00e+00 PHASE II CONJUGATION 1.75e-02 1.00e+00 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER 1.80e-02 1.00e+00 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 2.72e-02 1.00e+00 CYTOSOLIC SULFONATION OF SMALL MOLECULES 3.41e-02 1.00e+00 SIGNALING BY TGF BETA RECEPTOR COMPLEX

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.22e-05 8.24e-02 axonal dystrophy 3.74e-03 1.00e+00 thin placenta labyrinth 5.61e-03 1.00e+00 delayed gastrulation 5.61e-03 1.00e+00 abnormal vein morphology 5.61e-03 1.00e+00 testis degeneration 9.33e-03 1.00e+00 abnormal embryonic tissue physiology 9.34e-03 1.00e+00 intraventricular hemorrhage 9.34e-03 1.00e+00 abnormal medulla oblongata morphology 1.30e-02 1.00e+00 thin retinal outer plexiform layer 1.31e-02 1.00e+00 Purkinje cell degeneration 1.31e-02 1.00e+00 abnormal retinal layer morphology 1.49e-02 1.00e+00 abnormal photoreceptor inner segment morphology 1.68e-02 1.00e+00 abnormal retinal outer nuclear layer morphology 1.87e-02 1.00e+00 congestive heart failure 2.23e-02 1.00e+00 failure of heart looping 2.42e-02 1.00e+00 abnormal myocardial trabeculae morphology 2.42e-02 1.00e+00 abnormal dorsal root ganglion morphology 2.60e-02 1.00e+00 increased cardiomyocyte apoptosis 2.96e-02 1.00e+00 abnormal gametogenesis 3.15e-02 1.00e+00 abnormal retinal apoptosis

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

²FDR corrected p-value (Benjamini-Hochberg)