Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod40

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod40 Module size 63 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 146325 C16orf11 proline rich 35 84290 CAPNS2 calpain small subunit 2 114625 ERMAP erythroblast membrane associated protein (Scianna blood group) 64122 FN3K fructosamine 3 kinase 79672 FN3KRP fructosamine 3 kinase related protein 123722 FSD2 fibronectin type III and SPRY domain containing 2 25801 GCA grancalcin 8520 HAT1 histone acetyltransferase 1 8242 KDM5C lysine demethylase 5C 8284 KDM5D lysine demethylase 5D 4210 MEFV MEFV, pyrin innate immunity regulator 283948 NHLRC4 NHL repeat containing 4 5988 RFPL1 ret finger protein like 1 10739 RFPL2 ret finger protein like 2 10738 RFPL3 ret finger protein like 3 342931 RFPL4A ret finger protein like 4A 442247 RFPL4B ret finger protein like 4B 7732 RNF112 ring finger protein 112 84282 RNF135 ring finger protein 135 54546 RNF186 ring finger protein 186 80352 RNF39 ring finger protein 39 56948 SDR39U1 short chain dehydrogenase/reductase family 39U member 1 344558 SH3RF3 SH3 domain containing ring finger 3 6574 SLC20A1 solute carrier family 20 member 1 6575 SLC20A2 solute carrier family 20 member 2 3431 SP110 SP110 nuclear body protein 11262 SP140 SP140 nuclear body protein 93349 SP140L SP140 nuclear body protein like 10107 TRIM10 tripartite motif containing 10 81559 TRIM11 tripartite motif containing 11 89870 TRIM15 tripartite motif containing 15 51127 TRIM17 tripartite motif containing 17 7726 TRIM26 tripartite motif containing 26 11074 TRIM31 tripartite motif containing 31 53840 TRIM34 tripartite motif containing 34 202658 TRIM39-RPP21 TRIM39-RPP21 readthrough 89122 TRIM4 tripartite motif containing 4 135644 TRIM40 tripartite motif containing 40 90933 TRIM41 tripartite motif containing 41 129868 TRIM43 tripartite motif containing 43 79097 TRIM48 tripartite motif containing 48 57093 TRIM49 tripartite motif containing 49 283257 TRIM49B tripartite motif-containing 51F, pseudogene 642612 TRIM49C tripartite motif containing 49C 84767 TRIM51 tripartite motif-containing 51 84851 TRIM52 tripartite motif containing 52 25893 TRIM58 tripartite motif containing 58 445372 TRIM6-TRIM34 TRIM6-TRIM34 readthrough 166655 TRIM60 tripartite motif containing 60 391712 TRIM61 tripartite motif containing 61 642446 TRIM64B tripartite motif containing 64B 646754 TRIM64C tripartite motif containing 64C 9866 TRIM66 tripartite motif containing 66 55128 TRIM68 tripartite motif containing 68 140691 TRIM69 tripartite motif containing 69 81786 TRIM7 tripartite motif containing 7 493829 TRIM72 tripartite motif containing 72 375593 TRIM73 tripartite motif containing 73 378108 TRIM74 tripartite motif containing 74 339976 TRIML1 tripartite motif family like 1 205860 TRIML2 tripartite motif family like 2 79726 WDR59 WD repeat domain 59 84942 WDR73 WD repeat domain 73

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 1.52e-01 4.50e-05 Reactome Sodium-coupled phosphate cotransporters Transport of small molecules 1.51e-01 4.50e-05 GO histone demethylase activity (H3-K4 specific) molecular_function 6.89e-02 6.90e-08 GO negative regulation of viral entry into host cell biological_process 3.10e-02 9.35e-11 GO transferase activity molecular_function 2.58e-02 4.11e-06 GO negative regulation of viral release from host cell biological_process 1.17e-02 1.61e-07 GO protein autoubiquitination biological_process 1.06e-02 9.78e-10 Reactome Interferon gamma signaling Immune System 6.61e-03 2.45e-04 GO regulation of androgen receptor signaling pathway biological_process

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 1.78e-09 1.28e-06 protein modification by small protein conjugation 3.07e-09 2.15e-06 innate immune response 1.07e-08 6.94e-06 protein ubiquitination 1.51e-08 9.61e-06 regulation of viral release from host cell 2.87e-08 1.76e-05 negative regulation of viral entry into host cell 1.25e-07 6.95e-05 regulation of viral entry into host cell 1.29e-07 7.16e-05 negative regulation of viral process 2.11e-07 1.13e-04 regulation of sequence-specific DNA binding transcription factor activity 2.76e-07 1.45e-04 positive regulation of sequence-specific DNA binding transcription factor activity 4.59e-07 2.32e-04 negative regulation of viral release from host cell 6.99e-07 3.43e-04 response to interferon-gamma 7.94e-07 3.85e-04 regulation of viral life cycle 3.84e-06 1.63e-03 interferon-gamma-mediated signaling pathway 4.82e-06 1.34e-03 ubiquitin-protein transferase activity 6.41e-06 1.74e-03 ubiquitin-like protein transferase activity 9.92e-06 3.84e-03 regulation of viral process 1.58e-05 3.96e-03 inorganic phosphate transmembrane transporter activity 1.65e-05 6.06e-03 cellular response to interferon-gamma 3.92e-05 1.30e-02 histone H3-K4 demethylation 5.57e-05 1.24e-02 sodium-dependent phosphate transmembrane transporter activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.72e-03 1.87e-01 TRAF6 MEDIATED NFKB ACTIVATION 1.72e-03 1.87e-01 NFKB ACTIVATION THROUGH FADD RIP1 PATHWAY MEDIATED BY CASPASE 8 AND10 5.01e-03 4.58e-01 TRAF3 DEPENDENT IRF ACTIVATION PATHWAY 5.64e-03 5.04e-01 INNATE IMMUNE SYSTEM 5.96e-03 5.29e-01 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 6.73e-03 5.83e-01 TRAF6 MEDIATED IRF7 ACTIVATION 8.11e-03 6.19e-01 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 1.08e-02 7.78e-01 TRAF6 MEDIATED NFKB ACTIVATION 1.08e-02 7.78e-01 NFKB ACTIVATION THROUGH FADD RIP1 PATHWAY MEDIATED BY CASPASE 8 AND10 1.32e-02 9.18e-01 THE NLRP3 INFLAMMASOME 1.32e-02 9.18e-01 INFLAMMASOMES 1.45e-02 9.89e-01 INNATE IMMUNE SYSTEM 1.48e-02 1.00e+00 THE NLRP3 INFLAMMASOME 1.69e-02 1.00e+00 NUCLEOTIDE BINDING DOMAIN LEUCINE RICH REPEAT CONTAINING RECEPTOR NLR SIGNALING PATHWAYS 1.76e-02 1.00e+00 NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING 1.78e-02 1.00e+00 TRAF3 DEPENDENT IRF ACTIVATION PATHWAY 2.13e-02 1.00e+00 INFLAMMASOMES 2.16e-02 1.00e+00 NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING 2.39e-02 1.00e+00 SLC MEDIATED TRANSMEMBRANE TRANSPORT 2.46e-02 1.00e+00 NUCLEOTIDE BINDING DOMAIN LEUCINE RICH REPEAT CONTAINING RECEPTOR NLR SIGNALING PATHWAYS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.74e-03 1e+00 increased interleukin-18 secretion 3.74e-03 1e+00 decreased interleukin-3 secretion 3.74e-03 1e+00 increased interleukin-1 alpha secretion 5.61e-03 1e+00 increased interleukin-9 secretion 5.61e-03 1e+00 decreased macrophage apoptosis 7.47e-03 1e+00 echinocytosis 7.48e-03 1e+00 pale placenta 7.48e-03 1e+00 enlarged liver sinusoidal spaces 9.33e-03 1e+00 abnormal incisor color 1.12e-02 1e+00 decreased common myeloid progenitor cell number 1.12e-02 1e+00 schistocytosis 1.12e-02 1e+00 joint inflammation 1.30e-02 1e+00 abnormal lung interstitium morphology 1.30e-02 1e+00 abnormal fatty acid level 1.49e-02 1e+00 primary atelectasis 1.49e-02 1e+00 spherocytosis 1.49e-02 1e+00 eyelids fail to open 1.49e-02 1e+00 increased interleukin-12b secretion 1.49e-02 1e+00 arthritis 1.67e-02 1e+00 absent mandible

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

²FDR corrected p-value (Benjamini-Hochberg)