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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod233

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod233 Module size 30 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 684 BST2 bone marrow stromal cell antigen 2 151636 DTX3L deltex E3 ubiquitin ligase 3L 94240 EPSTI1 epithelial stromal interaction 1 441168 FAM26F calcium homeostasis modulator family member 6 115361 GBP4 guanylate binding protein 4 163351 GBP6 guanylate binding protein family member 6 388646 GBP7 guanylate binding protein 7 10561 IFI44 interferon induced protein 44 10964 IFI44L interferon induced protein 44 like 345611 IRGM immunity related GTPase M 3959 LGALS3BP galectin 3 binding protein 3965 LGALS9 galectin 9 284194 LGALS9B galectin 9B 654346 LGALS9C galectin 9C 51338 MS4A4A membrane spanning 4-domains A4A 64761 PARP12 poly(ADP-ribose) polymerase family member 12 54625 PARP14 poly(ADP-ribose) polymerase family member 14 165631 PARP15 poly(ADP-ribose) polymerase family member 15 83666 PARP9 poly(ADP-ribose) polymerase family member 9 100910270 PLAC8 uncharacterized LOC100910270 57664 PLEKHA4 pleckstrin homology domain containing A4 91543 RSAD2 radical S-adenosyl methionine domain containing 2 83597 RTP3 receptor transporter protein 3 64108 RTP4 receptor transporter protein 4 54809 SAMD9 sterile alpha motif domain containing 9 219285 SAMD9L sterile alpha motif domain containing 9 like 92610 TIFA TRAF interacting protein with forkhead associated domain 55281 TMEM140 transmembrane protein 140 11274 USP18 ubiquitin specific peptidase 18 373856 USP41 ubiquitin specific peptidase 41

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 5.82e-02 4.78e-05 GO protein insertion into membrane biological_process 3.69e-02 6.14e-05 GO positive regulation of double-strand break repair via nonhomologous end joining biological_process 3.48e-02 4.20e-08 GO NAD+ ADP-ribosyltransferase activity molecular_function 2.26e-02 4.78e-05 GO protein poly-ADP-ribosylation 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 3.22e-07 1.13e-04 NAD+ ADP-ribosyltransferase activity 3.26e-06 1.40e-03 response to virus 3.49e-06 1.49e-03 response to other organism 4.44e-06 1.85e-03 response to biotic stimulus 6.47e-06 1.75e-03 transferase activity, transferring pentosyl groups 1.20e-05 4.56e-03 defense response to other organism 1.76e-05 4.37e-03 olfactory receptor binding 2.13e-04 5.52e-02 innate immune response 3.05e-04 7.46e-02 endosomal vesicle fusion 3.36e-04 8.07e-02 protein insertion into membrane 3.37e-04 8.09e-02 response to interferon-gamma 3.47e-04 6.12e-02 GTP binding 3.51e-04 8.39e-02 negative regulation of viral genome replication 3.57e-04 6.27e-02 ribonucleoside binding 3.59e-04 6.30e-02 purine nucleoside binding 3.59e-04 6.30e-02 guanyl ribonucleotide binding 3.69e-04 6.45e-02 nucleoside binding 3.96e-04 9.25e-02 defense response to virus 4.11e-04 9.54e-02 regulation of viral life cycle 4.34e-04 9.96e-02 regulation of innate immune response

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 7.57e-07 1.34e-04 INTERFERON SIGNALING 1.35e-06 2.99e-04 INTERFERON GAMMA SIGNALING 1.53e-06 3.35e-04 INTERFERON SIGNALING 1.64e-06 3.56e-04 CYTOKINE SIGNALING IN IMMUNE SYSTEM 2.03e-06 3.38e-04 INTERFERON GAMMA SIGNALING 8.20e-06 1.25e-03 CYTOKINE SIGNALING IN IMMUNE SYSTEM 1.65e-03 1.81e-01 REGULATION OF IFNA SIGNALING 3.63e-03 3.13e-01 REGULATION OF IFNA SIGNALING 2.62e-02 1.00e+00 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 3.34e-02 1.00e+00 INTERFERON ALPHA BETA SIGNALING 3.70e-02 1.00e+00 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 4.70e-02 1.00e+00 INTERFERON ALPHA BETA SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 9.99e-04 9.02e-01 increased B cell proliferation 1.07e-03 9.34e-01 increased susceptibility to endotoxin shock 1.88e-03 1.00e+00 abnormal neutrophil morphology 2.25e-03 1.00e+00 increased leukocyte cell number 2.25e-03 1.00e+00 increased neutrophil cell number 3.74e-03 1.00e+00 spinning 5.47e-03 1.00e+00 anemia 5.61e-03 1.00e+00 increased follicular B cell number 5.61e-03 1.00e+00 enhanced humoral immune response 5.61e-03 1.00e+00 abnormal erythroblast morphology 7.47e-03 1.00e+00 increased T-helper 1 cell number 7.47e-03 1.00e+00 increased number of Howell-Jolly bodies 7.48e-03 1.00e+00 abnormal lymph node germinal center morphology 7.49e-03 1.00e+00 abnormal megakaryocyte morphology 9.33e-03 1.00e+00 decreased circulating interferon-alpha level 9.34e-03 1.00e+00 intracerebral hemorrhage 9.35e-03 1.00e+00 polychromatophilia 1.12e-02 1.00e+00 increased B cell apoptosis 1.12e-02 1.00e+00 enlarged third ventricle 1.12e-02 1.00e+00 increased susceptibility to induced arthritis

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

²FDR corrected p-value (Benjamini-Hochberg)