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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod82

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod82 Module size 18 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 25852 ARMC8 armadillo repeat containing 8 755 C21orf2 cilia and flagella associated protein 410 91050 CCDC149 coiled-coil domain containing 149 79018 GID4 GID complex subunit 4 homolog 54994 GID8 GID complex subunit 8 homolog 10296 MAEA macrophage erythroblast attacher 4289 MKLN1 muskelin 1 57610 RANBP10 RAN binding protein 10 55705 RANBP9 importin 9 64795 RMND5A required for meiotic nuclear division 5 homolog A 64777 RMND5B required for meiotic nuclear division 5 homolog B 84926 SPRYD3 SPRY domain containing 3 80232 WDR26 WD repeat domain 26 29799 YPEL1 yippee like 1 388403 YPEL2 yippee like 2 83719 YPEL3 yippee like 3 219539 YPEL4 yippee like 4 51646 YPEL5 yippee like 5

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 2.08e-02 2.45e-05 Reactome MET activates RAS signaling Signal Transduction

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 4.68e-09 1.93e-06 GID complex 6.12e-06 2.48e-03 proteasome-mediated ubiquitin-dependent protein catabolic process 6.50e-06 2.62e-03 proteasomal protein catabolic process 6.92e-06 2.78e-03 protein ubiquitination involved in ubiquitin-dependent protein catabolic process 4.97e-05 1.12e-02 ubiquitin-protein transferase activity 5.53e-05 1.24e-02 ubiquitin-like protein transferase activity 8.02e-05 2.41e-02 ubiquitin-dependent protein catabolic process 9.26e-05 2.74e-02 modification-dependent protein catabolic process 1.08e-04 3.12e-02 cellular protein catabolic process 1.08e-04 3.12e-02 proteolysis involved in cellular protein catabolic process 1.39e-04 3.86e-02 protein catabolic process 3.83e-04 9.01e-02 protein ubiquitination 5.13e-04 1.14e-01 protein modification by small protein conjugation 1.04e-03 1.51e-01 tertiary granule lumen 1.83e-03 2.43e-01 actomyosin contractile ring 1.95e-03 3.34e-01 positive regulation of cell aging 1.95e-03 3.34e-01 positive regulation of cellular senescence 1.95e-03 3.34e-01 erythrocyte maturation 1.95e-03 3.34e-01 enucleate erythrocyte differentiation 1.95e-03 3.34e-01 erythrocyte development

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.15e-02 8.9e-01 L1CAM INTERACTIONS 3.63e-02 1.0e+00 AXON GUIDANCE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 decreased primary ovarian follicle number 3.74e-03 1e+00 increased caudal vertebrae number 5.61e-03 1e+00 abnormal GABAergic neuron morphology 5.61e-03 1e+00 abnormal ovarian follicle number 5.61e-03 1e+00 abnormal spermatogonia proliferation 7.47e-03 1e+00 abnormal platelet dense granule physiology 7.50e-03 1e+00 increased nucleated erythrocyte cell number 9.34e-03 1e+00 abnormal megakaryocyte differentiation 9.34e-03 1e+00 abnormal female reproductive system physiology 9.35e-03 1e+00 abnormal spermatogonia morphology 9.36e-03 1e+00 abnormal startle reflex 1.30e-02 1e+00 abnormal platelet morphology 1.31e-02 1e+00 ovary cysts 2.05e-02 1e+00 decreased oocyte number 2.23e-02 1e+00 decreased macrophage cell number 2.23e-02 1e+00 abnormal male germ cell morphology 2.42e-02 1e+00 diluted coat color 2.60e-02 1e+00 abnormal spermatocyte morphology 2.61e-02 1e+00 short tibia 2.79e-02 1e+00 seminiferous tubule degeneration

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

²FDR corrected p-value (Benjamini-Hochberg)