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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod219

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod219 Module size 25 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 170691 ADAMTS17 ADAM metallopeptidase with thrombospondin type 1 motif 17 79747 ADGB androglobin 11132 CAPN10 calpain 10 11131 CAPN11 calpain 11 147968 CAPN12 calpain 12 92291 CAPN13 calpain 13 440854 CAPN14 calpain 14 824 CAPN2 calpain 2 825 CAPN3 calpain 3 726 CAPN5 calpain 5 827 CAPN6 calpain 6 23473 CAPN7 calpain 7 388743 CAPN8 calpain 8 10753 CAPN9 calpain 9 29082 CHMP4B charged multivesicular body protein 4A 92421 CHMP4C charged multivesicular body protein 4C 79643 CHMP6 charged multivesicular body protein 6 353288 KRT26 keratin 26 54799 MBTD1 mbt domain containing 1 10015 PDCD6IP programmed cell death 6 interacting protein 114822 RHPN1 rhophilin Rho GTPase binding protein 1 85415 RHPN2 rhophilin Rho GTPase binding protein 2 6650 SOLH calpain 15 53349 ZFYVE1 zinc finger FYVE-type containing 1 84936 ZFYVE19 zinc finger FYVE-type containing 19

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 5.40e-01 3.54e-30 GO calcium-dependent cysteine-type endopeptidase activity molecular_function 7.77e-02 6.89e-09 GO cell separation after cytokinesis biological_process 4.31e-02 6.70e-05 Reactome RHO GTPases Activate Rhotekin and Rhophilins Signal Transduction 2.56e-02 8.64e-07 GO vacuolar transport biological_process 1.41e-02 1.73e-08 GO viral budding via host ESCRT complex 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 0.00e+00 0.00e+00 cysteine-type endopeptidase activity 0.00e+00 0.00e+00 endopeptidase activity 0.00e+00 0.00e+00 cysteine-type peptidase activity 0.00e+00 0.00e+00 calcium-dependent cysteine-type endopeptidase activity 0.00e+00 0.00e+00 peptidase activity 2.74e-08 1.68e-05 cell separation after cytokinesis 4.42e-08 2.64e-05 viral budding via host ESCRT complex 5.61e-08 3.30e-05 viral budding 8.55e-08 4.89e-05 multivesicular body assembly 1.20e-07 6.70e-05 multivesicular body organization 1.20e-07 6.70e-05 multi-organism membrane organization 1.69e-07 9.18e-05 virion assembly 3.39e-07 1.75e-04 mitotic metaphase plate congression 4.75e-07 2.40e-04 ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway 4.96e-07 2.50e-04 metaphase plate congression 8.68e-07 4.18e-04 endosome organization 1.06e-06 3.09e-04 ESCRT III complex 1.64e-06 7.49e-04 establishment of chromosome localization 3.25e-06 1.40e-03 regulation of mitotic spindle assembly 3.61e-06 1.54e-03 mitotic sister chromatid segregation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.32e-06 3.81e-04 ENDOSOMAL SORTING COMPLEX REQUIRED FOR TRANSPORT ESCRT 6.05e-06 1.20e-03 ENDOSOMAL SORTING COMPLEX REQUIRED FOR TRANSPORT ESCRT 8.34e-06 1.26e-03 MEMBRANE TRAFFICKING 3.12e-04 4.25e-02 MEMBRANE TRAFFICKING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.52e-04 7.08e-01 increased susceptibility to injury 1.87e-03 1.00e+00 skeletal muscle degeneration 1.87e-03 1.00e+00 abnormal rib-vertebral column attachment 3.74e-03 1.00e+00 abnormal gastrocnemius morphology 3.74e-03 1.00e+00 abnormal skeletal muscle regeneration 3.75e-03 1.00e+00 abnormal interparietal bone morphology 3.75e-03 1.00e+00 abnormal tongue muscle morphology 5.61e-03 1.00e+00 pale placenta 5.61e-03 1.00e+00 abnormal soleus morphology 5.62e-03 1.00e+00 abnormal occipital bone morphology 7.47e-03 1.00e+00 abnormal tibialis anterior morphology 7.48e-03 1.00e+00 abnormal cervical axis morphology 7.49e-03 1.00e+00 transmission ratio distortion 7.49e-03 1.00e+00 abnormal thoracic cage morphology 7.50e-03 1.00e+00 abnormal vertebral column morphology 7.50e-03 1.00e+00 abnormal liver development 7.52e-03 1.00e+00 liver hypoplasia 9.36e-03 1.00e+00 rib bifurcation 1.12e-02 1.00e+00 abnormal cervical atlas morphology 1.30e-02 1.00e+00 abnormal sarcolemma morphology

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

²FDR corrected p-value (Benjamini-Hochberg)