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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod136

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod136 Module size 20 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 55726 ASUN integrator complex subunit 13 79034 C7orf26 chromosome 7 open reading frame 26 58493 INIP INTS3 and NABP interacting protein 26173 INTS1 integrator complex subunit 1 55174 INTS10 integrator complex subunit 10 57508 INTS2 integrator complex subunit 2 65123 INTS3 integrator complex subunit 3 92105 INTS4 integrator complex subunit 4 80789 INTS5 integrator complex subunit 5 26512 INTS6 integrator complex subunit 6 25896 INTS7 integrator complex subunit 7 55656 INTS8 integrator complex subunit 8 55756 INTS9 integrator complex subunit 9 64859 NABP1 nucleic acid binding protein 1 79035 NABP2 nucleic acid binding protein 2 203245 NAIF1 nuclear apoptosis inducing factor 1 8403 SOX14 SRY-box 14 83877 TM2D2 TM2 domain containing 2 81556 VWA9 integrator complex subunit 14 23613 ZMYND8 zinc finger MYND-type containing 8

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 5.03e-01 2.03e-29 GO snRNA processing biological_process 4.14e-02 1.14e-30 Reactome RNA polymerase II transcribes snRNA genes Gene expression (Transcription) 2.58e-02 5.97e-25 GO integrator complex cellular_component

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 transcription from RNA polymerase II promoter 0.00e+00 0.00e+00 snRNA transcription 0.00e+00 0.00e+00 snRNA transcription from RNA polymerase II promoter 0.00e+00 0.00e+00 ncRNA transcription 0.00e+00 0.00e+00 snRNA processing 0.00e+00 0.00e+00 snRNA metabolic process 0.00e+00 0.00e+00 DNA-directed RNA polymerase II, holoenzyme 0.00e+00 0.00e+00 integrator complex 3.80e-11 2.02e-08 SOSS complex 7.13e-09 4.72e-06 response to ionizing radiation 5.48e-08 1.97e-05 transferase complex 1.64e-06 7.49e-04 cell cycle checkpoint 2.80e-06 1.22e-03 response to radiation 1.23e-05 4.66e-03 mitotic cell cycle checkpoint 2.51e-05 8.77e-03 snRNA 3'-end processing 5.45e-05 1.73e-02 regulation of mitotic cell cycle 8.05e-05 2.42e-02 negative regulation of mitotic cell cycle 1.07e-04 3.09e-02 negative regulation of cell cycle 2.39e-04 6.09e-02 cellular response to DNA damage stimulus 4.33e-04 7.41e-02 single-stranded DNA binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.63e-03 1e+00 abnormal rib attachment 7.50e-03 1e+00 abnormal scapular spine morphology 7.51e-03 1e+00 abnormal embryo size 9.37e-03 1e+00 abnormal foot plate morphology 9.37e-03 1e+00 short scapula 9.39e-03 1e+00 primary atelectasis 1.12e-02 1e+00 absent fibula 1.12e-02 1e+00 absent deltoid tuberosity 1.15e-02 1e+00 embryonic lethality before implantation 1.18e-02 1e+00 complete preweaning lethality 1.31e-02 1e+00 abnormal premaxilla morphology 1.31e-02 1e+00 abnormal thoracic cage shape 1.31e-02 1e+00 abnormal rib development 1.31e-02 1e+00 abnormal deltoid tuberosity morphology 1.50e-02 1e+00 abnormal pulmonary alveolus wall morphology 1.68e-02 1e+00 small thoracic cage 2.05e-02 1e+00 abnormal rib-sternum attachment 2.06e-02 1e+00 decreased eosinophil cell number 2.07e-02 1e+00 increased embryonic tissue cell apoptosis 2.42e-02 1e+00 decreased bone volume

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

²FDR corrected p-value (Benjamini-Hochberg)