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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod92

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod92 Module size 30 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 844 CASQ1 calsequestrin 1 1674 DES desmin 4604 MYBPC1 myosin binding protein C, slow type 4606 MYBPC2 myosin binding protein C, fast type 4607 MYBPC3 myosin binding protein C, cardiac 4608 MYBPH myosin binding protein H 4621 MYH3 myosin heavy chain 3 4624 MYH6 myosin heavy chain 6 4626 MYH8 myosin heavy chain 8 4632 MYL1 myosin light chain 1 4633 MYL2 myosin light chain 2 4634 MYL3 myosin light chain 3 4635 MYL4 myosin light chain 4 9172 MYOM2 myomesin 2 4703 NEB nebulin 65083 NRAP nucleolar protein 6 8557 TCAP titin-cap 79041 TMEM38A transmembrane protein 38A 7111 TMOD1 tropomodulin 1 7135 TNNI1 troponin I1, slow skeletal type 7136 TNNI2 troponin I2, fast skeletal type 7137 TNNI3 troponin I3, cardiac type 7138 TNNT1 troponin T1, slow skeletal type 7139 TNNT2 troponin T2, cardiac type 7140 TNNT3 troponin T3, fast skeletal type 7168 TPM1 tropomyosin 1 7169 TPM2 tropomyosin 2 7170 TPM3 tropomyosin 3 7171 TPM4 tropomyosin 4 7273 TTN titin

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 3.94e-01 1.58e-68 Reactome Striated Muscle Contraction Muscle contraction 2.01e-01 1.63e-66 GO muscle filament sliding biological_process 5.09e-02 2.64e-16 GO myosin filament cellular_component 3.94e-02 1.32e-13 GO muscle alpha-actinin binding molecular_function 3.68e-02 5.25e-28 GO sarcomere organization biological_process 2.01e-02 7.65e-15 GO skeletal muscle myosin thick filament assembly biological_process 8.82e-03 1.48e-16 GO cardiac muscle fiber development biological_process 2.51e-03 9.05e-33 GO structural constituent of muscle molecular_function

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 0e+00 0e+00 actin-myosin filament sliding 0e+00 0e+00 striated muscle contraction 0e+00 0e+00 muscle system process 0e+00 0e+00 actin filament-based process 0e+00 0e+00 musculoskeletal movement 0e+00 0e+00 skeletal muscle contraction 0e+00 0e+00 regulation of ATPase activity 0e+00 0e+00 muscle contraction 0e+00 0e+00 actin-mediated cell contraction 0e+00 0e+00 regulation of muscle contraction 0e+00 0e+00 actin filament-based movement 0e+00 0e+00 muscle filament sliding 0e+00 0e+00 heart contraction 0e+00 0e+00 ventricular cardiac muscle tissue morphogenesis 0e+00 0e+00 actin filament organization 0e+00 0e+00 cardiac muscle contraction 0e+00 0e+00 circulatory system process 0e+00 0e+00 cardiac ventricle morphogenesis 0e+00 0e+00 striated muscle cell development 0e+00 0e+00 muscle structure development

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 MUSCLE CONTRACTION 0.00e+00 0.00e+00 STRIATED MUSCLE CONTRACTION 0.00e+00 0.00e+00 MUSCLE CONTRACTION 0.00e+00 0.00e+00 STRIATED MUSCLE CONTRACTION 3.99e-07 9.53e-05 SMOOTH MUSCLE CONTRACTION 1.00e-05 1.49e-03 SMOOTH MUSCLE CONTRACTION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 0.00e+00 0.00e+00 abnormal sarcomere morphology 7.73e-10 3.04e-05 cardiac interstitial fibrosis 1.24e-09 4.24e-05 abnormal myocardial fiber morphology 9.56e-09 2.46e-04 abnormal myocardial fiber physiology 1.58e-08 3.54e-04 decreased ventricle muscle contractility 4.67e-08 7.92e-04 dilated cardiomyopathy 6.25e-08 9.95e-04 skeletal muscle fiber atrophy 1.70e-07 2.17e-03 dystrophic cardiac calcinosis 5.68e-07 5.81e-03 abnormal muscle contractility 1.38e-06 1.12e-02 abnormal muscle physiology 1.39e-06 1.12e-02 abnormal cardiac muscle contractility 2.86e-06 1.97e-02 cardiac fibrosis 3.73e-06 2.33e-02 cardiac hypertrophy 8.87e-06 4.33e-02 congestive heart failure 1.20e-05 5.35e-02 abnormal heart left ventricle morphology 2.88e-05 9.93e-02 centrally nucleated skeletal muscle fibers 3.15e-05 1.06e-01 absent heartbeat 3.38e-05 1.10e-01 abnormal cardiac muscle relaxation 3.48e-05 1.12e-01 dilated heart left ventricle 4.25e-05 1.29e-01 abnormal myocardium layer morphology

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

²FDR corrected p-value (Benjamini-Hochberg)