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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod289

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod289 Module size 45 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 113622 ADPRHL1 ADP-ribosylhydrolase like 1 57538 ALPK3 alpha kinase 3 10930 APOBEC2 apolipoprotein B mRNA editing enzyme catalytic subunit 2 800 CALD1 caldesmon 1 845 CASQ2 calsequestrin 2 286097 EFHA2 mitochondrial calcium uptake family member 3 171484 FAM9C family with sequence similarity 9 member C 3270 HRC histidine rich calcium binding protein 91156 IGFN1 immunoglobulin-like and fibronectin type III domain containing 1 283284 IGSF22 immunoglobulin superfamily member 22 25802 LMOD1 leiomodin 1 442721 LMOD2 leiomodin 2 343263 MYBPHL myosin binding protein H like 4619 MYH1 myosin heavy chain 1 4628 MYH10 myosin heavy chain 10 4629 MYH11 myosin heavy chain 11 8735 MYH13 myosin heavy chain 13 57644 MYH14 myosin heavy chain 7B 4620 MYH2 myosin heavy chain 2 4625 MYH7 myosin heavy chain 7 4627 MYH9 myosin heavy chain 9 93408 MYL10 myosin light chain 10 10627 MYL12A myosin light chain 12A 103910 MYL12B myosin light chain 12B 4636 MYL5 myosin light chain 5 4637 MYL6 myosin light chain 6 140465 MYL6B myosin light chain 6B 58498 MYL7 myosin light chain 7 10398 MYL9 myosin light chain 9 29895 MYLPF myosin light chain, phosphorylatable, fast skeletal muscle 8736 MYOM1 myomesin 1 9499 MYOT myotilin 58529 MYOZ1 myozenin 1 23363 OBSL1 obscurin like 1 9033 PKD2L1 polycystin 2 like 1, transient receptor potential cation channel 134549 SHROOM1 shroom family member 1 57477 SHROOM4 shroom family member 4 23676 SMPX small muscle protein X-linked 6345 SRL sarcalumenin 29765 TMOD4 tropomodulin 4 7134 TNNC1 troponin C1, slow skeletal and cardiac type 7125 TNNC2 troponin C2, fast skeletal type 10345 TRDN triadin 140803 TRPM6 transient receptor potential cation channel subfamily M member 6 80737 VWA7 von Willebrand factor A domain containing 7

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 3.08e-01 3.79e-21 GO muscle myosin complex cellular_component 2.84e-01 1.75e-09 GO sarcoplasmic reticulum lumen cellular_component 1.38e-01 1.40e-24 Reactome Smooth Muscle Contraction Muscle contraction 1.23e-01 1.35e-15 Reactome EPHA-mediated growth cone collapse Developmental Biology 1.18e-01 2.86e-12 GO striated muscle thin filament cellular_component 9.87e-02 2.40e-15 Reactome RHO GTPases activate CIT Signal Transduction 8.95e-02 4.14e-11 GO actin-dependent ATPase activity molecular_function 5.30e-02 8.22e-09 GO myofibril assembly biological_process 4.42e-02 1.23e-08 GO regulation of muscle contraction biological_process 4.27e-02 4.50e-08 GO muscle alpha-actinin binding molecular_function 3.06e-02 3.70e-37 GO muscle contraction biological_process 2.45e-02 2.42e-14 Reactome RHO GTPases activate PAKs Signal Transduction 1.89e-02 6.66e-15 Reactome RHO GTPases Activate ROCKs Signal Transduction 1.30e-02 1.62e-14 Reactome Sema4D induced cell migration and growth-cone collapse Developmental Biology 4.48e-03 6.03e-09 GO M band cellular_component 1.87e-03 3.38e-08 GO tropomyosin binding molecular_function 1.16e-03 9.34e-11 GO myosin complex cellular_component 3.18e-04 3.29e-06 GO actomyosin 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 0e+00 0e+00 muscle system process 0e+00 0e+00 muscle contraction 0e+00 0e+00 supramolecular fiber organization 0e+00 0e+00 actin filament-based process 0e+00 0e+00 muscle structure development 0e+00 0e+00 striated muscle contraction 0e+00 0e+00 striated muscle cell differentiation 0e+00 0e+00 myofibril assembly 0e+00 0e+00 striated muscle cell development 0e+00 0e+00 actomyosin structure organization 0e+00 0e+00 actin cytoskeleton organization 0e+00 0e+00 contractile fiber 0e+00 0e+00 supramolecular fiber 0e+00 0e+00 sarcomere 0e+00 0e+00 myofibril 0e+00 0e+00 myosin complex 0e+00 0e+00 muscle myosin complex 0e+00 0e+00 myosin II complex 0e+00 0e+00 myosin filament 0e+00 0e+00 actin cytoskeleton

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 SEMA4D INDUCED CELL MIGRATION AND GROWTH CONE COLLAPSE 0.00e+00 0.00e+00 SEMA4D IN SEMAPHORIN SIGNALING 0.00e+00 0.00e+00 SMOOTH MUSCLE CONTRACTION 0.00e+00 0.00e+00 MUSCLE CONTRACTION 0.00e+00 0.00e+00 SEMA4D INDUCED CELL MIGRATION AND GROWTH CONE COLLAPSE 0.00e+00 0.00e+00 SEMA4D IN SEMAPHORIN SIGNALING 0.00e+00 0.00e+00 SMOOTH MUSCLE CONTRACTION 8.78e-11 2.41e-08 SEMAPHORIN INTERACTIONS 2.23e-10 7.87e-08 SEMAPHORIN INTERACTIONS 2.22e-07 4.17e-05 AXON GUIDANCE 1.64e-06 3.56e-04 AXON GUIDANCE 4.58e-05 7.71e-03 DEVELOPMENTAL BIOLOGY 4.22e-03 3.98e-01 STRIATED MUSCLE CONTRACTION 4.53e-03 3.78e-01 STRIATED MUSCLE CONTRACTION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.90e-06 1.98e-02 abnormal myocardial fiber morphology 3.40e-06 2.20e-02 abnormal sarcoplasmic reticulum morphology 1.01e-05 4.74e-02 dilated heart left ventricle 3.80e-05 1.19e-01 decreased cardiac muscle contractility 4.67e-05 1.36e-01 abnormal skeletal muscle fiber type ratio 9.51e-05 2.18e-01 dilated cardiomyopathy 3.84e-04 5.20e-01 enlarged heart atrium 7.29e-04 7.55e-01 abnormal intercalated disc morphology 8.65e-04 8.31e-01 cardiac hypertrophy 1.02e-03 9.10e-01 thin ventricular wall 1.12e-03 9.61e-01 abnormal muscle physiology 1.47e-03 1.00e+00 abnormal muscle contractility 1.57e-03 1.00e+00 abnormal fetal cardiomyocyte morphology 1.82e-03 1.00e+00 increased heart weight 2.93e-03 1.00e+00 impaired skeletal muscle contractility 3.38e-03 1.00e+00 thick ventricular wall 3.38e-03 1.00e+00 abnormal sarcomere morphology 5.61e-03 1.00e+00 impaired contractility of urinary bladder detrusor smooth muscle 6.31e-03 1.00e+00 decreased grip strength 7.47e-03 1.00e+00 abnormal placenta fetal blood space morphology

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

²FDR corrected p-value (Benjamini-Hochberg)