Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod18

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod18 Module size 63 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 137735 ABRA actin binding Rho activating protein 88 ACTN2 actinin alpha 2 9823 ARMCX2 armadillo repeat containing X-linked 2 51233 C22orf43 aspartate rich 1 57530 CGN cingulin 1152 CKB creatine kinase B 1158 CKM creatine kinase, M-type 1160 CKMT2 creatine kinase, mitochondrial 2 202333 CMYA5 cardiomyopathy associated 5 1410 CRYAB crystallin alpha B 8048 CSRP3 cysteine and glycine rich protein 3 1756 DMD dystrophin 8291 DYSF dysferlin 80303 EFHD1 EF-hand domain family member D1 133584 EGFLAM EGF like, fibronectin type III and laminin G domains 7430 EZR ezrin 296026 FIBP olfactory receptor 773 54676 GTPBP2 GTP binding protein 2 83872 HMCN1 hemicentin 1 100528019 HSPB2-C11orf52 HSPB2-C11orf52 readthrough (NMD candidate) 8988 HSPB3 heat shock protein family B (small) member 3 126393 HSPB6 heat shock protein family B (small) member 6 27129 HSPB7 heat shock protein family B (small) member 7 26548 ITGB1BP2 integrin subunit beta 1 binding protein 2 79734 KCTD17 potassium channel tetramerization domain containing 17 23510 KCTD2 potassium channel tetramerization domain containing 2 54442 KCTD5 potassium channel tetramerization domain containing 5 150082 LCA5L LCA5L, lebercilin like 11155 LDB3 LIM domain binding 3 56203 LMOD3 leiomodin 3 29967 LRP12 LDL receptor related protein 12 4151 MB myoglobin 23164 MPRIP myosin phosphatase Rho interacting protein 4638 MYLK myosin light chain kinase 127294 MYOM3 myomesin 3 51778 MYOZ2 myozenin 2 91977 MYOZ3 myozenin 3 84665 MYPN myopalladin 91624 NEXN nexilin F-actin binding protein 390916 NUDT19 nudix hydrolase 19 5341 PLEK pleckstrin 57480 PLEKHG1 pleckstrin homology and RhoGEF domain containing G1 26030 PLEKHG3 pleckstrin homology and RhoGEF domain containing G3 6261 RYR1 ryanodine receptor 1 6263 RYR3 ryanodine receptor 3 298544 SH3BGR SH3 domain binding glutamate-rich protein like 3 10580 SORBS1 sorbin and SH3 domain containing 1 10174 SORBS3 sorbin and SH3 domain containing 3 81493 SYNC syncoilin, intermediate filament protein 11346 SYNPO synaptopodin 255104 TMCO4 transmembrane and coiled-coil domains 4 55151 TMEM38B transmembrane protein 38B 22954 TRIM32 tripartite motif containing 32 84676 TRIM63 tripartite motif containing 63 54822 TRPM7 transient receptor potential cation channel subfamily M member 7 80705 TSGA10 testis specific 10 7289 TULP3 tubby like protein 3 167838 TXLNB taxilin beta 55665 URGCP upregulator of cell proliferation 7414 VCL vinculin 7431 VIM vimentin 165904 XIRP1 xin actin binding repeat containing 1 129446 XIRP2 xin actin binding repeat containing 2

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 1.58e-01 6.69e-05 GO ryanodine-sensitive calcium-release channel activity molecular_function 1.49e-01 1.27e-06 GO telethonin binding molecular_function 7.30e-02 4.31e-06 GO creatine metabolic process biological_process 7.28e-02 4.31e-06 Reactome Creatine metabolism Metabolism 6.51e-02 1.68e-23 GO Z disc cellular_component 3.91e-02 8.13e-08 Reactome Smooth Muscle Contraction Muscle contraction 3.75e-02 2.88e-05 GO cullin family protein binding molecular_function 3.03e-02 3.97e-04 GO dystroglycan binding molecular_function 2.80e-02 1.01e-02 Reactome Intracellular oxygen transport Transport of small molecules 2.35e-02 4.11e-08 GO M band cellular_component 2.05e-02 4.65e-05 GO structural constituent of eye lens molecular_function 1.27e-02 1.74e-12 GO muscle contraction biological_process 5.47e-03 7.03e-05 GO myosin binding 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 0.00e+00 0.00e+00 muscle system process 0.00e+00 0.00e+00 muscle contraction 0.00e+00 0.00e+00 actin filament-based process 0.00e+00 0.00e+00 actin cytoskeleton organization 0.00e+00 0.00e+00 Z disc 0.00e+00 0.00e+00 I band 0.00e+00 0.00e+00 sarcomere 8.07e-20 4.78e-17 myofibril 2.07e-19 1.23e-16 contractile fiber 1.73e-16 1.22e-13 actin binding 2.49e-11 2.19e-08 striated muscle cell development 8.32e-11 4.33e-08 supramolecular fiber 1.31e-10 1.07e-07 muscle cell development 2.16e-10 1.74e-07 actomyosin structure organization 2.90e-09 2.04e-06 striated muscle cell differentiation 4.27e-09 2.92e-06 myofibril assembly 1.36e-08 8.71e-06 muscle structure development 3.05e-08 1.13e-05 actin cytoskeleton 7.04e-08 4.08e-05 muscle cell differentiation 1.26e-07 7.00e-05 supramolecular fiber organization

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.74e-11 1.40e-08 MUSCLE CONTRACTION 8.69e-10 2.13e-07 MUSCLE CONTRACTION 4.44e-07 1.05e-04 SMOOTH MUSCLE CONTRACTION 7.56e-07 1.34e-04 SMOOTH MUSCLE CONTRACTION 7.58e-05 1.21e-02 STRIATED MUSCLE CONTRACTION 4.37e-04 4.80e-02 STRIATED MUSCLE CONTRACTION 1.51e-03 1.68e-01 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2 1.67e-03 1.59e-01 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2 8.73e-03 6.58e-01 PLATELET ACTIVATION SIGNALING AND AGGREGATION 9.03e-03 6.76e-01 UNBLOCKING OF NMDA RECEPTOR GLUTAMATE BINDING AND ACTIVATION 1.03e-02 8.15e-01 PLATELET ACTIVATION SIGNALING AND AGGREGATION 1.60e-02 1.00e+00 METABOLISM OF AMINO ACIDS AND DERIVATIVES 1.62e-02 1.00e+00 CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF CAMKII 1.98e-02 1.00e+00 RAS ACTIVATION UOPN CA2 INFUX THROUGH NMDA RECEPTOR 2.00e-02 1.00e+00 CASPASE MEDIATED CLEAVAGE OF CYTOSKELETAL PROTEINS 2.59e-02 1.00e+00 TGF BETA RECEPTOR SIGNALING IN EMT EPITHELIAL TO MESENCHYMAL TRANSITION 3.39e-02 1.00e+00 CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF RAS 3.63e-02 1.00e+00 TGF BETA RECEPTOR SIGNALING IN EMT EPITHELIAL TO MESENCHYMAL TRANSITION 3.72e-02 1.00e+00 CASPASE MEDIATED CLEAVAGE OF CYTOSKELETAL PROTEINS 4.19e-02 1.00e+00 RECYCLING PATHWAY OF L1

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 9.36e-09 2.44e-04 decreased cardiac muscle contractility 9.37e-09 2.44e-04 increased variability of skeletal muscle fiber size 4.16e-08 7.17e-04 myopathy 3.47e-07 3.91e-03 abnormal intercalated disc morphology 3.90e-07 4.28e-03 centrally nucleated skeletal muscle fibers 1.04e-06 9.04e-03 abnormal skeletal muscle morphology 2.13e-06 1.54e-02 cardiac hypertrophy 4.85e-06 2.87e-02 abnormal muscle contractility 1.46e-05 6.08e-02 decreased skeletal muscle fiber size 1.52e-05 6.25e-02 abnormal skeletal muscle fiber morphology 2.01e-05 7.62e-02 impaired skeletal muscle contractility 5.85e-05 1.59e-01 skeletal muscle fiber necrosis 7.06e-05 1.79e-01 abnormal muscle physiology 7.29e-05 1.83e-01 abnormal myocardial fiber morphology 7.32e-05 1.83e-01 increased skeletal muscle fiber size 8.85e-05 2.09e-01 abnormal Z lines 1.82e-04 3.30e-01 dilated heart left ventricle 1.95e-04 3.43e-01 increased circulating creatine kinase level 2.30e-04 3.79e-01 skeletal muscle endomysial fibrosis 2.84e-04 4.36e-01 increased quadriceps weight

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

²FDR corrected p-value (Benjamini-Hochberg)