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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod313

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod313 Module size 62 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 58 ACTA1 actin, alpha 1, skeletal muscle 60 ACTB actin beta 87 ACTN1 actinin alpha 1 81 ACTN4 actinin alpha 4 101 ADAM8 ADAM metallopeptidase domain 8 56999 ADAMTS9 ADAM metallopeptidase with thrombospondin type 1 motif 9 134265 AFAP1L1 actin filament associated protein 1 like 1 116986 AGAP2 ArfGAP with GTPase domain, ankyrin repeat and PH domain 2 199 AIF1 allograft inflammatory factor 1 10677 AVIL advillin 9854 C2CD2L C2CD2 like 93664 CADPS2 calcium dependent secretion activator 2 157922 CAMSAP1 calmodulin regulated spectrin associated protein 1 80790 CMIP c-Maf inducing protein 1773 DNASE1 deoxyribonuclease 1 1808 DRP2 dihydropyrimidinase like 2 1837 DTNA dystrobrevin alpha 1838 DTNB dystrobrevin beta 2035 EPB41 erythrocyte membrane protein band 4.1 2038 EPB42 erythrocyte membrane protein band 4.2 2039 EPB49 dematin actin binding protein 54751 FBLIM1 filamin binding LIM protein 1 283807 FBXL22 F-box and leucine rich repeat protein 22 10979 FERMT2 fermitin family member 2 83706 FERMT3 fermitin family member 3 2316 FLNA filamin A 2317 FLNB filamin B 2318 FLNC filamin C 6624 FSCN1 fascin actin-bundling protein 1 25794 FSCN2 fascin actin-bundling protein 2, retinal 29999 FSCN3 fascin actin-bundling protein 3 63940 GPSM3 G protein signaling modulator 3 2995 GYPC glycophorin C (Gerbich blood group) 8826 IQGAP1 IQ motif containing GTPase activating protein 1 386618 KCTD4 potassium channel tetramerization domain containing 4 3927 LASP1 LIM and SH3 protein 1 9404 LPXN leupaxin 10529 NEBL nebulette 10611 PDLIM5 PDZ and LIM domain 5 221692 PHACTR1 phosphatase and actin regulator 1 117157 SH2D1B SH2 domain containing 1B 140710 SOGA1 suppressor of glucose, autophagy associated 1 23255 SOGA2 microtubule crosslinking factor 1 387104 SOGA3 SOGA family member 3 6708 SPTA1 spectrin alpha, erythrocytic 1 6709 SPTAN1 spectrin alpha, non-erythrocytic 1 6710 SPTB spectrin beta, erythrocytic 6711 SPTBN1 spectrin beta, non-erythrocytic 1 6712 SPTBN2 spectrin beta, non-erythrocytic 2 57731 SPTBN4 spectrin beta, non-erythrocytic 4 51332 SPTBN5 spectrin beta, non-erythrocytic 5 6840 SVIL supervillin 10178 TENM1 teneurin transmembrane protein 1 57451 TENM2 teneurin transmembrane protein 2 55714 TENM3 teneurin transmembrane protein 3 7041 TGFB1I1 transforming growth factor beta 1 induced transcript 1 128229 TSACC TSSK6 activating cochaperone 7402 UTRN utrophin 7429 VIL1 villin 1 50853 VILL villin like 9948 WDR1 WD repeat domain 1 7791 ZYX zyxin

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 5.51e-01 2.00e-23 GO actin filament capping biological_process 1.06e-01 1.43e-09 Reactome Cell-extracellular matrix interactions Cell-Cell communication 8.61e-02 3.39e-12 GO podosome cellular_component 8.04e-02 4.09e-06 GO invadopodium cellular_component 7.94e-02 2.79e-09 GO cell junction assembly biological_process 7.64e-02 3.77e-09 GO cortical cytoskeleton cellular_component 5.95e-02 2.99e-04 GO self proteolysis biological_process 5.84e-02 2.37e-13 GO stress fiber cellular_component 4.48e-02 8.48e-09 Reactome Nephrin family interactions Cell-Cell communication 4.01e-02 2.99e-04 GO microtubule minus-end cellular_component 1.20e-02 6.53e-09 GO actin filament bundle assembly biological_process 8.35e-03 3.84e-04 GO integrin activation biological_process 7.50e-03 3.41e-14 GO structural constituent of cytoskeleton molecular_function 3.78e-03 4.46e-12 Reactome Interaction between L1 and Ankyrins Developmental Biology

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 actin filament organization 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 negative regulation of protein polymerization 0.00e+00 0.00e+00 regulation of actin polymerization or depolymerization 0.00e+00 0.00e+00 regulation of protein complex disassembly 0.00e+00 0.00e+00 regulation of actin filament length 0.00e+00 0.00e+00 negative regulation of actin filament depolymerization 0.00e+00 0.00e+00 regulation of actin filament depolymerization 0.00e+00 0.00e+00 negative regulation of actin filament polymerization 0.00e+00 0.00e+00 actin filament capping 0.00e+00 0.00e+00 negative regulation of protein complex disassembly 0.00e+00 0.00e+00 actin cytoskeleton 0.00e+00 0.00e+00 cortical cytoskeleton 0.00e+00 0.00e+00 cell cortex 0.00e+00 0.00e+00 spectrin 0.00e+00 0.00e+00 actin filament binding 0.00e+00 0.00e+00 actin binding 0.00e+00 0.00e+00 structural constituent of cytoskeleton 6.41e-11 5.43e-08 regulation of actin filament polymerization

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 INTERACTION BETWEEN L1 AND ANKYRINS 0.00e+00 0.00e+00 INTERACTION BETWEEN L1 AND ANKYRINS 3.46e-10 8.93e-08 NCAM SIGNALING FOR NEURITE OUT GROWTH 7.12e-10 1.77e-07 NEPHRIN INTERACTIONS 1.62e-09 3.86e-07 L1CAM INTERACTIONS 2.05e-09 6.50e-07 NEPHRIN INTERACTIONS 4.93e-09 1.49e-06 NCAM SIGNALING FOR NEURITE OUT GROWTH 6.77e-09 2.02e-06 CELL CELL COMMUNICATION 8.66e-09 2.56e-06 L1CAM INTERACTIONS 1.83e-08 3.90e-06 CELL CELL COMMUNICATION 6.55e-08 1.30e-05 CELL EXTRACELLULAR MATRIX INTERACTIONS 4.49e-07 1.06e-04 CELL EXTRACELLULAR MATRIX INTERACTIONS 6.88e-06 1.06e-03 AXON GUIDANCE 1.98e-05 3.58e-03 AXON GUIDANCE 2.17e-04 3.08e-02 CELL JUNCTION ORGANIZATION 4.83e-04 6.24e-02 DEVELOPMENTAL BIOLOGY 9.38e-04 9.52e-02 CELL JUNCTION ORGANIZATION 1.88e-03 1.76e-01 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2 2.58e-03 2.65e-01 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2 1.43e-02 9.78e-01 PLATELET ACTIVATION SIGNALING AND AGGREGATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 7.15e-07 6.90e-03 spherocytosis 8.30e-06 4.10e-02 anisopoikilocytosis 9.14e-06 4.43e-02 decreased cellular hemoglobin content 4.33e-05 1.29e-01 increased kidney iron level 7.81e-05 1.93e-01 renal tubular necrosis 1.24e-04 2.59e-01 abnormal erythrocyte morphology 3.39e-04 4.84e-01 thrombosis 4.58e-04 5.76e-01 reticulocytosis 5.09e-04 6.11e-01 tubular nephritis 5.32e-04 6.31e-01 hemolytic anemia 7.63e-04 7.68e-01 increased erythrocyte clearance 7.64e-04 7.68e-01 hemolysis 1.15e-03 9.76e-01 scoliosis 1.17e-03 9.85e-01 increased erythrocyte protoporphyrin level 1.55e-03 1.00e+00 increased nucleated erythrocyte cell number 1.56e-03 1.00e+00 low mean erythrocyte cell number 1.61e-03 1.00e+00 schistocytosis 1.63e-03 1.00e+00 abnormal reticulocyte morphology 1.85e-03 1.00e+00 jaundice 1.97e-03 1.00e+00 enlarged testis

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

²FDR corrected p-value (Benjamini-Hochberg)