Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod377

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod377 Module size 85 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 25890 ABI3BP ABI family member 3 binding protein 84830 ADTRP androgen dependent TFPI regulating protein 7726 AFP tripartite motif containing 26 140564 APOBEC3D apolipoprotein B mRNA editing enzyme catalytic subunit 3D 9530 BAG4 BCL2 associated athanogene 4 577 BAI3 adhesion G protein-coupled receptor B3 8412 BCAR3 BCAR3, NSP family adaptor protein 636 BICD1 BICD cargo adaptor 1 54766 BTG4 BTG anti-proliferation factor 4 201895 C4orf34 small integral membrane protein 14 146439 CCDC64B BICD family like cargo adaptor 2 83987 CCDC8 coiled-coil domain containing 8 10970 CKAP4 cytoskeleton associated protein 4 113540 CMTM1 CKLF like MARVEL transmembrane domain containing 1 1389 CREBL2 cAMP responsive element binding protein like 2 51379 CRLF3 cytokine receptor like factor 3 49860 CRNN cornulin 64478 CSMD1 CUB and Sushi multiple domains 1 1465 CSRP1 cysteine and glycine rich protein 1 151871 DPPA2 developmental pluripotency associated 2 29904 EEF2K eukaryotic elongation factor 2 kinase 116496 FAM129A family with sequence similarity 129 member A 83648 FAM167A family with sequence similarity 167 member A 253725 FAM21C WASH complex subunit 2C 81553 FAM49A family with sequence similarity 49 member A 100287045 FAM90A26P family with sequence similarity 90 member A26 81545 FBXO38 F-box protein 38 84978 FRMD5 FERM domain containing 5 2579 GAGE12I G antigen 7 26749 GAGE2E G antigen 2E 80772 GLTPD1 ceramide-1-phosphate transfer protein 64395 GMCL1 germ cell-less, spermatogenesis associated 1 10456 HAX1 HCLS1 associated protein X-1 64342 HS1BP3 HCLS1 binding protein 3 3064 HTT huntingtin 389123 IQCF2 IQ motif containing F2 115207 KCTD12 potassium channel tetramerization domain containing 12 23313 KIAA0930 KIAA0930 3875 KRT18 keratin 18 337879 KRTAP8-1 keratin associated protein 8-1 388533 KRTDAP keratinocyte differentiation associated protein 56891 LGALS14 galectin 14 4000 LMNA lamin A/C 84823 LMNB2 lamin B2 130576 LYPD6B LY6/PLAUR domain containing 6B 145748 LYSMD4 LysM domain containing 4 685131 MEA1 male-enhanced antigen 1 90523 MLIP muscular LMNA interacting protein 92154 MTSS1L MTSS1L, I-BAR domain containing 4745 NELL1 neural EGFL like 1 11188 NISCH nischarin 5311 PKD2 polycystin 2, transient receptor potential cation channel 26279 PLA2G2D phospholipase A2 group IID 79983 POF1B POF1B, actin binding protein 55624 POMGNT1 protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) 5504 PPP1R2 protein phosphatase 1 regulatory inhibitor subunit 2 64792 RABL5 intraflagellar transport 22 55698 RADIL Rap associating with DIL domain 125950 RAVER1 ribonucleoprotein, PTB binding 1 84060 RBM48 RNA binding motif protein 48 57096 RPGRIP1 RPGR interacting protein 1 23322 RPGRIP1L RPGRIP1 like 51507 RTFDC1 replication termination factor 2 6284 S100A13 S100 calcium binding protein A13 10807 SDCCAG3 endosome associated trafficking regulator 1 9919 SEC16A SEC16 homolog A, endoplasmic reticulum export factor 6462 SHBG sex hormone binding globulin 6570 SLC18A1 solute carrier family 18 member A1 132203 SNTN sentan, cilia apical structure protein 23161 SNX13 sorting nexin 13 9043 SPAG9 sperm associated antigen 9 90864 SPSB3 splA/ryanodine receptor domain and SOCS box containing 3 284297 SSC5D scavenger receptor cysteine rich family member with 5 domains 140290 TCP10L t-complex 10 like 29844 TFPT TCF3 fusion partner 56889 TM9SF3 transmembrane 9 superfamily member 3 7009 TMBIM6 transmembrane BAX inhibitor motif containing 6 26146 TRAF3IP1 TRAF3 interacting protein 1 57159 TRIM54 tripartite motif containing 54 114088 TRIM9 tripartite motif containing 9 59341 TRPV4 transient receptor potential cation channel subfamily V member 4 155382 VPS37D VPS37D, ESCRT-I subunit 646799 ZAR1L zygote arrest 1 like 25946 ZNF385A zinc finger protein 385A 23053 ZSWIM8 zinc finger SWIM-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 5.82e-02 4.01e-04 GO lamellar body cellular_component 2.68e-02 1.15e-02 Reactome Breakdown of the nuclear lamina Programmed Cell Death 2.68e-02 1.15e-02 Reactome MTF1 activates gene expression Cellular responses to external stimuli 2.38e-02 1.15e-02 Reactome Signaling by plasma membrane FGFR1 fusions Disease 1.17e-02 9.36e-04 GO dynactin binding molecular_function 9.81e-03 9.36e-04 GO ruffle assembly biological_process

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 8.04e-05 2.42e-02 positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity 1.70e-04 4.57e-02 regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity 1.76e-04 3.38e-02 dynactin binding 1.90e-04 3.44e-02 lamin filament 2.76e-04 5.01e-02 phosphatidylinositol binding 5.38e-04 1.19e-01 ruffle assembly 7.45e-04 1.55e-01 positive regulation of peptidyl-serine phosphorylation 7.88e-04 1.63e-01 endomembrane system organization 1.03e-03 1.50e-01 nuclear lamina 1.29e-03 2.43e-01 microtubule-based process 1.46e-03 2.69e-01 regulation of phosphatase activity 1.66e-03 2.98e-01 intracellular mRNA localization 1.74e-03 2.34e-01 ciliary transition zone 1.83e-03 3.22e-01 regulation of peptidyl-serine phosphorylation 1.86e-03 3.26e-01 positive regulation of protein depolymerization 2.45e-03 4.01e-01 retrograde transport, endosome to plasma membrane 2.62e-03 3.30e-01 nuclear envelope 2.93e-03 4.64e-01 cellular response to osmotic stress 2.96e-03 4.67e-01 microtubule cytoskeleton organization 2.98e-03 3.97e-01 lipid binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.66e-02 1e+00 MEMBRANE BINDING AND TARGETTING OF GAG PROTEINS 1.79e-02 1e+00 MTORC1 MEDIATED SIGNALLING 1.88e-02 1e+00 MTORC1 MEDIATED SIGNALLING 2.19e-02 1e+00 NA CL DEPENDENT NEUROTRANSMITTER TRANSPORTERS 2.30e-02 1e+00 MEMBRANE BINDING AND TARGETTING OF GAG PROTEINS 2.45e-02 1e+00 ACYL CHAIN REMODELLING OF PG 2.65e-02 1e+00 ACYL CHAIN REMODELLING OF PI 2.96e-02 1e+00 ENDOSOMAL SORTING COMPLEX REQUIRED FOR TRANSPORT ESCRT 3.39e-02 1e+00 ACYL CHAIN REMODELLING OF PS 3.55e-02 1e+00 AMINE COMPOUND SLC TRANSPORTERS 3.97e-02 1e+00 ENDOSOMAL SORTING COMPLEX REQUIRED FOR TRANSPORT ESCRT 4.22e-02 1e+00 PKB MEDIATED EVENTS 4.48e-02 1e+00 ACYL CHAIN REMODELLING OF PC 4.59e-02 1e+00 ACYL CHAIN REMODELLING OF PI 4.59e-02 1e+00 ACYL CHAIN REMODELLING OF PG 4.65e-02 1e+00 ACYL CHAIN REMODELLING OF PE 4.67e-02 1e+00 NA CL DEPENDENT NEUROTRANSMITTER TRANSPORTERS 4.74e-02 1e+00 ACYL CHAIN REMODELLING OF PS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.09e-04 6.8e-01 abnormal cell nucleus morphology 1.88e-03 1.0e+00 abnormal extraembryonic endoderm formation 4.17e-03 1.0e+00 left pulmonary isomerism 4.39e-03 1.0e+00 abnormal forebrain morphology 5.31e-03 1.0e+00 decreased retinal ganglion cell number 5.54e-03 1.0e+00 dystrophic muscle 6.60e-03 1.0e+00 myocardial fiber degeneration 6.87e-03 1.0e+00 bradykinesia 7.03e-03 1.0e+00 abnormal stratification in cerebral cortex 7.42e-03 1.0e+00 abnormal neuron physiology 9.22e-03 1.0e+00 decreased skeletal muscle fiber size 9.37e-03 1.0e+00 abnormal hepatic vein morphology 1.02e-02 1.0e+00 dextrocardia 1.14e-02 1.0e+00 dilated cardiomyopathy 1.31e-02 1.0e+00 abnormal frontonasal suture morphology 1.31e-02 1.0e+00 small xiphoid process 1.31e-02 1.0e+00 sebaceous gland hypoplasia 1.31e-02 1.0e+00 brain atrophy 1.35e-02 1.0e+00 liver fibrosis 1.49e-02 1.0e+00 increased Reichert's membrane thickness

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

²FDR corrected p-value (Benjamini-Hochberg)