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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod2

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod2 Module size 88 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 84334 APOPT1 apoptogenic 1, mitochondrial 93436 ARMC6 armadillo repeat containing 6 64225 ATL2 atlastin GTPase 2 8455 ATRN attractin 80115 BAIAP2L2 BAI1 associated protein 2 like 2 146227 BEAN1 brain expressed associated with NEDD4 1 259282 BOD1L1 biorientation of chromosomes in cell division 1 like 1 55108 BSDC1 BSD domain containing 1 91298 C12orf29 chromosome 12 open reading frame 29 55017 C14orf119 chromosome 14 open reading frame 119 148423 C1orf52 chromosome 1 open reading frame 52 100129271 C1orf68 chromosome 1 open reading frame 68 114905 C1QTNF7 C1q and TNF related 7 150248 C22orf15 chromosome 22 open reading frame 15 51614 C2orf47 ERGIC and golgi 3 255119 C4orf22 cilia and flagella associated protein 299 56951 C5orf15 chromosome 5 open reading frame 15 375444 C5orf34 chromosome 5 open reading frame 34 84933 C8orf76 chromosome 8 open reading frame 76 51531 C9orf156 tRNA methyltransferase O 112942 CCDC104 cilia and flagella associated protein 36 55610 CCDC132 VPS50, EARP/GARPII complex subunit 79879 CCDC134 coiled-coil domain containing 134 285331 CCDC66 coiled-coil domain containing 66 221960 CCZ1B CCZ1 homolog B, vacuolar protein trafficking and biogenesis associated 91368 CDKN2AIPNL CDKN2A interacting protein N-terminal like 153241 CEP120 centrosomal protein 120 112616 CMTM7 CKLF like MARVEL transmembrane domain containing 7 1534 CYB561 cytochrome b561 347442 DCAF8L2 DDB1 and CUL4 associated factor 8 like 2 1687 DFNA5 gasdermin E 392617 ELFN1 extracellular leucine rich repeat and fibronectin type III domain containing 1 256364 EML3 echinoderm microtubule associated protein like 3 157697 ERICH1 glutamate rich 1 2171 FABP5 fatty acid binding protein 5 84498 FAM120B family with sequence similarity 120B 283635 FAM177A1 family with sequence similarity 177 member A1 29902 FAM216A family with sequence similarity 216 member A 404636 FAM45A family with sequence similarity 45 member A 151354 FAM84A family with sequence similarity 84 member A 28982 FLVCR1 feline leukemia virus subgroup C cellular receptor 1 54914 FOCAD focadhesin 55303 GIMAP4 GTPase, IMAP family member 4 54856 GON4L gon-4 like 284110 GSDMA gasdermin A 79792 GSDMD gasdermin D 63897 HEATR6 HEAT repeat containing 6 135114 HINT3 histidine triad nucleotide binding protein 3 79366 HMGN5 high mobility group nucleosome binding domain 5 285148 IAH1 isoamyl acetate hydrolyzing esterase 1 (putative) 27177 IL36B interleukin 36 beta 150771 ITPRIPL1 ITPRIP like 1 222658 KCTD20 potassium channel tetramerization domain containing 20 143888 KDELC2 KDEL motif containing 2 85459 KIAA1731 centrosomal protein 295 448834 KPRP keratinocyte proline rich protein 51108 METTL9 methyltransferase like 9 4826 NNAT neuronatin 84304 NUDT22 nudix hydrolase 22 54940 OCIAD1 OCIA domain containing 1 79668 PARP8 poly(ADP-ribose) polymerase family member 8 22990 PCNX pecanex 1 23187 PHLDB1 pleckstrin homology like domain family B member 1 63895 PIEZO2 piezo type mechanosensitive ion channel component 2 149041 RC3H1 ring finger and CCCH-type domains 1 113178 SCAMP4 secretory carrier membrane protein 4 54549 SDK2 sidekick cell adhesion molecule 2 253512 SLC25A30 solute carrier family 25 member 30 57228 SMAGP small cell adhesion glycoprotein 8303 SNN stannin 57231 SNX14 sorting nexin 14 284612 SYPL2 synaptophysin like 2 54868 TMEM104 transmembrane protein 104 375346 TMEM110 STIM activating enhancer 54972 TMEM132A transmembrane protein 132A 29058 TMEM230 transmembrane protein 230 169693 TMEM252 transmembrane protein 252 55116 TMEM39B transmembrane protein 39B 126259 TMIGD2 transmembrane and immunoglobulin domain containing 2 91978 TPGS1 tubulin polyglutamylase complex subunit 1 131601 TPRA1 transmembrane protein adipocyte associated 1 80305 TRABD TraB domain containing 9830 TRIM14 tripartite motif containing 14 54795 TRPM4 transient receptor potential cation channel subfamily M member 4 92181 UBTD2 ubiquitin domain containing 2 80217 WDR96 cilia and flagella associated protein 43 29066 ZC3H7A zinc finger CCCH-type containing 7A 57683 ZDBF2 zinc finger DBF-type 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 1.20e-01 5.47e-03 Reactome SDK interactions Cell-Cell communication 1.25e-02 4.75e-04 GO pyroptosis 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 1.22e-03 2.32e-01 hemopoiesis 2.11e-03 2.95e-01 phosphatidylinositol bisphosphate binding 2.15e-03 3.61e-01 spleen development 2.29e-03 3.80e-01 immune system development 2.95e-03 4.66e-01 regulation of activated T cell proliferation 3.90e-03 5.71e-01 pyroptosis 3.95e-03 5.77e-01 membrane depolarization during bundle of His cell action potential 4.49e-03 5.60e-01 phosphatidylinositol phosphate binding 4.81e-03 5.94e-01 phosphatidylglycerol binding 4.81e-03 5.94e-01 cardiolipin binding 5.49e-03 5.97e-01 clathrin complex 5.52e-03 7.52e-01 eye photoreceptor cell differentiation 5.84e-03 7.72e-01 B-1 B cell differentiation 5.89e-03 7.74e-01 membrane depolarization during Purkinje myocyte cell action potential 5.89e-03 7.74e-01 membrane depolarization during AV node cell action potential 5.93e-03 7.79e-01 retina morphogenesis in camera-type eye 7.32e-03 7.43e-01 integral component of synaptic vesicle membrane 7.78e-03 9.47e-01 T follicular helper cell differentiation 7.93e-03 9.55e-01 positive regulation of adipose tissue development 9.54e-03 1.00e+00 phospholipid binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.61e-03 1.78e-01 IRON UPTAKE AND TRANSPORT 1.69e-03 1.85e-01 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.41e-03 1e+00 decreased rib number 3.74e-03 1e+00 increased T follicular helper cell number 5.61e-03 1e+00 ileum inflammation 6.71e-03 1e+00 decreased total body fat amount 7.47e-03 1e+00 abnormal intraepithelial T cell number 7.48e-03 1e+00 reticulocytopenia 7.48e-03 1e+00 abnormal effector T cell morphology 7.48e-03 1e+00 crypts of Lieberkuhn abscesses 9.34e-03 1e+00 cecum inflammation 9.35e-03 1e+00 abnormal thymus development 1.12e-02 1e+00 abnormal skeletal muscle fiber triad morphology 1.12e-02 1e+00 abnormal impulsive behavior control 1.31e-02 1e+00 increased synaptic depression 1.31e-02 1e+00 abnormal response to novelty 1.31e-02 1e+00 absent B cells 1.49e-02 1e+00 spongiform encephalopathy 1.67e-02 1e+00 decreased red blood cell distribution width 1.68e-02 1e+00 abnormal sarcoplasmic reticulum morphology 1.68e-02 1e+00 abnormal Meckel's cartilage morphology 1.68e-02 1e+00 small intestinal inflammation

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

²FDR corrected p-value (Benjamini-Hochberg)