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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod227

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod227 Module size 54 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 83596 BCL2L12 BCL2 like 12 91272 BOD1 biorientation of chromosomes in cell division 1 102288414 C11orf48 chromosome 11 open reading frame 98 745 C11orf9 myelin regulatory factor 123207 C15orf40 chromosome 15 open reading frame 40 388289 C16orf47 chromosome 16 open reading frame 47 128061 C1orf131 chromosome 1 open reading frame 131 285237 C3orf38 chromosome 3 open reading frame 38 84317 CCDC115 coiled-coil domain containing 115 84318 CCDC77 coiled-coil domain containing 77 53344 CHIC1 cysteine rich hydrophobic domain 1 54875 CNTLN centlein 116228 COX20 cytochrome c oxidase assembly factor COX20 151835 CPNE9 copine family member 9 64693 CTAGE1 cutaneous T cell lymphoma-associated antigen 1 644538 CXorf69 small integral membrane protein 10 400830 DEFB132 defensin beta 132 352909 DNAAF3 dynein axonemal assembly factor 3 116151 FAM210B family with sequence similarity 210 member B 51571 FAM49B family with sequence similarity 49 member B 128876 FAM83C family with sequence similarity 83 member C 127943 FCRLB Fc receptor like B 257144 GCSAM germinal center associated signaling and motility 221393 GPR115 adhesion G protein-coupled receptor F4 1880 GPR183 G protein-coupled receptor 183 654502 IQCJ IQ motif containing J 306469 KIAA1430 cilia and flagella associated protein 97 147183 KRT25 keratin 25 84918 LRP11 LDL receptor related protein 11 116068 LYSMD3 LysM domain containing 3 84328 LZIC leucine zipper and CTNNBIP1 domain containing 256714 MAP7D2 MAP7 domain containing 2 79649 MAP7D3 MAP7 domain containing 3 4493 MT1E metallothionein 1E 80023 NRSN2 neurensin 2 93034 NT5C1B 5'-nucleotidase, cytosolic IB 79701 OGFOD3 2-oxoglutarate and iron dependent oxygenase domain containing 3 10761 PLAC1 placenta specific 1 50512 PODXL2 podocalyxin like 2 400736 PRAMEF13 PRAME family member 13 729528 PRAMEF14 PRAME family member 14 65122 PRAMEF2 PRAME family member 2 122651 RNASE11 ribonuclease A family member 11 (inactive) 6248 RSC1A1 regulator of solute carriers 1 25914 RTTN rotatin 152579 SCFD2 sec1 family domain containing 2 652991 SKOR2 SKI family transcriptional corepressor 2 26010 SPATS2L spermatogenesis associated serine rich 2 like 11322 TMC6 transmembrane channel like 6 92305 TMEM129 transmembrane protein 129 84187 TMEM164 transmembrane protein 164 129787 TMEM18 transmembrane protein 18 144406 WDR66 WD repeat domain 66 NA ZHX1-C8ORF76

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 1.30e-02 2.78e-04 GO centriole-centriole cohesion biological_process 3.95e-03 3.49e-06 GO negative regulation of cell differentiation 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 4.62e-04 1.05e-01 microtubule cytoskeleton organization 1.95e-03 3.34e-01 T follicular helper cell differentiation 2.94e-03 3.93e-01 protein kinase binding 3.52e-03 4.20e-01 microtubule organizing center 3.90e-03 5.71e-01 inhibition of cysteine-type endopeptidase activity involved in apoptotic process 3.90e-03 5.71e-01 negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator 3.90e-03 5.71e-01 negative regulation of lymphocyte migration 3.90e-03 5.71e-01 T cell chemotaxis 3.90e-03 5.71e-01 dendritic cell chemotaxis 4.84e-03 6.78e-01 microtubule-based process 5.02e-03 6.15e-01 kinase binding 5.48e-03 6.62e-01 oxysterol binding 5.84e-03 7.72e-01 centriole-centriole cohesion 5.84e-03 7.72e-01 regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator 5.84e-03 7.72e-01 leukocyte tethering or rolling 5.85e-03 7.72e-01 dendritic cell migration 5.90e-03 7.76e-01 negative regulation of cell differentiation 5.90e-03 7.76e-01 cellular protein complex assembly 7.78e-03 9.47e-01 negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator 7.78e-03 9.47e-01 negative regulation of cellular senescence

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.72e-03 1.87e-01 PURINE CATABOLISM 5.16e-03 4.69e-01 PURINE METABOLISM 8.32e-03 6.31e-01 PURINE CATABOLISM 8.54e-03 7.07e-01 BETA DEFENSINS 8.55e-03 7.08e-01 DEFENSINS 1.33e-02 9.24e-01 BETA DEFENSINS 1.33e-02 9.24e-01 DEFENSINS 2.61e-02 1.00e+00 METABOLISM OF NUCLEOTIDES 3.72e-02 1.00e+00 INNATE IMMUNE SYSTEM 4.23e-02 1.00e+00 PURINE METABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 abnormal cerebellar granule cell precursor proliferation 1.88e-03 1e+00 abdominal situs ambiguus 1.88e-03 1e+00 abnormal aortic arch morphology 2.72e-03 1e+00 abnormal food intake 3.74e-03 1e+00 abnormal intestinal glucose absorption 3.74e-03 1e+00 increased circulating interferon-alpha level 3.74e-03 1e+00 increased curvature of guard hairs 3.74e-03 1e+00 abdominal situs inversus 3.76e-03 1e+00 right aortic arch 5.61e-03 1e+00 notochord degeneration 5.61e-03 1e+00 decreased myeloid dendritic cell number 5.61e-03 1e+00 increased placenta weight 5.61e-03 1e+00 abnormal placenta junctional zone morphology 5.61e-03 1e+00 dual inferior vena cava 7.47e-03 1e+00 abnormal Purkinje cell differentiation 7.48e-03 1e+00 reduced cerebellar foliation 7.48e-03 1e+00 decreased plasma cell number 7.48e-03 1e+00 decreased plasmacytoid dendritic cell number 7.48e-03 1e+00 increased spongiotrophoblast size 7.48e-03 1e+00 abnormal vein morphology

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

²FDR corrected p-value (Benjamini-Hochberg)