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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod32

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod32 Module size 72 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 195827 AAED1 peroxiredoxin like 2C 54890 ALKBH5 alkB homolog 5, RNA demethylase 389289 ANXA2R annexin A2 receptor 79000 AUNIP aurora kinase A and ninein interacting protein 399726 C10orf114 cancer susceptibility 10 90488 C12orf23 transmembrane protein 263 387882 C12orf75 chromosome 12 open reading frame 75 148137 C19orf55 proline and serine rich 3 84886 C1orf198 chromosome 1 open reading frame 198 10882 C1QL1 complement C1q like 1 388969 C2orf68 chromosome 2 open reading frame 68 285315 C3orf33 chromosome 3 open reading frame 33 132720 C4orf32 family with sequence similarity 241 member A 285636 C5orf51 chromosome 5 open reading frame 51 222166 C7orf41 maturin, neural progenitor differentiation regulator homolog 79886 CAAP1 caspase activity and apoptosis inhibitor 1 113201 CASC4 cancer susceptibility 4 25790 CCDC19 cilia and flagella associated protein 45 128338 DRAM2 DNA damage regulated autophagy modulator 2 55184 DZANK1 double zinc ribbon and ankyrin repeat domains 1 1994 ELAVL1 ELAV like RNA binding protein 1 284611 FAM102B family with sequence similarity 102 member B 90736 FAM104B family with sequence similarity 104 member B 54491 FAM105A OTU deubiquitinase with linear linkage specificity like 83641 FAM107B family with sequence similarity 107 member B 158293 FAM120AOS family with sequence similarity 120A opposite strand 131408 FAM131A family with sequence similarity 131 member A 57700 FAM160B1 family with sequence similarity 160 member B1 55719 FAM178A SMC5-SMC6 complex localization factor 2 63939 FAM217B family with sequence similarity 217 member B 57184 FAM219B family with sequence similarity 219 member B 374986 FAM73A mitoguardin 1 113828 FAM83F family with sequence similarity 83 member F 114984 FLYWCH2 FLYWCH family member 2 390637 GDPGP1 GDP-D-glucose phosphorylase 1 160897 GPR180 G protein-coupled receptor 180 492311 IGIP IgA inducing protein 23366 KIAA0895 KIAA0895 143458 LDLRAD3 low density lipoprotein receptor class A domain containing 3 90007 MIDN midnolin 91283 MSANTD3 Myb/SANT DNA binding domain containing 3 439921 MXRA7 matrix remodeling associated 7 91663 MYADM myeloid associated differentiation marker 342897 NCCRP1 non-specific cytotoxic cell receptor protein 1 homolog (zebrafish) 734 OSGIN2 oxidative stress induced growth inhibitor family member 2 57157 PHTF2 putative homeodomain transcription factor 2 11098 PRSS23 serine protease 23 285498 RNF212 ring finger protein 212 51093 RRNAD1 ribosomal RNA adenine dimethylase domain containing 1 64766 S100PBP S100P binding protein 55776 SAYSD1 SAYSVFN motif domain containing 1 133383 SETD9 SET domain containing 9 387640 SKIDA1 SKI/DACH domain containing 1 55652 SLC48A1 solute carrier family 48 member 1 79086 SMIM7 small integral membrane protein 7 154007 SNRNP48 small nuclear ribonucleoprotein U11/U12 subunit 48 64089 SNX16 sorting nexin 16 399979 SNX19 sorting nexin 19 84336 TMEM101 transmembrane protein 101 10360 TMEM123 nucleophosmin/nucleoplasmin 3 55654 TMEM127 transmembrane protein 127 79847 TMEM180 major facilitator superfamily domain containing 13A 23670 TMEM2 cell migration inducing hyaluronidase 2 131920 TMEM207 transmembrane protein 207 85019 TMEM241 transmembrane protein 241 120939 TMEM52B transmembrane protein 52B 729264 TP53TG3 TP53 target 3D 286319 TUSC1 tumor suppressor candidate 1 54621 VSIG10 V-set and immunoglobulin domain containing 10 152002 XXYLT1 xyloside xylosyltransferase 1 84327 ZBED3 zinc finger BED-type containing 3 90204 ZSWIM1 zinc finger SWIM-type containing 1

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 2.8e-02 4.88e-03 GO protein linear deubiquitination 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 2.69e-04 6.73e-02 negative regulation of phosphorylation 3.36e-04 8.07e-02 cellular component maintenance 1.02e-03 1.56e-01 N-methyltransferase activity 1.02e-03 1.56e-01 oxidative RNA demethylase activity 1.95e-03 3.34e-01 negative regulation of heterotypic cell-cell adhesion 1.95e-03 3.34e-01 regulation of heterotypic cell-cell adhesion 2.61e-03 4.22e-01 negative regulation of protein phosphorylation 3.69e-03 5.58e-01 negative regulation of intracellular signal transduction 3.89e-03 5.71e-01 meiotic gene conversion 3.89e-03 5.71e-01 secretory granule maturation 3.90e-03 5.71e-01 gene conversion 3.91e-03 4.53e-01 early endosome 4.60e-03 5.19e-01 early endosome membrane 5.84e-03 7.72e-01 chiasma assembly 5.84e-03 7.72e-01 GDP-fucose transport 5.84e-03 7.72e-01 oxidative single-stranded RNA demethylation 5.84e-03 7.72e-01 positive regulation of cell size 6.66e-03 6.95e-01 extrinsic component of endosome membrane 6.74e-03 7.85e-01 GDP-fucose transmembrane transporter activity 7.32e-03 8.37e-01 rRNA (adenine-N6,N6-)-dimethyltransferase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.44e-03 2.52e-01 REGULATION OF MRNA STABILITY BY PROTEINS THAT BIND AU RICH ELEMENTS 9.86e-03 7.92e-01 METABOLISM OF MRNA 9.92e-03 7.95e-01 METABOLISM OF RNA

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.59e-03 1e+00 decreased lumbar vertebrae number 3.71e-03 1e+00 increased sacral vertebrae number 5.68e-03 1e+00 placental labyrinth hypoplasia 7.56e-03 1e+00 abnormal artery morphology 9.33e-03 1e+00 abnormal spongiotrophoblast cell morphology 9.34e-03 1e+00 decreased spongiotrophoblast size 9.34e-03 1e+00 abnormal chorionic plate morphology 1.12e-02 1e+00 abnormal maternal decidual layer morphology 1.12e-02 1e+00 abnormal pupil morphology 1.30e-02 1e+00 increased circulating thyroxine level 1.31e-02 1e+00 decreased bone marrow cell number 1.49e-02 1e+00 abnormal lysosome physiology 1.87e-02 1e+00 abnormal auditory brainstem response 2.05e-02 1e+00 decreased trophoblast giant cell number 2.05e-02 1e+00 increased trabecular bone thickness 2.23e-02 1e+00 decreased NK T cell number 2.25e-02 1e+00 abnormal vertebral arch morphology 2.54e-02 1e+00 decreased blood urea nitrogen level 2.78e-02 1e+00 decreased circulating chloride level 2.78e-02 1e+00 increased mean corpuscular hemoglobin concentration

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

²FDR corrected p-value (Benjamini-Hochberg)