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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod348

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod348 Module size 67 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 64746 ACBD3 acyl-CoA binding domain containing 3 79026 AHNAK AHNAK nucleoprotein 445815 AKAP2 PALM2-AKAP2 readthrough 151254 ALS2CR11 C2 calcium dependent domain containing 6 311 ANXA11 annexin A11 307 ANXA4 annexin A4 308 ANXA5 annexin A5 310 ANXA7 annexin A7 25814 ATXN10 ataxin 10 9529 BAG5 BCL2 associated athanogene 5 60686 C14orf93 chromosome 14 open reading frame 93 56005 C19orf10 myeloid derived growth factor 128989 C22orf25 transport and golgi organization 2 homolog 146849 CCDC42 coiled-coil domain containing 42 80279 CDK5RAP3 CDK5 regulatory subunit associated protein 3 23059 CLUAP1 clusterin associated protein 1 116840 CNTROB centrobin, centriole duplication and spindle assembly protein 8895 CPNE3 copine 3 131034 CPNE4 copine 4 22979 EFR3B EFR3 homolog B 23344 ESYT1 extended synaptotagmin 1 257415 FAM133B family with sequence similarity 133 member B 10922 FASTK Fas activated serine/threonine kinase 23014 FBXO21 F-box protein 21 96459 FNIP1 folliculin interacting protein 1 23131 GPATCH8 G-patch domain containing 8 64645 HIAT1 major facilitator superfamily domain containing 14A 84641 HIATL1 major facilitator superfamily domain containing 14B 23240 KIAA0922 transmembrane 131 like 10542 LAMTOR5 late endosomal/lysosomal adaptor, MAPK and MTOR activator 5 4134 MAP4 microtubule associated protein 4 84804 MFSD9 major facilitator superfamily domain containing 9 93621 MRFAP1 Morf4 family associated protein 1 26292 MYCBP MYC binding protein 64943 NT5DC2 5'-nucleotidase domain containing 2 134492 NUDCD2 NudC domain containing 2 54726 OTUD4 OTU deubiquitinase 4 5074 PAWR pro-apoptotic WT1 regulator 144100 PLEKHA7 pleckstrin homology domain containing A7 307235 RBFA ribosome binding factor A 155435 RBM33 RNA binding motif protein 33 6281 S100A10 S100 calcium binding protein A10 6282 S100A11 S100 calcium binding protein A11 6277 S100A6 S100 calcium binding protein A6 283514 SIAH3 siah E3 ubiquitin protein ligase family member 3 57606 SLAIN2 SLAIN motif family member 2 5002 SLC22A18 solute carrier family 22 member 18 57210 SLC45A4 solute carrier family 45 member 4 124460 SNX20 sorting nexin 20 50861 STMN3 stathmin 3 30851 TAX1BP3 Tax1 binding protein 3 84897 TBRG1 transforming growth factor beta regulator 1 7053 TGM3 transglutaminase 3 221981 THSD7A thrombospondin type 1 domain containing 7A 283578 TMED8 transmembrane p24 trafficking protein family member 8 51754 TMEM8B transmembrane protein 8B 83590 TMUB1 transmembrane and ubiquitin like domain containing 1 55521 TRIM36 tripartite motif containing 36 91107 TRIM47 tripartite motif containing 47 55833 UBAP2 ubiquitin associated protein 2 92912 UBE2Q2 ubiquitin conjugating enzyme E2 Q2 134111 UBE2QL1 ubiquitin conjugating enzyme E2 Q family like 1 9958 USP15 ubiquitin specific peptidase 15 23264 ZC3H7B zinc finger CCCH-type containing 7B 51663 ZFR zinc finger RNA binding protein 9204 ZMYM6 zinc finger MYM-type containing 6 23140 ZZEF1 zinc finger ZZ-type and EF-hand domain 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 1.09e-01 8.47e-08 GO S100 protein binding molecular_function 4.50e-02 1.83e-10 GO calcium-dependent phospholipid binding molecular_function 8.86e-03 2.42e-08 GO calcium-dependent protein binding molecular_function

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 1.76e-08 7.74e-06 S100 protein binding 2.88e-08 1.21e-05 calcium-dependent protein binding 2.46e-07 8.80e-05 calcium-dependent phospholipid binding 1.79e-04 3.43e-02 phospholipid binding 1.83e-04 3.50e-02 phospholipase inhibitor activity 1.93e-04 3.66e-02 lipid binding 3.59e-04 6.30e-02 calcium ion binding 3.84e-04 6.67e-02 lipase inhibitor activity 1.45e-03 2.67e-01 response to calcium ion 1.91e-03 3.33e-01 negative regulation of cellular protein catabolic process 1.95e-03 2.76e-01 ubiquitin conjugating enzyme activity 2.42e-03 3.33e-01 ATPase regulator activity 2.66e-03 4.29e-01 negative regulation of T cell proliferation 2.92e-03 3.91e-01 NF-kappaB binding 3.24e-03 5.02e-01 negative regulation of lymphocyte proliferation 3.24e-03 5.02e-01 negative regulation of mononuclear cell proliferation 3.24e-03 5.02e-01 negative regulation of leukocyte proliferation 3.34e-03 5.14e-01 microtubule polymerization or depolymerization 3.36e-03 4.04e-01 microtubule organizing center 3.66e-03 5.55e-01 cytoplasmic microtubule organization

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.20e-02 9.20e-01 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 1.21e-02 9.26e-01 ORGANIC CATION ANION ZWITTERION TRANSPORT 1.33e-02 9.97e-01 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 1.39e-02 9.57e-01 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 1.58e-02 1.00e+00 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 1.66e-02 1.00e+00 ORGANIC CATION ANION ZWITTERION TRANSPORT 3.95e-02 1.00e+00 ACTIVATION OF CHAPERONE GENES BY XBP1S 3.95e-02 1.00e+00 ACTIVATION OF CHAPERONE GENES BY XBP1S 4.63e-02 1.00e+00 UNFOLDED PROTEIN RESPONSE 4.67e-02 1.00e+00 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 4.70e-02 1.00e+00 UNFOLDED PROTEIN RESPONSE

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 hair cortex keratinization 1.87e-03 1e+00 decreased zigzag hair amount 1.87e-03 1e+00 increased curvature of hairs 1.87e-03 1e+00 loss of vibrissae 1.87e-03 1e+00 thin hair shaft 3.74e-03 1e+00 decreased interleukin-23 secretion 5.61e-03 1e+00 brittle hair 5.62e-03 1e+00 decreased IgG1 level 7.48e-03 1e+00 decreased abdominal adipose tissue amount 9.34e-03 1e+00 abnormal hair cuticle 1.12e-02 1e+00 absent B cells 1.30e-02 1e+00 increased growth rate 1.30e-02 1e+00 decreased embryonic cilium length 1.30e-02 1e+00 abnormal lateral plate mesoderm morphology 1.31e-02 1e+00 decreased transitional stage B cell number 1.49e-02 1e+00 abnormal zigzag hair morphology 1.49e-02 1e+00 enlarged pancreatic islets 1.50e-02 1e+00 decreased pre-B cell number 1.67e-02 1e+00 abnormal ion homeostasis 1.68e-02 1e+00 increased pro-B cell number

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

²FDR corrected p-value (Benjamini-Hochberg)