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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod250

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod250 Module size 65 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 9048 ARTN artemin 55653 BCAS4 breast carcinoma amplified sequence 4 81688 C6orf62 chromosome 6 open reading frame 62 201973 CCDC111 primase and DNA directed polymerase 153733 CCDC112 coiled-coil domain containing 112 56882 CDC42SE1 CDC42 small effector 1 1048 CEACAM5 carcinoembryonic antigen related cell adhesion molecule 5 1088 CEACAM8 carcinoembryonic antigen related cell adhesion molecule 8 145508 CEP128 centrosomal protein 128 161198 CLEC14A C-type lectin domain containing 14A 50856 CLEC4A C-type lectin domain family 4 member A 338339 CLEC4D C-type lectin domain family 4 member D 26253 CLEC4E C-type lectin domain family 4 member E 8418 CMAHP cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene 10321 CRISP3 cysteine rich secretory protein 3 54849 DEF8 differentially expressed in FDCP 8 homolog 1668 DEFA3 defensin alpha 3 1671 DEFA6 defensin alpha 6 22862 FNDC3A fibronectin type III domain containing 3A 84075 FSCB fibrous sheath CABYR binding protein 2676 GFRA3 GDNF family receptor alpha 3 144321 GLIPR1L2 GLIPR1 like 2 152007 GLIPR2 GLI pathogenesis related 2 51280 GOLM1 golgi membrane protein 1 402665 IGLON5 IgLON family member 5 55540 IL17RB interleukin 17 receptor B 10008 KCNE3 potassium voltage-gated channel subfamily E regulatory subunit 3 541468 LURAP1 leucine rich adaptor protein 1 11320 MGAT4A alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A 4249 MGAT5 alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase 25832 NBPF14 NBPF member 14 56901 NDUFA4L2 NDUFA4, mitochondrial complex associated like 2 5064 PALM paralemmin 100303755 PET117 PET117 homolog 54477 PLEKHA5 pleckstrin homology domain containing A5 65121 PRAMEF1 PRAME family member 1 NA PRAMEF16 51052 PRLH prolactin releasing hormone 283571 PROX2 prospero homeobox 2 5623 PSPN persephin 353091 RAET1G retinoic acid early transcript 1G 80328 RAET1L UL16 binding protein 2 5068 REG3A regenerating family member 3 alpha 768211 RELL1 RELT like 1 285613 RELL2 RELT like 2 289635 RELT RELT-like 1 26150 RIBC2 RIB43A domain with coiled-coils 2 6275 S100A4 S100 calcium binding protein A4 374897 SBSN suprabasin 10647 SCGB1D2 secretoglobin family 1D member 2 404552 SCGB1D4 secretoglobin family 1D member 4 4246 SCGB2A1 secretoglobin family 2A member 1 4250 SCGB2A2 secretoglobin family 2A member 2 6623 SNCG synuclein gamma 83874 TBC1D10A TBC1 domain family member 10A 374618 TEX9 testis expressed 9 84948 TIGD5 tigger transposable element derived 5 23023 TMCC1 transmembrane and coiled-coil domain family 1 65084 TMEM135 transmembrane protein 135 131616 TMEM42 transmembrane protein 42 145567 TTC7B tetratricopeptide repeat domain 7B 80328 ULBP2 UL16 binding protein 2 79465 ULBP3 UL16 binding protein 3 152098 ZCWPW2 zinc finger CW-type and PWWP domain containing 2 158506 ZNF645 Cbl proto-oncogene like 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 1.83e-01 1.21e-08 GO natural killer cell lectin-like receptor binding molecular_function 5.65e-02 2.21e-04 GO membrane disruption in other organism biological_process 4.01e-02 2.84e-08 GO susceptibility to natural killer cell mediated cytotoxicity biological_process 3.77e-03 3.54e-04 Reactome Alpha-defensins Immune System 1.94e-03 8.39e-05 Reactome Dectin-2 family Immune System

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 1.14e-08 7.36e-06 cell killing 4.19e-08 1.71e-05 natural killer cell lectin-like receptor binding 2.39e-07 1.27e-04 innate immune response 4.09e-07 1.28e-04 anchored component of membrane 7.08e-07 3.47e-04 natural killer cell mediated cytotoxicity 9.86e-07 4.69e-04 natural killer cell mediated immunity 1.99e-06 8.93e-04 leukocyte mediated cytotoxicity 1.65e-05 6.06e-03 C-terminal protein lipidation 2.29e-05 5.58e-03 antigen binding 6.82e-05 2.10e-02 post-translational protein modification 1.78e-04 4.75e-02 T cell differentiation involved in immune response 3.38e-04 5.98e-02 carbohydrate binding 3.66e-04 8.68e-02 leukocyte mediated immunity 4.52e-04 1.03e-01 stimulatory C-type lectin receptor signaling pathway 5.19e-04 1.15e-01 protein lipidation 5.74e-04 1.25e-01 lipoprotein biosynthetic process 5.83e-04 1.27e-01 defense response to bacterium 7.82e-04 1.62e-01 antimicrobial humoral response 9.03e-04 1.82e-01 response to bacterium 1.19e-03 2.27e-01 autonomic nervous system development

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.78e-04 2.59e-02 N GLYCAN ANTENNAE ELONGATION 1.93e-04 2.29e-02 N GLYCAN ANTENNAE ELONGATION 1.96e-04 2.33e-02 N GLYCAN ANTENNAE ELONGATION IN THE MEDIAL TRANS GOLGI 4.30e-04 5.64e-02 DEFENSINS 4.32e-04 5.66e-02 NCAM1 INTERACTIONS 4.76e-04 5.19e-02 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 5.00e-04 6.43e-02 N GLYCAN ANTENNAE ELONGATION IN THE MEDIAL TRANS GOLGI 6.89e-04 7.21e-02 DEFENSINS 1.01e-03 1.19e-01 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 1.03e-03 1.21e-01 NCAM SIGNALING FOR NEURITE OUT GROWTH 1.59e-03 1.52e-01 NCAM1 INTERACTIONS 2.02e-03 1.88e-01 NCAM SIGNALING FOR NEURITE OUT GROWTH 2.99e-03 2.64e-01 ASPARAGINE N LINKED GLYCOSYLATION 4.75e-03 4.38e-01 IMMUNOREGULATORY INTERACTIONS BETWEEN A LYMPHOID AND A NON LYMPHOID CELL 8.01e-03 6.72e-01 ASPARAGINE N LINKED GLYCOSYLATION 1.15e-02 8.90e-01 INNATE IMMUNE SYSTEM 1.27e-02 8.92e-01 IMMUNOREGULATORY INTERACTIONS BETWEEN A LYMPHOID AND A NON LYMPHOID CELL 1.71e-02 1.00e+00 INNATE IMMUNE SYSTEM 1.78e-02 1.00e+00 AXON GUIDANCE 2.95e-02 1.00e+00 POST TRANSLATIONAL PROTEIN MODIFICATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.76e-05 6.95e-02 abnormal interleukin-17 secretion 4.23e-05 1.28e-01 abnormal chemokine secretion 1.46e-04 2.92e-01 abnormal sympathetic neuron morphology 1.48e-04 2.93e-01 abnormal superior cervical ganglion morphology 1.75e-04 3.23e-01 abnormal interferon-gamma secretion 1.81e-04 3.29e-01 abnormal sympathetic ganglion morphology 3.92e-04 5.25e-01 abnormal immune serum protein physiology 4.24e-04 5.51e-01 small superior cervical ganglion 9.69e-04 8.90e-01 increased interleukin-10 secretion 1.45e-03 1.00e+00 blepharoptosis 1.79e-03 1.00e+00 decreased sensitivity to xenobiotic induced morbidity/mortality 2.01e-03 1.00e+00 decreased dendritic cell number 2.85e-03 1.00e+00 decreased interleukin-10 secretion 3.74e-03 1.00e+00 abnormal sympathetic system morphology 4.72e-03 1.00e+00 hepatic steatosis 6.25e-03 1.00e+00 decreased susceptibility to type IV hypersensitivity reaction 7.17e-03 1.00e+00 abnormal Sertoli cell morphology 7.20e-03 1.00e+00 decreased susceptibility to experimental autoimmune encephalomyelitis 7.47e-03 1.00e+00 impaired cellular glucose import 7.48e-03 1.00e+00 glomerular capillary thrombosis

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

²FDR corrected p-value (Benjamini-Hochberg)