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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod266

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod266 Module size 85 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 11096 ADAMTS5 ADAM metallopeptidase with thrombospondin type 1 motif 5 11173 ADAMTS7 ADAM metallopeptidase with thrombospondin type 1 motif 7 92949 ADAMTSL1 ADAMTS like 1 54507 ADAMTSL4 ADAMTS like 4 80830 APOL6 apolipoprotein L6 145173 B3GALTL beta 3-glucosyltransferase 84752 B3GNT9 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9 145497 C14orf166B leucine rich repeat containing 74A 256302 C17orf103 N-acetyltransferase domain containing 1 494514 C18orf56 TYMS opposite strand 126526 C19orf47 chromosome 19 open reading frame 47 152816 C4orf26 odontogenesis associated phosphoprotein 140947 C5orf20 dendritic cell associated nuclear protein 157773 C8orf48 chromosome 8 open reading frame 48 28952 CCDC22 coiled-coil domain containing 22 25901 CCDC28A coiled-coil domain containing 28A 11314 CD300A CD300a molecule 9936 CD302 CD302 molecule 966 CD59 CD59 molecule (CD59 blood group) 5199 CFP complement factor properdin 348174 CLEC18A C-type lectin domain family 18 member A 51397 COMMD10 COMM domain containing 10 51122 COMMD2 COMM domain containing 2 23412 COMMD3 COMM domain containing 3 149951 COMMD7 COMM domain containing 7 54951 COMMD8 COMM domain containing 8 29099 COMMD9 COMM domain containing 9 1415 CRYBB2 crystallin beta B2 1470 CST2 cystatin SA 303794 DGCR6 DiGeorge syndrome critical region gene 6 58524 DMRT3 doublesex and mab-3 related transcription factor 3 84677 DSCR8 Down syndrome critical region 8 2014 EMP3 epithelial membrane protein 3 79843 FAM124B family with sequence similarity 124 member B 284418 FAM71E2 family with sequence similarity 71 member E2 84985 FAM83A family with sequence similarity 83 member A 80028 FBXL18 F-box and leucine rich repeat protein 18 3321 IGSF3 immunoglobulin superfamily member 3 93185 IGSF8 immunoglobulin superfamily member 8 284359 IZUMO1 izumo sperm-egg fusion 1 9929 JOSD1 Josephin domain containing 1 9766 KIAA0247 sushi domain containing 6 3887 KRT81 keratin 81 386672 KRTAP10-4 keratin associated protein 10-4 140258 KRTAP13-1 keratin associated protein 13-1 337972 KRTAP19-5 keratin associated protein 19-5 4045 LSAMP limbic system associated membrane protein 4121 MAN1A1 mannosidase alpha class 1A member 1 10905 MAN1A2 mannosidase alpha class 1A member 2 57134 MAN1C1 mannosidase alpha class 1C member 1 4124 MAN2A1 mannosidase alpha class 2A member 1 4122 MAN2A2 mannosidase alpha class 2A member 2 116255 MGAT1 monoacylglycerol O-acyltransferase 1 94273 MGAT2 mannosyl (alpha-1,6-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase 4248 MGAT3 mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase 11282 MGAT4B alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase B 25834 MGAT4C MGAT4 family member C 146664 MGAT5B alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B 4340 MOG myelin oligodendrocyte glycoprotein 4601 MXI1 MAX interactor 1, dimerization protein 257194 NEGR1 neuronal growth regulator 1 296562 NPDC1 neural proliferation, differentiation and control, 1 4879 NPPB natriuretic peptide B 23467 NPTXR neuronal pentraxin receptor 50863 NTM neurotrimin 4978 OPCML opioid binding protein/cell adhesion molecule like 5025 P2RX4 purinergic receptor P2X 4 9127 P2RX6 purinergic receptor P2X 6 22822 PHLDA1 pleckstrin homology like domain family A member 1 23275 POFUT2 protein O-fucosyltransferase 2 338324 S100A7A S100 calcium binding protein A7A 124935 SLC43A2 solute carrier family 43 member 2 10252 SPRY1 sprouty RTK signaling antagonist 1 10253 SPRY2 sprouty RTK signaling antagonist 2 10251 SPRY3 sprouty RTK signaling antagonist 3 81848 SPRY4 sprouty RTK signaling antagonist 4 140732 SUN5 Sad1 and UNC84 domain containing 5 51298 THEG theg spermatid protein 128218 TMEM125 transmembrane protein 125 58986 TMEM8A transmembrane protein 8A 55503 TRPV6 transient receptor potential cation channel subfamily V member 6 81619 TSPAN14 tetraspanin 14 10867 TSPAN9 tetraspanin 9 25844 YIPF3 Yip1 domain family member 3 79038 ZFYVE21 zinc finger FYVE-type containing 21

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 3.81e-01 3.90e-03 Reactome Reactions specific to the hybrid N-glycan synthesis pathway Metabolism of proteins 3.29e-01 1.05e-09 Reactome N-glycan trimming and elongation in the cis-Golgi Metabolism of proteins 2.29e-01 5.67e-08 Reactome Progressive trimming of alpha-1,2-linked mannose residues from Man9/8/7GlcNAc2 to produce Man5GlcNAc2 Metabolism of proteins 1.21e-01 7.79e-03 Reactome Interaction between PHLDA1 and AURKA Cell Cycle 1.19e-01 8.21e-12 GO N-glycan processing biological_process 1.12e-01 2.06e-07 GO negative regulation of fibroblast growth factor receptor signaling pathway biological_process 6.06e-02 8.26e-09 Reactome O-glycosylation of TSR domain-containing proteins Metabolism of proteins 5.95e-02 6.07e-10 Reactome N-glycan antennae elongation in the medial/trans-Golgi Metabolism of proteins 4.80e-02 9.77e-07 GO negative regulation of Ras protein signal transduction biological_process 4.76e-02 3.11e-04 GO purinergic nucleotide receptor activity molecular_function 3.57e-02 3.11e-04 GO extracellularly ATP-gated cation channel activity molecular_function 3.26e-02 6.68e-06 Reactome Reactions specific to the complex N-glycan synthesis pathway Metabolism of proteins 2.32e-02 3.53e-07 GO negative regulation of MAP kinase activity biological_process 1.10e-02 7.01e-09 GO protein N-linked glycosylation 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 0.00e+00 0.00e+00 protein O-linked fucosylation 1.40e-17 1.33e-14 protein glycosylation 1.40e-17 1.33e-14 macromolecule glycosylation 1.64e-17 1.56e-14 glycoprotein biosynthetic process 2.75e-17 2.61e-14 glycosylation 1.86e-16 1.76e-13 glycoprotein metabolic process 7.53e-11 6.32e-08 N-glycan processing 2.13e-09 1.52e-06 fucosylation 4.00e-09 1.94e-06 alpha-mannosidase activity 6.53e-09 3.05e-06 mannosidase activity 2.13e-08 9.22e-06 acetylglucosaminyltransferase activity 1.14e-07 6.38e-05 protein deglycosylation 2.60e-07 1.37e-04 Golgi apparatus mannose trimming 5.90e-07 1.95e-04 transferase activity, transferring hexosyl groups 2.08e-06 9.30e-04 protein O-linked glycosylation 2.65e-06 7.74e-04 mannosyl-oligosaccharide 1,2-alpha-mannosidase activity 5.63e-06 1.54e-03 transferase activity, transferring glycosyl groups 9.08e-06 2.39e-03 UDP-glycosyltransferase activity 1.03e-05 2.52e-03 Golgi membrane 1.21e-05 4.60e-03 protein N-linked glycosylation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 ASPARAGINE N LINKED GLYCOSYLATION 0.00e+00 0.00e+00 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 0.00e+00 0.00e+00 ASPARAGINE N LINKED GLYCOSYLATION 0.00e+00 0.00e+00 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 0.00e+00 0.00e+00 POST TRANSLATIONAL PROTEIN MODIFICATION 1.99e-10 7.05e-08 POST TRANSLATIONAL PROTEIN MODIFICATION 1.24e-09 2.99e-07 N GLYCAN ANTENNAE ELONGATION IN THE MEDIAL TRANS GOLGI 1.89e-09 6.01e-07 N GLYCAN ANTENNAE ELONGATION IN THE MEDIAL TRANS GOLGI 2.91e-04 3.99e-02 EGFR DOWNREGULATION 4.47e-04 4.90e-02 N GLYCAN ANTENNAE ELONGATION 6.03e-04 7.59e-02 N GLYCAN ANTENNAE ELONGATION 6.50e-04 6.83e-02 EGFR DOWNREGULATION 6.92e-04 8.51e-02 SIGNALING BY EGFR IN CANCER 1.08e-03 1.08e-01 SIGNALING BY EGFR IN CANCER 1.72e-03 1.87e-01 SPRY REGULATION OF FGF SIGNALING 1.73e-03 1.88e-01 NEGATIVE REGULATION OF FGFR SIGNALING 6.30e-03 5.53e-01 SIGNALING BY FGFR 1.18e-02 8.41e-01 SPRY REGULATION OF FGF SIGNALING 1.19e-02 8.47e-01 NEGATIVE REGULATION OF FGFR SIGNALING 2.04e-02 1.00e+00 SIGNALING BY FGFR

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.20e-04 3.69e-01 hematuria 2.52e-04 4.01e-01 supernumerary teeth 3.11e-04 4.59e-01 reticulocytosis 1.06e-03 9.29e-01 decreased susceptibility to injury 1.51e-03 1.00e+00 malocclusion 5.61e-03 1.00e+00 increased Deiters cell number 5.61e-03 1.00e+00 ectopic ureter 5.62e-03 1.00e+00 erythroblastosis 7.48e-03 1.00e+00 abnormal tail position or orientation 7.48e-03 1.00e+00 blind ureter 7.48e-03 1.00e+00 increased Purkinje cell number 9.16e-03 1.00e+00 decreased susceptibility to induced arthritis 9.34e-03 1.00e+00 ectopic ureteric bud 9.34e-03 1.00e+00 necrospermia 9.34e-03 1.00e+00 hemoglobinuria 9.37e-03 1.00e+00 increased partial thromboplastin time 9.41e-03 1.00e+00 increased urine protein level 9.81e-03 1.00e+00 impaired swimming 1.12e-02 1.00e+00 abnormal vascular endothelial cell differentiation 1.12e-02 1.00e+00 abnormal pillar cell morphology

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

²FDR corrected p-value (Benjamini-Hochberg)