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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod212

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod212 Module size 47 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 122970 ACOT4 acyl-CoA thioesterase 4 56052 ALG1 ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase 440138 ALG11 ALG11, alpha-1,2-mannosyltransferase 79868 ALG13 ALG13, UDP-N-acetylglucosaminyltransferase subunit 199857 ALG14 ALG14, UDP-N-acetylglucosaminyltransferase subunit 200810 ALG1L ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase like 85365 ALG2 ALG2, alpha-1,3/1,6-mannosyltransferase 287983 ALG3 ALG3, alpha-1,3- mannosyltransferase 29880 ALG5 ALG5, dolichyl-phosphate beta-glucosyltransferase 29929 ALG6 ALG6, alpha-1,3-glucosyltransferase 146712 B3GNTL1 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase like 1 22845 DOLK dolichol kinase 57171 DOLPP1 dolichyldiphosphatase 1 1798 DPAGT1 dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 8813 DPM1 dolichyl-phosphate mannosyltransferase subunit 1, catalytic 29640 DPM2 dolichyl-phosphate mannosyltransferase subunit 2, regulatory 502017 DPM3 dolichyl-phosphate mannosyltransferase subunit 3 161247 FITM1 fat storage inducing transmembrane protein 1 128486 FITM2 fat storage inducing transmembrane protein 2 2762 GMDS GDP-mannose 4,6-dehydratase 29926 GMPPA GDP-mannose pyrophosphorylase A 29925 GMPPB GDP-mannose pyrophosphorylase B 27430 MAT2B methionine adenosyltransferase 2B 9526 MPDU1 mannose-P-dolichol utilization defect 1 363464 PIGA phosphatidylinositol glycan anchor biosynthesis, class A 9488 PIGB phosphatidylinositol glycan anchor biosynthesis class B 5279 PIGC phosphatidylinositol glycan anchor biosynthesis class C 5281 PIGF phosphatidylinositol glycan anchor biosynthesis class F 54872 PIGG phosphatidylinositol glycan anchor biosynthesis class G 5283 PIGH phosphatidylinositol glycan anchor biosynthesis class H 10026 PIGK phosphatidylinositol glycan anchor biosynthesis class K 9487 PIGL phosphatidylinositol glycan anchor biosynthesis class L 93183 PIGM phosphatidylinositol glycan anchor biosynthesis class M 23556 PIGN phosphatidylinositol glycan anchor biosynthesis class N 84720 PIGO phosphatidylinositol glycan anchor biosynthesis class O 51227 PIGP phosphatidylinositol glycan anchor biosynthesis class P 9091 PIGQ phosphatidylinositol glycan anchor biosynthesis class Q 94005 PIGS phosphatidylinositol glycan anchor biosynthesis class S 51604 PIGT phosphatidylinositol glycan anchor biosynthesis class T 128869 PIGU phosphatidylinositol glycan anchor biosynthesis class U 54965 PIGX phosphatidylinositol glycan anchor biosynthesis class X 84992 PIGY phosphatidylinositol glycan anchor biosynthesis class Y 100996939 PYURF PIGY upstream reading frame 84074 QRICH2 glutamine rich 2 91869 RFT1 RFT1 homolog 23483 TGDS TDP-glucose 4,6-dehydratase 85025 TMEM60 transmembrane protein 60

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 3.41e-01 5.60e-10 GO attachment of GPI anchor to protein biological_process 3.31e-01 7.35e-38 Reactome Synthesis of glycosylphosphatidylinositol (GPI) Metabolism of proteins 3.29e-01 2.81e-18 GO dolichol-linked oligosaccharide biosynthetic process biological_process 2.55e-01 1.87e-43 GO GPI anchor biosynthetic process biological_process 2.52e-01 9.45e-22 GO glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex cellular_component 1.48e-01 1.57e-08 Reactome Synthesis of dolichyl-phosphate mannose Metabolism of proteins 1.07e-01 9.56e-05 Reactome Lipid particle organization Metabolism 8.14e-02 5.90e-32 Reactome Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein Metabolism of proteins 7.85e-02 6.38e-05 Reactome Synthesis of GDP-mannose Metabolism of proteins 4.55e-02 5.12e-03 Reactome Synthesis of dolichyl-phosphate-glucose Metabolism of proteins 3.69e-02 1.30e-09 Reactome Attachment of GPI anchor to uPAR Metabolism of proteins 1.27e-02 1.08e-15 GO integral component of endoplasmic reticulum membrane cellular_component 2.98e-05 5.26e-37 Reactome Post-translational modification: synthesis of GPI-anchored proteins Metabolism of proteins

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 0e+00 0e+00 protein glycosylation 0e+00 0e+00 phosphatidylinositol biosynthetic process 0e+00 0e+00 lipoprotein metabolic process 0e+00 0e+00 phospholipid metabolic process 0e+00 0e+00 lipoprotein biosynthetic process 0e+00 0e+00 glycolipid metabolic process 0e+00 0e+00 membrane lipid metabolic process 0e+00 0e+00 glycosylation 0e+00 0e+00 glycerolipid metabolic process 0e+00 0e+00 mannosylation 0e+00 0e+00 preassembly of GPI anchor in ER membrane 0e+00 0e+00 glycoprotein biosynthetic process 0e+00 0e+00 protein lipidation 0e+00 0e+00 lipid biosynthetic process 0e+00 0e+00 phospholipid biosynthetic process 0e+00 0e+00 glycolipid biosynthetic process 0e+00 0e+00 phosphatidylinositol metabolic process 0e+00 0e+00 glycerophospholipid metabolic process 0e+00 0e+00 macromolecule glycosylation 0e+00 0e+00 GPI anchor metabolic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 ASPARAGINE N LINKED GLYCOSYLATION 0e+00 0e+00 POST TRANSLATIONAL PROTEIN MODIFICATION 0e+00 0e+00 SYNTHESIS OF SUBSTRATES IN N GLYCAN BIOSYTHESIS 0e+00 0e+00 BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN 0e+00 0e+00 SYNTHESIS OF GLYCOSYLPHOSPHATIDYLINOSITOL GPI 0e+00 0e+00 POST TRANSLATIONAL MODIFICATION SYNTHESIS OF GPI ANCHORED PROTEINS 0e+00 0e+00 ASPARAGINE N LINKED GLYCOSYLATION 0e+00 0e+00 POST TRANSLATIONAL PROTEIN MODIFICATION 0e+00 0e+00 SYNTHESIS OF SUBSTRATES IN N GLYCAN BIOSYTHESIS 0e+00 0e+00 BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN 0e+00 0e+00 SYNTHESIS OF GLYCOSYLPHOSPHATIDYLINOSITOL GPI 0e+00 0e+00 POST TRANSLATIONAL MODIFICATION SYNTHESIS OF GPI ANCHORED PROTEINS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.75e-03 1e+00 increased circulating chloride level 3.75e-03 1e+00 forebrain hypoplasia 3.77e-03 1e+00 abnormal craniofacial bone morphology 7.47e-03 1e+00 coloboma 7.51e-03 1e+00 abnormal cartilage development 7.54e-03 1e+00 abnormal visceral yolk sac morphology 1.12e-02 1e+00 abnormal left-right axis patterning 1.13e-02 1e+00 incomplete embryo turning 1.14e-02 1e+00 abnormal cranium morphology 1.49e-02 1e+00 increased circulating iron level 1.49e-02 1e+00 abnormal plasma membrane morphology 1.51e-02 1e+00 microphthalmia 1.88e-02 1e+00 abnormal brain development 2.23e-02 1e+00 abnormal gastrulation 3.35e-02 1e+00 increased circulating alkaline phosphatase level 3.40e-02 1e+00 complete preweaning lethality 3.76e-02 1e+00 decreased circulating glucose level 4.40e-02 1e+00 failure of blastocyst to hatch from the zona pellucida 4.77e-02 1e+00 increased rib number

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

²FDR corrected p-value (Benjamini-Hochberg)