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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod223

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod223 Module size 44 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 84002 B3GNT5 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5 93010 B3GNT7 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7 374907 B3GNT8 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 8 9334 B4GALT5 beta-1,4-galactosyltransferase 5 56913 C1GALT1 core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 29071 C1GALT1C1 C1GALT1 specific chaperone 1 2589 GALNT1 polypeptide N-acetylgalactosaminyltransferase 1 55568 GALNT10 polypeptide N-acetylgalactosaminyltransferase 10 63917 GALNT11 polypeptide N-acetylgalactosaminyltransferase 11 79695 GALNT12 polypeptide N-acetylgalactosaminyltransferase 12 117248 GALNT13 polypeptide N-acetylgalactosaminyltransferase 15 79623 GALNT14 polypeptide N-acetylgalactosaminyltransferase 14 2590 GALNT2 polypeptide N-acetylgalactosaminyltransferase 2 2591 GALNT3 polypeptide N-acetylgalactosaminyltransferase 3 8693 GALNT4 polypeptide N-acetylgalactosaminyltransferase 4 11227 GALNT5 polypeptide N-acetylgalactosaminyltransferase 5 11226 GALNT6 polypeptide N-acetylgalactosaminyltransferase 6 51809 GALNT7 polypeptide N-acetylgalactosaminyltransferase 7 26290 GALNT8 polypeptide N-acetylgalactosaminyltransferase 8 79623 GALNTL2 polypeptide N-acetylgalactosaminyltransferase 14 2650 GCNT1 glucosaminyl (N-acetyl) transferase 1, core 2 9245 GCNT3 glucosaminyl (N-acetyl) transferase 3, mucin type 51301 GCNT4 glucosaminyl (N-acetyl) transferase 4, core 2 4582 MUC1 mucin 1, cell surface associated 10071 MUC12 mucin 12, cell surface associated 56667 MUC13 mucin 13, cell surface associated 143662 MUC15 mucin 15, cell surface associated 94025 MUC16 mucin 16, cell surface associated 140453 MUC17 mucin 17, cell surface associated 283463 MUC19 mucin 19, oligomeric 4583 MUC2 mucin 2, oligomeric mucus/gel-forming 200958 MUC20 mucin 20, cell surface associated 394263 MUC21 mucin 21, cell surface associated 57876 MUC3A mucin 3B, cell surface associated 4585 MUC4 mucin 4, cell surface associated 4586 MUC5AC mucin 5AC, oligomeric mucus/gel-forming 727897 MUC5B mucin 5B, oligomeric mucus/gel-forming 4588 MUC6 mucin 6, oligomeric mucus/gel-forming 4589 MUC7 mucin 7, secreted 118430 MUCL1 mucin like 1 6480 ST6GAL1 ST6 beta-galactoside alpha-2,6-sialyltransferase 1 55808 ST6GALNAC1 ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 10610 ST6GALNAC2 ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 27090 ST6GALNAC4 ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 4

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 2.79e-01 1.90e-103 GO O-glycan processing biological_process 2.10e-01 5.38e-108 Reactome O-linked glycosylation of mucins Metabolism of proteins 1.24e-01 5.43e-31 GO polypeptide N-acetylgalactosaminyltransferase activity molecular_function 1.10e-01 2.75e-45 Reactome Defective GALNT3 causes familial hyperphosphatemic tumoral calcinosis (HFTC) Disease 1.08e-01 2.75e-45 Reactome Defective GALNT12 causes colorectal cancer 1 (CRCS1) Disease 1.06e-01 2.75e-45 Reactome Defective C1GALT1C1 causes Tn polyagglutination syndrome (TNPS) Disease 7.67e-02 2.91e-07 GO alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity molecular_function 6.17e-03 2.39e-08 GO sialyltransferase activity 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 0e+00 0e+00 protein O-linked glycosylation 0e+00 0e+00 glycoprotein biosynthetic process 0e+00 0e+00 glycoprotein metabolic process 0e+00 0e+00 protein glycosylation 0e+00 0e+00 macromolecule glycosylation 0e+00 0e+00 glycosylation 0e+00 0e+00 O-glycan processing 0e+00 0e+00 stimulatory C-type lectin receptor signaling pathway 0e+00 0e+00 immune response-regulating signaling pathway 0e+00 0e+00 positive regulation of innate immune response 0e+00 0e+00 activation of innate immune response 0e+00 0e+00 immune response-activating signal transduction 0e+00 0e+00 immune response-regulating cell surface receptor signaling pathway 0e+00 0e+00 innate immune response-activating signal transduction 0e+00 0e+00 regulation of innate immune response 0e+00 0e+00 immune response-activating cell surface receptor signaling pathway 0e+00 0e+00 positive regulation of immune response 0e+00 0e+00 Golgi membrane 0e+00 0e+00 Golgi lumen 0e+00 0e+00 transferase activity, transferring glycosyl groups

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 TERMINATION OF O GLYCAN BIOSYNTHESIS 0.00e+00 0.00e+00 POST TRANSLATIONAL PROTEIN MODIFICATION 0.00e+00 0.00e+00 O LINKED GLYCOSYLATION OF MUCINS 0.00e+00 0.00e+00 TERMINATION OF O GLYCAN BIOSYNTHESIS 0.00e+00 0.00e+00 POST TRANSLATIONAL PROTEIN MODIFICATION 0.00e+00 0.00e+00 O LINKED GLYCOSYLATION OF MUCINS 1.05e-04 1.62e-02 N GLYCAN ANTENNAE ELONGATION 1.58e-04 2.33e-02 N GLYCAN ANTENNAE ELONGATION IN THE MEDIAL TRANS GOLGI 5.85e-04 6.23e-02 N GLYCAN ANTENNAE ELONGATION 5.96e-04 6.34e-02 N GLYCAN ANTENNAE ELONGATION IN THE MEDIAL TRANS GOLGI 1.27e-03 1.24e-01 KERATAN SULFATE BIOSYNTHESIS 1.36e-03 1.53e-01 KERATAN SULFATE BIOSYNTHESIS 1.46e-03 1.63e-01 KERATAN SULFATE KERATIN METABOLISM 1.64e-03 1.56e-01 KERATAN SULFATE KERATIN METABOLISM 9.53e-03 7.72e-01 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 1.09e-02 7.84e-01 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 2.16e-02 1.00e+00 GLYCOSAMINOGLYCAN METABOLISM 4.72e-02 1.00e+00 GLYCOSAMINOGLYCAN METABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.64e-05 1.15e-01 abnormal intestinal mucosa morphology 1.48e-04 2.93e-01 spinal hemorrhage 2.93e-04 4.42e-01 abnormal intestinal absorption 8.37e-04 8.15e-01 increased neutrophil cell number 1.47e-03 1.00e+00 abnormal leukocyte tethering or rolling 1.57e-03 1.00e+00 abnormal intestinal goblet cell morphology 3.09e-03 1.00e+00 decreased IgA level 3.74e-03 1.00e+00 increased response to stress-induced hyperthermia 3.74e-03 1.00e+00 calcified aorta 3.74e-03 1.00e+00 melena 3.74e-03 1.00e+00 decreased pulmonary ventilation 3.75e-03 1.00e+00 absent spleen marginal zone 3.97e-03 1.00e+00 increased lymphocyte cell number 4.81e-03 1.00e+00 enlarged lymph nodes 5.43e-03 1.00e+00 increased susceptibility to induced colitis 5.61e-03 1.00e+00 calcified skin 5.61e-03 1.00e+00 dilated mitochondria 5.61e-03 1.00e+00 increased macrophage apoptosis 7.47e-03 1.00e+00 decreased interleukin-23 secretion 9.33e-03 1.00e+00 thin zona pellucida

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

²FDR corrected p-value (Benjamini-Hochberg)