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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod122

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod122 Module size 37 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10678 B3GNT2 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2 10331 B3GNT3 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3 79369 B3GNT4 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4 647024 C6orf132 chromosome 6 open reading frame 132 151887 CCDC80 coiled-coil domain containing 80 81494 CFHR5 complement factor H related 5 8534 CHST1 carbohydrate sulfotransferase 1 9435 CHST2 carbohydrate sulfotransferase 2 23563 CHST5 carbohydrate sulfotransferase 5 4166 CHST6 carbohydrate sulfotransferase 6 57452 GALNTL1 polypeptide N-acetylgalactosaminyltransferase 16 374378 GALNTL4 polypeptide N-acetylgalactosaminyltransferase 18 168391 GALNTL5 polypeptide N-acetylgalactosaminyltransferase like 5 442117 GALNTL6 polypeptide N-acetylgalactosaminyltransferase like 6 3346 HTN1 histatin 1 3347 HTN3 histatin 3 4065 LY75 lymphocyte antigen 75 100526664 LY75-CD302 LY75-CD302 readthrough 9842 PLEKHM1 pleckstrin homology and RUN domain containing M1 100528030 POC1B-GALNT4 POC1B-GALNT4 readthrough 5554 PRH1 proline rich protein HaeIII subfamily 1 58503 PROL1 opiorphin prepropeptide 11272 PRR4 proline rich 4 10559 SLC35A1 solute carrier family 35 member A1 6482 ST3GAL1 ST3 beta-galactoside alpha-2,3-sialyltransferase 1 6483 ST3GAL2 ST3 beta-galactoside alpha-2,3-sialyltransferase 2 6487 ST3GAL3 ST3 beta-galactoside alpha-2,3-sialyltransferase 3 6484 ST3GAL4 ST3 beta-galactoside alpha-2,3-sialyltransferase 4 256435 ST6GALNAC3 ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 81849 ST6GALNAC5 ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5 30815 ST6GALNAC6 ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 6 51046 ST8SIA3 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3 7903 ST8SIA4 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4 29906 ST8SIA5 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5 6779 STATH statherin 64409 WBSCR17 polypeptide N-acetylgalactosaminyltransferase 17 10406 WFDC2 WAP four-disulfide core domain 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 2.38e-01 2.64e-10 GO N-acetylglucosamine 6-O-sulfotransferase activity molecular_function 1.26e-01 6.64e-21 GO sialylation biological_process 9.76e-02 1.20e-24 GO keratan sulfate biosynthetic process biological_process 9.55e-02 1.20e-24 Reactome Keratan sulfate biosynthesis Metabolism 8.97e-02 1.08e-23 Reactome Sialic acid metabolism Metabolism of proteins 7.19e-02 9.47e-10 GO ganglioside biosynthetic process biological_process 4.98e-02 9.58e-08 GO alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity molecular_function 4.53e-02 1.13e-10 GO beta-galactoside (CMP) alpha-2,3-sialyltransferase activity molecular_function 3.18e-02 9.58e-08 GO alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity molecular_function 1.93e-02 5.72e-07 GO N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity molecular_function 1.89e-02 9.73e-18 Reactome O-linked glycosylation of mucins Metabolism of proteins 1.33e-02 4.01e-07 GO glycosphingolipid biosynthetic process biological_process 7.19e-03 1.53e-05 GO biomineral tissue development biological_process 3.48e-03 7.86e-07 GO glycoprotein metabolic process biological_process 1.79e-03 1.80e-16 GO protein glycosylation biological_process 1.51e-04 7.48e-09 GO oligosaccharide biosynthetic process 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 glycoprotein biosynthetic process 0.00e+00 0.00e+00 glycoprotein metabolic process 0.00e+00 0.00e+00 protein glycosylation 0.00e+00 0.00e+00 macromolecule glycosylation 0.00e+00 0.00e+00 glycosylation 0.00e+00 0.00e+00 keratan sulfate metabolic process 0.00e+00 0.00e+00 carbohydrate metabolic process 0.00e+00 0.00e+00 glycosaminoglycan biosynthetic process 0.00e+00 0.00e+00 keratan sulfate biosynthetic process 0.00e+00 0.00e+00 glycosaminoglycan metabolic process 0.00e+00 0.00e+00 oligosaccharide metabolic process 0.00e+00 0.00e+00 sialylation 0.00e+00 0.00e+00 Golgi membrane 0.00e+00 0.00e+00 intrinsic component of Golgi membrane 0.00e+00 0.00e+00 transferase activity, transferring glycosyl groups 0.00e+00 0.00e+00 sialyltransferase activity 9.98e-12 8.98e-09 protein N-linked glycosylation via asparagine 7.41e-11 3.88e-08 integral component of Golgi membrane 4.40e-10 3.42e-07 protein N-linked glycosylation 4.41e-10 3.42e-07 O-glycan processing

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 POST TRANSLATIONAL PROTEIN MODIFICATION 0.00e+00 0.00e+00 O LINKED GLYCOSYLATION OF MUCINS 0.00e+00 0.00e+00 KERATAN SULFATE BIOSYNTHESIS 0.00e+00 0.00e+00 GLYCOSAMINOGLYCAN METABOLISM 0.00e+00 0.00e+00 KERATAN SULFATE KERATIN METABOLISM 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 KERATAN SULFATE BIOSYNTHESIS 0.00e+00 0.00e+00 KERATAN SULFATE KERATIN METABOLISM 2.47e-11 7.13e-09 GLYCOSAMINOGLYCAN METABOLISM 1.22e-09 3.99e-07 METABOLISM OF CARBOHYDRATES 4.52e-09 1.02e-06 METABOLISM OF CARBOHYDRATES 1.36e-07 2.60e-05 TERMINATION OF O GLYCAN BIOSYNTHESIS 9.03e-07 2.05e-04 TERMINATION OF O GLYCAN BIOSYNTHESIS 4.63e-02 1.00e+00 N GLYCAN ANTENNAE ELONGATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.41e-04 6.37e-01 abnormal leukocyte migration 1.24e-03 1.00e+00 increased T cell number 3.32e-03 1.00e+00 increased bleeding time 3.76e-03 1.00e+00 abnormal olfactory epithelium morphology 7.48e-03 1.00e+00 increased aggression towards mice 7.48e-03 1.00e+00 enhanced lipolysis 7.50e-03 1.00e+00 pancreatic islet hyperplasia 1.12e-02 1.00e+00 increased spleen germinal center size 1.30e-02 1.00e+00 decreased corneal stroma thickness 1.30e-02 1.00e+00 decreased cornea thickness 1.31e-02 1.00e+00 increased interleukin-1 beta secretion 1.49e-02 1.00e+00 abnormal corneal stroma morphology 1.68e-02 1.00e+00 abnormal olfaction 1.69e-02 1.00e+00 increased susceptibility to weight gain 1.88e-02 1.00e+00 increased food intake 2.05e-02 1.00e+00 increased insulin secretion 2.24e-02 1.00e+00 reduced long term depression 2.25e-02 1.00e+00 increased neuron apoptosis 2.42e-02 1.00e+00 abnormal leukocyte tethering or rolling 2.42e-02 1.00e+00 abnormal CD8-positive, alpha beta T cell morphology

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

²FDR corrected p-value (Benjamini-Hochberg)