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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod76

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod76 Module size 22 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 8708 B3GALT1 beta-1,3-galactosyltransferase 1 8707 B3GALT2 beta-1,3-galactosyltransferase 2 10317 B3GALT5 beta-1,3-galactosyltransferase 5 10678 B3GNT1 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2 2683 B4GALT1 beta-1,4-galactosyltransferase 1 8704 B4GALT2 beta-1,4-galactosyltransferase 2 8703 B4GALT3 beta-1,4-galactosyltransferase 3 8702 B4GALT4 beta-1,4-galactosyltransferase 4 2523 FUT1 fucosyltransferase 1 (H blood group) 2524 FUT2 fucosyltransferase 2 2525 FUT3 fucosyltransferase 3 (Lewis blood group) 2526 FUT4 fucosyltransferase 4 2527 FUT5 fucosyltransferase 5 2528 FUT6 fucosyltransferase 6 2529 FUT7 fucosyltransferase 7 10690 FUT9 fucosyltransferase 9 2651 GCNT2 glucosaminyl (N-acetyl) transferase 2 (I blood group) 120071 GYLTL1B LARGE xylosyl- and glucuronyltransferase 2 9215 LARGE LARGE xylosyl- and glucuronyltransferase 1 10402 ST3GAL6 ST3 beta-galactoside alpha-2,3-sialyltransferase 6 84620 ST6GAL2 ST6 beta-galactoside alpha-2,6-sialyltransferase 2 6489 ST8SIA1 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1

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 4.64e-01 3.62e-24 GO fucosyltransferase activity molecular_function 2.51e-01 7.46e-11 GO beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity molecular_function 1.67e-01 6.64e-23 GO fucosylation biological_process 1.18e-01 1.86e-12 GO oligosaccharide biosynthetic process biological_process 3.87e-02 4.17e-35 GO protein glycosylation biological_process 2.07e-03 4.15e-07 GO UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase 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 0.00e+00 0.00e+00 protein glycosylation 0.00e+00 0.00e+00 glycosylation 0.00e+00 0.00e+00 glycoprotein biosynthetic process 0.00e+00 0.00e+00 glycoprotein metabolic process 0.00e+00 0.00e+00 macromolecule glycosylation 0.00e+00 0.00e+00 carbohydrate metabolic process 0.00e+00 0.00e+00 fucosylation 0.00e+00 0.00e+00 L-fucose catabolic process 0.00e+00 0.00e+00 fucose metabolic process 0.00e+00 0.00e+00 Golgi cisterna membrane 0.00e+00 0.00e+00 Golgi membrane 0.00e+00 0.00e+00 Golgi cisterna 0.00e+00 0.00e+00 Golgi stack 0.00e+00 0.00e+00 transferase activity, transferring glycosyl groups 0.00e+00 0.00e+00 transferase activity, transferring hexosyl groups 0.00e+00 0.00e+00 UDP-galactosyltransferase activity 0.00e+00 0.00e+00 galactosyltransferase activity 0.00e+00 0.00e+00 fucosyltransferase activity 0.00e+00 0.00e+00 alpha-(1->3)-fucosyltransferase activity 1.35e-11 8.87e-09 N-acetyllactosamine synthase activity

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 KERATAN SULFATE BIOSYNTHESIS 3.08e-12 1.20e-09 KERATAN SULFATE BIOSYNTHESIS 7.76e-12 2.27e-09 KERATAN SULFATE KERATIN METABOLISM 3.22e-11 1.21e-08 KERATAN SULFATE KERATIN METABOLISM 9.69e-09 2.14e-06 GLYCOSAMINOGLYCAN METABOLISM 1.34e-08 3.86e-06 N GLYCAN ANTENNAE ELONGATION 1.49e-08 4.27e-06 GLYCOSAMINOGLYCAN METABOLISM 2.33e-08 6.55e-06 N GLYCAN ANTENNAE ELONGATION IN THE MEDIAL TRANS GOLGI 5.30e-08 1.07e-05 N GLYCAN ANTENNAE ELONGATION 8.47e-08 1.67e-05 METABOLISM OF CARBOHYDRATES 9.40e-08 1.84e-05 N GLYCAN ANTENNAE ELONGATION IN THE MEDIAL TRANS GOLGI 1.76e-07 4.43e-05 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 4.43e-07 1.05e-04 METABOLISM OF CARBOHYDRATES 1.65e-06 2.77e-04 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 1.67e-06 3.61e-04 ASPARAGINE N LINKED GLYCOSYLATION 8.34e-06 1.26e-03 ASPARAGINE N LINKED GLYCOSYLATION 1.89e-05 2.71e-03 POST TRANSLATIONAL PROTEIN MODIFICATION 5.26e-05 8.74e-03 POST TRANSLATIONAL PROTEIN MODIFICATION 4.78e-04 6.18e-02 PRE NOTCH PROCESSING IN GOLGI 1.42e-03 1.37e-01 PRE NOTCH PROCESSING IN GOLGI

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.43e-05 5.98e-02 abnormal leukocyte tethering or rolling 5.88e-05 1.59e-01 impaired neutrophil recruitment 4.02e-03 1.00e+00 abnormal leukocyte physiology 4.05e-03 1.00e+00 decreased susceptibility to type IV hypersensitivity reaction 5.37e-03 1.00e+00 increased circulating creatinine level 5.61e-03 1.00e+00 abnormal nervous system regeneration 5.63e-03 1.00e+00 dystocia 9.37e-03 1.00e+00 disorganized retinal outer plexiform layer 9.37e-03 1.00e+00 vitreal fibroplasia 9.37e-03 1.00e+00 abnormal pulmonary alveolar system morphology 1.12e-02 1.00e+00 abnormal cerebellar lobule formation 1.12e-02 1.00e+00 abnormal granulocyte physiology 1.12e-02 1.00e+00 decreased coping response 1.12e-02 1.00e+00 skeletal muscle endomysial fibrosis 1.12e-02 1.00e+00 disorganized retinal ganglion layer 1.49e-02 1.00e+00 thin retinal outer plexiform layer 1.50e-02 1.00e+00 skeletal muscle fiber degeneration 1.50e-02 1.00e+00 skeletal muscle degeneration 1.50e-02 1.00e+00 abnormal retinal outer plexiform layer morphology 1.50e-02 1.00e+00 vitreous body deposition

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

²FDR corrected p-value (Benjamini-Hochberg)