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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod337

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod337 Module size 40 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 203 AK1 adenylate kinase 1 204 AK2 adenylate kinase 2 50808 AK3 adenylate kinase 3 205 AK4 adenylate kinase 4 26289 AK5 adenylate kinase 5 122481 AK7 adenylate kinase 7 158067 AK8 adenylate kinase 8 51727 CMPK1 cytidine/uridine monophosphate kinase 1 146223 CMTM4 CKLF like MARVEL transmembrane domain containing 4 1503 CTPS1 CTP synthase 1 56474 CTPS2 CTP synthase 2 58511 DNASE2B deoxyribonuclease 2 beta 954 ENTPD2 ectonucleoside triphosphate diphosphohydrolase 2 27349 MCAT malonyl-CoA-acyl carrier protein transacylase 4830 NME1 NME/NM23 nucleoside diphosphate kinase 1 654364 NME1-NME2 NME1-NME2 readthrough 4831 NME2 NME/NM23 nucleoside diphosphate kinase 2 4832 NME3 NME/NM23 nucleoside diphosphate kinase 3 4833 NME4 NME/NM23 nucleoside diphosphate kinase 4 8382 NME5 NME/NM23 family member 5 10201 NME6 NME/NM23 nucleoside diphosphate kinase 6 29922 NME7 NME/NM23 family member 7 347736 NME9 NME/NM23 family member 9 84284 NTPCR nucleoside-triphosphatase, cancer-related 87178 PNPT1 polyribonucleotide nucleotidyltransferase 1 9533 POLR1C RNA polymerase I and III subunit C 83480 PUS3 pseudouridylate synthase 3 126789 PUSL1 pseudouridylate synthase like 1 29927 SEC61A1 Sec61 translocon alpha 1 subunit 55176 SEC61A2 Sec61 translocon alpha 2 subunit 84193 SETD3 SET domain containing 3 54093 SETD4 SET domain containing 4 6723 SRM spermidine synthase 79188 TMEM43 transmembrane protein 43 79799 UGT2A3 UDP glucuronosyltransferase family 2 member A3 7365 UGT2B10 UDP glucuronosyltransferase family 2 member B10 7366 UGT2B15 UDP glucuronosyltransferase family 2 member B15 54490 UGT2B28 UDP glucuronosyltransferase family 2 member B28 133688 UGT3A1 UDP glycosyltransferase family 3 member A1 167127 UGT3A2 UDP glycosyltransferase family 3 member A2

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 3.54e-01 4.55e-24 GO CTP biosynthetic process biological_process 3.12e-01 2.95e-36 GO nucleoside diphosphate phosphorylation biological_process 2.98e-01 5.18e-18 GO adenylate kinase activity molecular_function 1.28e-01 7.36e-30 GO nucleobase-containing small molecule interconversion biological_process 1.06e-01 5.64e-12 GO UDP-glycosyltransferase activity molecular_function 4.97e-02 1.01e-11 Reactome Glucuronidation Metabolism 4.37e-02 1.70e-04 GO posttranslational protein targeting to endoplasmic reticulum membrane biological_process 3.14e-02 2.12e-04 GO peptidyl-lysine monomethylation biological_process 3.14e-02 2.12e-04 GO nucleoside-triphosphatase activity molecular_function 3.14e-02 2.12e-04 GO pseudouridine synthase activity molecular_function 8.03e-03 3.57e-30 GO nucleoside diphosphate kinase activity molecular_function 2.08e-03 3.33e-19 GO nucleoside monophosphate phosphorylation 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 0e+00 0e+00 nucleotide phosphorylation 0e+00 0e+00 purine nucleotide metabolic process 0e+00 0e+00 nucleobase-containing small molecule metabolic process 0e+00 0e+00 purine nucleotide biosynthetic process 0e+00 0e+00 pyrimidine ribonucleotide biosynthetic process 0e+00 0e+00 nucleotide biosynthetic process 0e+00 0e+00 nucleoside diphosphate metabolic process 0e+00 0e+00 nucleoside triphosphate biosynthetic process 0e+00 0e+00 ribonucleotide metabolic process 0e+00 0e+00 pyrimidine nucleotide metabolic process 0e+00 0e+00 nucleoside diphosphate phosphorylation 0e+00 0e+00 pyrimidine nucleotide biosynthetic process 0e+00 0e+00 nucleotide metabolic process 0e+00 0e+00 nucleobase-containing small molecule interconversion 0e+00 0e+00 purine-containing compound biosynthetic process 0e+00 0e+00 ribose phosphate biosynthetic process 0e+00 0e+00 CTP biosynthetic process 0e+00 0e+00 GTP biosynthetic process 0e+00 0e+00 GTP metabolic process 0e+00 0e+00 nucleoside metabolic process

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 METABOLISM OF NUCLEOTIDES 0.00e+00 0.00e+00 SYNTHESIS AND INTERCONVERSION OF NUCLEOTIDE DI AND TRIPHOSPHATES 0.00e+00 0.00e+00 METABOLISM OF NUCLEOTIDES 0.00e+00 0.00e+00 SYNTHESIS AND INTERCONVERSION OF NUCLEOTIDE DI AND TRIPHOSPHATES 2.57e-04 2.98e-02 ER PHAGOSOME PATHWAY 5.12e-04 5.54e-02 GLUCURONIDATION 1.08e-03 1.26e-01 ER PHAGOSOME PATHWAY 1.14e-03 1.13e-01 ANTIGEN PROCESSING CROSS PRESENTATION 4.68e-03 4.33e-01 ANTIGEN PROCESSING CROSS PRESENTATION 5.46e-03 4.91e-01 GLUCURONIDATION 1.23e-02 8.72e-01 PHASE II CONJUGATION 2.12e-02 1.00e+00 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE 2.16e-02 1.00e+00 RNA POL III CHAIN ELONGATION 2.16e-02 1.00e+00 RNA POL III TRANSCRIPTION 2.16e-02 1.00e+00 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 2 PROMOTER 2.16e-02 1.00e+00 RNA POL III TRANSCRIPTION TERMINATION 2.16e-02 1.00e+00 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 3 PROMOTER 2.45e-02 1.00e+00 RNA POL I TRANSCRIPTION TERMINATION 2.51e-02 1.00e+00 RNA POL I TRANSCRIPTION TERMINATION 2.69e-02 1.00e+00 RNA POL I TRANSCRIPTION INITIATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.41e-06 1.69e-02 hydroencephaly 3.23e-05 1.07e-01 abnormal internal nares morphology 4.84e-05 1.39e-01 impaired mucociliary clearance 2.86e-04 4.38e-01 abnormal respiratory motile cilium physiology 5.72e-04 6.58e-01 domed cranium 6.92e-04 7.31e-01 dilated lateral ventricles 1.87e-03 1.00e+00 abnormal pancreatic delta cell morphology 3.74e-03 1.00e+00 liver cirrhosis 3.74e-03 1.00e+00 increased pancreatic delta cell number 6.91e-03 1.00e+00 arrest of spermatogenesis 7.47e-03 1.00e+00 abnormal maxillary sinus morphology 7.48e-03 1.00e+00 rhinitis 9.33e-03 1.00e+00 abnormal tricarboxylic acid cycle 9.33e-03 1.00e+00 abnormal gustatory papillae taste bud morphology 9.34e-03 1.00e+00 abnormal pancreatic islet cell apoptosis 1.12e-02 1.00e+00 increased pancreatic alpha cell number 1.17e-02 1.00e+00 abnormal glucose homeostasis 1.31e-02 1.00e+00 abnormal head shape 1.31e-02 1.00e+00 intraventricular hemorrhage 1.49e-02 1.00e+00 increased circulating glucagon level

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

²FDR corrected p-value (Benjamini-Hochberg)