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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod22

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod22 Module size 42 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 24184 ADK adenylate kinase 2 158 ADSL adenylosuccinate lyase 270 AMPD1 adenosine monophosphate deaminase 1 271 AMPD2 adenosine monophosphate deaminase 2 272 AMPD3 adenosine monophosphate deaminase 3 353 APRT adenine phosphoribosyltransferase 124583 CANT1 calcium activated nucleotidase 1 978 CDA cytidine deaminase 129607 CMPK2 cytidine/uridine monophosphate kinase 2 1633 DCK deoxycytidine kinase 953 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 956 ENTPD3 ectonucleoside triphosphate diphosphohydrolase 3 9583 ENTPD4 ectonucleoside triphosphate diphosphohydrolase 4 957 ENTPD5 ectonucleoside triphosphate diphosphohydrolase 5 955 ENTPD6 ectonucleoside triphosphate diphosphohydrolase 6 (putative) 377841 ENTPD8 ectonucleoside triphosphate diphosphohydrolase 8 2766 GMPR guanosine monophosphate reductase 51292 GMPR2 guanosine monophosphate reductase 2 3251 HPRT1 hypoxanthine phosphoribosyltransferase 1 3704 ITPA inosine triphosphatase 100360582 NT5C 5', 3'-nucleotidase, cytosolic 84618 NT5C1A 5'-nucleotidase, cytosolic IA 100526794 NT5C1B-RDH14 NT5C1B-RDH14 readthrough 22978 NT5C2 5'-nucleotidase, cytosolic II 51251 NT5C3 5'-nucleotidase, cytosolic IIIA 4907 NT5E 5'-nucleotidase ecto 56953 NT5M 5',3'-nucleotidase, mitochondrial 131870 NUDT16 nudix hydrolase 16 5136 PDE1A phosphodiesterase 1A 5153 PDE1B phosphodiesterase 1B 5137 PDE1C phosphodiesterase 1C 5139 PDE3A phosphodiesterase 3A 5147 PDE6D phosphodiesterase 6D 5151 PDE8A phosphodiesterase 8A 5539 PNP pancreatic polypeptide 9154 SLC28A1 solute carrier family 28 member 1 9153 SLC28A2 solute carrier family 28 member 2 64078 SLC28A3 solute carrier family 28 member 3 1890 TYMP thymidine phosphorylase 7371 UCK2 uridine-cytidine kinase 2 7378 UPP1 uridine phosphorylase 1 151531 UPP2 uridine phosphorylase 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 6.15e-01 1.26e-08 Reactome Cam-PDE 1 activation Signal Transduction 2.88e-01 1.21e-35 Reactome Nucleotide salvage Metabolism 2.03e-01 3.52e-15 GO nucleoside-diphosphatase activity molecular_function 2.03e-01 3.52e-15 Reactome Phosphate bond hydrolysis by NTPDase proteins Metabolism 1.57e-01 8.43e-17 GO pyrimidine nucleoside catabolic process biological_process 1.50e-01 4.62e-37 Reactome Nucleobase catabolism Metabolism 1.37e-01 3.74e-13 GO 5'-nucleotidase activity molecular_function 1.36e-01 5.19e-25 GO purine-containing compound salvage biological_process 1.34e-01 5.19e-25 Reactome Purine salvage Metabolism 1.14e-01 1.26e-08 GO AMP deaminase activity molecular_function 1.11e-01 4.39e-07 GO nucleoside transmembrane transporter activity molecular_function 1.11e-01 4.39e-07 Reactome Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane Transport of small molecules 4.21e-02 3.74e-08 GO 3',5'-cyclic-AMP phosphodiesterase activity molecular_function 2.92e-02 7.14e-03 Reactome ARL13B-mediated ciliary trafficking of INPP5E Organelle biogenesis and maintenance 1.77e-02 1.30e-57 Reactome Metabolism of nucleotides Metabolism 7.20e-03 1.06e-07 GO 3',5'-cyclic-GMP phosphodiesterase activity molecular_function 8.60e-04 2.14e-13 GO purine nucleotide catabolic 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 0e+00 0e+00 purine nucleotide metabolic process 0e+00 0e+00 nucleobase-containing small molecule metabolic process 0e+00 0e+00 ribonucleotide metabolic process 0e+00 0e+00 nucleoside metabolic process 0e+00 0e+00 purine-containing compound salvage 0e+00 0e+00 purine nucleoside metabolic process 0e+00 0e+00 purine-containing compound biosynthetic process 0e+00 0e+00 glycosyl compound metabolic process 0e+00 0e+00 nucleotide metabolic process 0e+00 0e+00 ribonucleoside monophosphate biosynthetic process 0e+00 0e+00 nucleotide biosynthetic process 0e+00 0e+00 purine nucleotide salvage 0e+00 0e+00 nucleoside monophosphate biosynthetic process 0e+00 0e+00 nucleoside phosphate catabolic process 0e+00 0e+00 aromatic compound catabolic process 0e+00 0e+00 nucleotide catabolic process 0e+00 0e+00 purine ribonucleotide catabolic process 0e+00 0e+00 purine nucleotide catabolic process 0e+00 0e+00 organophosphate catabolic process 0e+00 0e+00 pyrimidine 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 PURINE METABOLISM 0.00e+00 0.00e+00 PURINE SALVAGE 0.00e+00 0.00e+00 PYRIMIDINE CATABOLISM 0.00e+00 0.00e+00 PYRIMIDINE METABOLISM 0.00e+00 0.00e+00 METABOLISM OF NUCLEOTIDES 0.00e+00 0.00e+00 PURINE METABOLISM 0.00e+00 0.00e+00 PURINE SALVAGE 0.00e+00 0.00e+00 PYRIMIDINE CATABOLISM 0.00e+00 0.00e+00 PYRIMIDINE METABOLISM 4.30e-09 1.31e-06 PURINE CATABOLISM 8.71e-09 1.92e-06 PURINE CATABOLISM 2.32e-04 3.27e-02 CGMP EFFECTS 2.99e-04 3.42e-02 CGMP EFFECTS 4.62e-04 6.01e-02 NITRIC OXIDE STIMULATES GUANYLATE CYCLASE 6.56e-04 6.89e-02 TRANSPORT OF VITAMINS NUCLEOSIDES AND RELATED MOLECULES 6.84e-04 7.17e-02 NITRIC OXIDE STIMULATES GUANYLATE CYCLASE 1.64e-03 1.80e-01 TRANSPORT OF VITAMINS NUCLEOSIDES AND RELATED MOLECULES 3.61e-03 3.12e-01 G ALPHA S SIGNALLING EVENTS 4.42e-03 4.13e-01 CA DEPENDENT EVENTS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.67e-08 5.16e-04 abnormal nucleotide metabolism 1.68e-04 3.15e-01 abnormal enzyme/coenzyme level 5.47e-04 6.42e-01 renal fibrosis 1.30e-03 1.00e+00 podocyte foot process effacement 4.30e-03 1.00e+00 abnormal vascular endothelial cell physiology 5.62e-03 1.00e+00 absent Z lines 7.49e-03 1.00e+00 increased effector memory CD8-positive, alpha-beta T cell number 7.83e-03 1.00e+00 decreased circulating serum albumin level 8.89e-03 1.00e+00 abnormal platelet physiology 9.33e-03 1.00e+00 nephrolithiasis 9.33e-03 1.00e+00 spleen fibrosis 9.35e-03 1.00e+00 increased effector memory CD4-positive, alpha-beta T cell number 9.36e-03 1.00e+00 pyelonephritis 9.37e-03 1.00e+00 phenotypic reversion 9.79e-03 1.00e+00 decreased B cell number 1.12e-02 1.00e+00 increased aggression toward humans 1.12e-02 1.00e+00 decreased coronary flow rate 1.12e-02 1.00e+00 abnormal habituation to a new environment 1.12e-02 1.00e+00 absent spleen white pulp 1.18e-02 1.00e+00 increased urine protein level

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

²FDR corrected p-value (Benjamini-Hochberg)