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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod169

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod169 Module size 41 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 79841 AGBL2 ATP/GTP binding protein like 2 84871 AGBL4 ATP/GTP binding protein like 4 60509 AGBL5 ATP/GTP binding protein like 5 537 ATP6AP1 ATPase H+ transporting accessory protein 1 92270 ATP6AP1L ATPase H+ transporting accessory protein 1 like 10159 ATP6AP2 ATPase H+ transporting accessory protein 2 535 ATP6V0A1 ATPase H+ transporting V0 subunit a1 23545 ATP6V0A2 ATPase H+ transporting V0 subunit a2 50617 ATP6V0A4 ATPase H+ transporting V0 subunit a4 533 ATP6V0B ATPase H+ transporting V0 subunit b 527 ATP6V0C ATPase H+ transporting V0 subunit c 9114 ATP6V0D1 ATPase H+ transporting V0 subunit d1 245972 ATP6V0D2 ATPase H+ transporting V0 subunit d2 8992 ATP6V0E1 ATPase H+ transporting V0 subunit e1 155066 ATP6V0E2 ATPase H+ transporting V0 subunit e2 523 ATP6V1A ATPase H+ transporting V1 subunit A 525 ATP6V1B1 ATPase H+ transporting V1 subunit B1 526 ATP6V1B2 ATPase H+ transporting V1 subunit B2 528 ATP6V1C1 ATPase H+ transporting V1 subunit C1 245973 ATP6V1C2 ATPase H+ transporting V1 subunit C2 51382 ATP6V1D ATPase H+ transporting V1 subunit D 529 ATP6V1E1 ATPase H+ transporting V1 subunit E1 90423 ATP6V1E2 ATPase H+ transporting V1 subunit E2 9296 ATP6V1F ATPase H+ transporting V1 subunit F 9550 ATP6V1G1 ATPase H+ transporting V1 subunit G1 534 ATP6V1G2 ATPase H+ transporting V1 subunit G2 100532737 ATP6V1G2-DDX39B ATP6V1G2-DDX39B readthrough (NMD candidate) 127124 ATP6V1G3 ATPase H+ transporting V1 subunit G3 51606 ATP6V1H ATPase H+ transporting V1 subunit H 1371 CPO coproporphyrinogen oxidase 1657 DMXL1 Dmx like 1 23312 DMXL2 Dmx like 2 90231 KIAA2013 KIAA2013 64077 LHPP phospholysine phosphohistidine inorganic pyrophosphate phosphatase 5464 PPA1 pyrophosphatase (inorganic) 1 27068 PPA2 pyrophosphatase (inorganic) 2 10312 TCIRG1 T cell immune regulator 1, ATPase H+ transporting V0 subunit a3 2152 TF coagulation factor III, tissue factor 7037 TFRC transferrin receptor 201931 TMEM192 transmembrane protein 192 147007 TMEM199 transmembrane protein 199

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 3.18e-01 4.67e-08 GO inorganic diphosphatase activity molecular_function 2.89e-01 5.29e-06 Reactome Pyrophosphate hydrolysis Metabolism 2.37e-01 1.26e-68 Reactome Transferrin endocytosis and recycling Transport of small molecules 2.24e-01 2.96e-65 Reactome Insulin receptor recycling Signal Transduction 1.87e-01 9.29e-35 GO vacuolar proton-transporting V-type ATPase complex cellular_component 1.67e-01 1.57e-53 GO proton-transporting ATPase activity, rotational mechanism molecular_function 9.37e-02 3.70e-31 GO vacuolar acidification biological_process 6.88e-02 1.88e-65 GO transferrin transport biological_process 4.81e-02 1.12e-51 GO ATP hydrolysis coupled proton transport biological_process 4.04e-02 4.96e-07 GO metallocarboxypeptidase activity molecular_function 2.45e-02 2.56e-57 Reactome ROS, RNS production in phagocytes Immune System

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 proton transport 0e+00 0e+00 monovalent inorganic cation transport 0e+00 0e+00 ATP hydrolysis coupled proton transport 0e+00 0e+00 regulation of pH 0e+00 0e+00 cation transmembrane transport 0e+00 0e+00 cellular response to peptide hormone stimulus 0e+00 0e+00 cellular response to organonitrogen compound 0e+00 0e+00 transferrin transport 0e+00 0e+00 ATP hydrolysis coupled transmembrane transport 0e+00 0e+00 hydrogen ion transmembrane transport 0e+00 0e+00 phagosome maturation 0e+00 0e+00 phagosome acidification 0e+00 0e+00 pH reduction 0e+00 0e+00 response to hormone 0e+00 0e+00 response to peptide hormone 0e+00 0e+00 regulation of intracellular pH 0e+00 0e+00 intracellular pH reduction 0e+00 0e+00 regulation of autophagy 0e+00 0e+00 regulation of macroautophagy 0e+00 0e+00 ion homeostasis

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 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 0.00e+00 0.00e+00 TRANSFERRIN ENDOCYTOSIS AND RECYCLING 0.00e+00 0.00e+00 INSULIN RECEPTOR RECYCLING 0.00e+00 0.00e+00 SIGNALING BY INSULIN RECEPTOR 0.00e+00 0.00e+00 LATENT INFECTION OF HOMO SAPIENS WITH MYCOBACTERIUM TUBERCULOSIS 0.00e+00 0.00e+00 IRON UPTAKE AND TRANSPORT 0.00e+00 0.00e+00 TRANSFERRIN ENDOCYTOSIS AND RECYCLING 0.00e+00 0.00e+00 INSULIN RECEPTOR RECYCLING 0.00e+00 0.00e+00 SIGNALING BY INSULIN RECEPTOR 0.00e+00 0.00e+00 LATENT INFECTION OF HOMO SAPIENS WITH MYCOBACTERIUM TUBERCULOSIS 0.00e+00 0.00e+00 IRON UPTAKE AND TRANSPORT 2.37e-03 2.16e-01 TRNA AMINOACYLATION 5.48e-03 4.93e-01 TRNA AMINOACYLATION 3.30e-02 1.00e+00 MITOCHONDRIAL TRNA AMINOACYLATION 3.84e-02 1.00e+00 CYTOSOLIC TRNA AMINOACYLATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.26e-04 4.72e-01 acidosis 7.75e-04 7.76e-01 abnormal iron homeostasis 1.24e-03 1.00e+00 osteopetrosis 1.34e-03 1.00e+00 decreased mean corpuscular volume 2.59e-03 1.00e+00 abnormal osteoclast morphology 5.42e-03 1.00e+00 circling 5.61e-03 1.00e+00 abnormal pH regulation 5.62e-03 1.00e+00 dilated scala media 5.64e-03 1.00e+00 failure of secondary bone resorption 7.48e-03 1.00e+00 decreased liver iron level 7.49e-03 1.00e+00 decreased vitamin D level 7.50e-03 1.00e+00 abnormal response to novel odor 9.33e-03 1.00e+00 abnormal intestinal mineral absorption 9.33e-03 1.00e+00 abnormal renal transport 9.34e-03 1.00e+00 cystolithiasis 9.36e-03 1.00e+00 clubfoot 1.12e-02 1.00e+00 delayed tooth eruption 1.12e-02 1.00e+00 hypochromic microcytic anemia 1.12e-02 1.00e+00 spherocytosis 1.31e-02 1.00e+00 decreased circulating bicarbonate level

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

²FDR corrected p-value (Benjamini-Hochberg)