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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod292

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod292 Module size 22 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 479 ATP12A ATPase H+/K+ transporting non-gastric alpha2 subunit 57130 ATP13A1 ATPase 13A1 487 ATP2A1 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1 488 ATP2A2 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 489 ATP2A3 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3 490 ATP2B1 ATPase plasma membrane Ca2+ transporting 1 491 ATP2B2 ATPase plasma membrane Ca2+ transporting 2 492 ATP2B3 ATPase plasma membrane Ca2+ transporting 3 493 ATP2B4 ATPase plasma membrane Ca2+ transporting 4 27032 ATP2C1 ATPase secretory pathway Ca2+ transporting 1 9914 ATP2C2 ATPase secretory pathway Ca2+ transporting 2 495 ATP4A ATPase H+/K+ transporting subunit alpha 496 ATP4B ATPase H+/K+ transporting subunit beta 152078 C3orf55 PQ loop repeat containing 2 like 54097 FAM3B family with sequence similarity 3 member B 93210 PGAP3 post-GPI attachment to proteins 3 5350 PLN phospholamban 54896 PQLC2 PQ loop repeat containing 2 80024 SLC24A6 solute carrier family 8 member B1 55334 SLC39A9 solute carrier family 39 member 9 6547 SLC8A3 solute carrier family 8 member A3 6588 SLN sarcolipin

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 4.29e-01 2.58e-27 GO calcium-transporting ATPase activity molecular_function 2.37e-01 1.81e-23 Reactome Reduction of cytosolic Ca++ levels Hemostasis 5.06e-02 2.09e-30 Reactome Ion transport by P-type ATPases Transport of small molecules 4.81e-02 6.62e-27 GO ATP hydrolysis coupled cation transmembrane transport biological_process 2.46e-02 3.26e-07 GO sodium:potassium-exchanging ATPase activity molecular_function 1.40e-02 4.15e-07 GO cellular potassium ion homeostasis 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 calcium ion transport 0.00e+00 0.00e+00 metal ion transport 0.00e+00 0.00e+00 divalent metal ion transport 0.00e+00 0.00e+00 cation transmembrane transport 0.00e+00 0.00e+00 ATP hydrolysis coupled transmembrane transport 0.00e+00 0.00e+00 regulation of cardiac conduction 0.00e+00 0.00e+00 ATP hydrolysis coupled cation transmembrane transport 0.00e+00 0.00e+00 calcium ion transmembrane transport 0.00e+00 0.00e+00 ATPase coupled ion transmembrane transporter activity 0.00e+00 0.00e+00 ATPase activity, coupled to transmembrane movement of substances 0.00e+00 0.00e+00 ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism 0.00e+00 0.00e+00 cation-transporting ATPase activity 0.00e+00 0.00e+00 calcium-transporting ATPase activity 0.00e+00 0.00e+00 ATPase activity, coupled 0.00e+00 0.00e+00 ATPase activity, coupled to movement of substances 0.00e+00 0.00e+00 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances 2.89e-11 2.52e-08 ion homeostasis 4.53e-11 3.89e-08 cellular calcium ion homeostasis 7.43e-11 6.25e-08 calcium ion homeostasis 7.91e-11 4.87e-08 ATPase 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 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 0.00e+00 0.00e+00 PLATELET CALCIUM HOMEOSTASIS 0.00e+00 0.00e+00 ION CHANNEL TRANSPORT 0.00e+00 0.00e+00 ION TRANSPORT BY P TYPE ATPASES 0.00e+00 0.00e+00 ION CHANNEL TRANSPORT 0.00e+00 0.00e+00 ION TRANSPORT BY P TYPE ATPASES 1.73e-12 5.11e-10 PLATELET CALCIUM HOMEOSTASIS 1.21e-09 2.92e-07 PLATELET HOMEOSTASIS 1.85e-09 5.90e-07 PLATELET HOMEOSTASIS 8.36e-06 1.26e-03 PRE NOTCH PROCESSING IN GOLGI 1.13e-05 2.14e-03 PRE NOTCH PROCESSING IN GOLGI 5.62e-05 9.29e-03 PRE NOTCH EXPRESSION AND PROCESSING 5.80e-05 7.71e-03 PRE NOTCH EXPRESSION AND PROCESSING 3.51e-04 3.95e-02 SIGNALING BY NOTCH 7.57e-04 9.21e-02 SIGNALING BY NOTCH 2.24e-02 1.00e+00 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 4.44e-02 1.00e+00 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.73e-05 6.94e-02 increased esophageal papilloma incidence 9.01e-05 2.12e-01 abnormal gastric gland morphology 9.02e-05 2.12e-01 increased circulating gastrin level 1.43e-04 2.88e-01 fatigue 2.48e-04 3.97e-01 increased stomach pH 3.85e-04 5.21e-01 abnormal gastric chief cell morphology 6.05e-04 6.78e-01 increased skin papilloma incidence 7.38e-04 7.59e-01 increased squamous cell carcinoma incidence 8.72e-04 8.34e-01 abnormal gastric parietal cell morphology 1.75e-03 1.00e+00 abnormal calcium ion homeostasis 1.88e-03 1.00e+00 decreased threshold for auditory brainstem response 5.61e-03 1.00e+00 esophageal epithelium hyperplasia 5.62e-03 1.00e+00 ascending aorta hypoplasia 5.62e-03 1.00e+00 gastric cysts 5.62e-03 1.00e+00 decreased organ of Corti supporting cell number 5.63e-03 1.00e+00 increased Purkinje cell number 5.64e-03 1.00e+00 abnormal Golgi apparatus morphology 5.64e-03 1.00e+00 vestibular saccular degeneration 5.64e-03 1.00e+00 absent pillar cells 7.49e-03 1.00e+00 gastric metaplasia

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

²FDR corrected p-value (Benjamini-Hochberg)