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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod288

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod288 Module size 25 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 57194 ATP10A ATPase phospholipid transporting 10A (putative) 23120 ATP10B ATPase phospholipid transporting 10B (putative) 57205 ATP10D ATPase phospholipid transporting 10D (putative) 23250 ATP11A ATPase phospholipid transporting 11A 23200 ATP11B ATPase phospholipid transporting 11B (putative) 286410 ATP11C ATPase phospholipid transporting 11C 10396 ATP8A1 ATPase phospholipid transporting 8A1 51761 ATP8A2 ATPase phospholipid transporting 8A2 5205 ATP8B1 ATPase phospholipid transporting 8B1 57198 ATP8B2 ATPase phospholipid transporting 8B2 148229 ATP8B3 ATPase phospholipid transporting 8B3 79895 ATP8B4 ATPase phospholipid transporting 8B4 (putative) 65258 MPPE1 metallophosphoesterase 1 4948 OCA2 OCA2 melanosomal transmembrane protein 6550 SLC9A3 solute carrier family 9 member A3 84679 SLC9A6 solute carrier family 9 member A7 84679 SLC9A7 solute carrier family 9 member A7 23315 SLC9A8 solute carrier family 9 member A8 285195 SLC9A9 solute carrier family 9 member A9 285335 SLC9C1 solute carrier family 9 member C1 284525 SLC9C2 solute carrier family 9 member C2 (putative) 55002 TMCO3 transmembrane and coiled-coil domains 3 55754 TMEM30A transmembrane protein 30A 161291 TMEM30B transmembrane protein 30B 644444 TMEM30C transmembrane protein 30C, pseudogene

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 5.26e-01 2.70e-39 GO phospholipid-translocating ATPase activity molecular_function 3.54e-01 1.30e-18 GO potassium:proton antiporter activity molecular_function 8.15e-02 1.57e-33 GO phospholipid translocation biological_process 7.79e-02 6.76e-18 GO sodium:proton antiporter activity molecular_function 8.73e-03 4.50e-17 GO sodium ion import across plasma membrane 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 sodium ion import 0.00e+00 0.00e+00 sodium ion import across plasma membrane 0.00e+00 0.00e+00 anion transport 0.00e+00 0.00e+00 lipid transport 0.00e+00 0.00e+00 regulation of membrane lipid distribution 0.00e+00 0.00e+00 phospholipid translocation 0.00e+00 0.00e+00 phospholipid transport 0.00e+00 0.00e+00 lipid localization 0.00e+00 0.00e+00 organic anion transport 0.00e+00 0.00e+00 solute:proton antiporter activity 0.00e+00 0.00e+00 potassium:proton antiporter activity 0.00e+00 0.00e+00 sodium:proton antiporter activity 0.00e+00 0.00e+00 monovalent cation:proton antiporter activity 0.00e+00 0.00e+00 magnesium ion binding 0.00e+00 0.00e+00 phospholipid transporter activity 0.00e+00 0.00e+00 lipid transporter activity 0.00e+00 0.00e+00 ATPase activity, coupled to movement of substances 0.00e+00 0.00e+00 phospholipid-translocating ATPase activity 3.40e-11 2.16e-08 cation:cation antiporter activity 1.25e-10 1.03e-07 import into cell

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 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 7.67e-05 1.22e-02 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 1.11e-04 1.40e-02 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 8.84e-04 1.06e-01 SLC MEDIATED TRANSMEMBRANE TRANSPORT 1.02e-03 1.02e-01 SLC MEDIATED TRANSMEMBRANE TRANSPORT

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.16e-04 2.49e-01 abnormal retinal pigmentation 1.52e-03 1.00e+00 complete preweaning lethality 3.35e-03 1.00e+00 increased circulating bilirubin level 3.74e-03 1.00e+00 chromatolysis 3.75e-03 1.00e+00 nervous 4.05e-03 1.00e+00 increased or absent threshold for auditory brainstem response 5.62e-03 1.00e+00 increased circulating tyrosine level 7.11e-03 1.00e+00 abnormal coat/hair pigmentation 7.49e-03 1.00e+00 pancreas necrosis 7.50e-03 1.00e+00 ocular albinism 9.33e-03 1.00e+00 esophageal epithelium hyperplasia 9.34e-03 1.00e+00 retinal pigment epithelium hyperplasia 9.34e-03 1.00e+00 abnormal blood pH regulation 9.34e-03 1.00e+00 dilated efferent ductules of testis 9.34e-03 1.00e+00 abnormal circulating HDL cholesterol level 9.35e-03 1.00e+00 decreased B-1b cell number 9.35e-03 1.00e+00 enlarged sperm head 9.36e-03 1.00e+00 optic nerve degeneration 9.36e-03 1.00e+00 phenotypic reversion 9.37e-03 1.00e+00 variegated coat color

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

²FDR corrected p-value (Benjamini-Hochberg)