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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod295

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod295 Module size 39 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 154467 CCDC167 coiled-coil domain containing 167 54535 CCHCR1 coiled-coil alpha-helical rod protein 1 1356 CP ceruloplasmin 221154 EFHA1 mitochondrial calcium uptake 2 2172 FABP6 fatty acid binding protein 6 57817 HAMP hepcidin antimicrobial peptide 90550 MCU mitochondrial calcium uniporter 196410 METTL7B methyltransferase like 7B 10367 MICU1 mitochondrial calcium uptake 1 10577 NPC2 NPC intracellular cholesterol transporter 2 5097 PCDH1 protocadherin 1 79849 PDZD3 PDZ domain containing 3 6038 RNASE4 ribonuclease A family member 4 6554 SLC10A1 solute carrier family 10 member 1 6555 SLC10A2 solute carrier family 10 member 2 8273 SLC10A3 solute carrier family 10 member 3 201780 SLC10A4 solute carrier family 10 member 4 347051 SLC10A5 solute carrier family 10 member 5 345274 SLC10A6 solute carrier family 10 member 6 6581 SLC22A3 solute carrier family 22 member 3 30061 SLC40A1 solute carrier family 40 member 1 54946 SLC41A3 solute carrier family 41 member 3 6579 SLCO1A2 solute carrier organic anion transporter family member 1A2 10599 SLCO1B1 solute carrier organic anion transporter family member 1B1 28234 SLCO1B3 solute carrier organic anion transporter family member 1B3 338821 SLCO1B7 solute carrier organic anion transporter family member 1B7 (putative) 53919 SLCO1C1 solute carrier organic anion transporter family member 1C1 28232 SLCO3A1 solute carrier organic anion transporter family member 3A1 57213 SPRYD7 SPRY domain containing 7 6770 STAR steroidogenic acute regulatory protein 80765 STARD5 StAR related lipid transfer domain containing 5 7051 TGM1 transglutaminase 1 27283 TINAG tubulointerstitial nephritis antigen 55365 TMEM176A transmembrane protein 176A 28959 TMEM176B transmembrane protein 176B 120224 TMEM45B transmembrane protein 45B 79001 VKORC1 vitamin K epoxide reductase complex subunit 1 219654 ZCCHC24 zinc finger CCHC-type containing 24 100506144 ZMYM6NB transmembrane protein 35B

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 2.45e-01 4.92e-27 GO bile acid and bile salt transport biological_process 1.52e-01 3.35e-05 GO uniplex complex cellular_component 9.62e-02 1.27e-11 Reactome Transport of organic anions Transport of small molecules 6.57e-02 4.36e-16 Reactome Recycling of bile acids and salts Metabolism 3.11e-02 3.10e-13 GO sodium-independent organic anion transmembrane transporter activity molecular_function 2.85e-02 5.58e-03 Reactome Metabolism of vitamin K Metabolism 2.52e-02 1.50e-04 GO intracellular cholesterol transport biological_process 1.43e-02 3.77e-08 GO organic anion transport biological_process 1.30e-02 5.58e-06 GO cholesterol transporter activity molecular_function 1.10e-02 3.10e-13 GO sodium-independent organic anion transport 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 lipid transport 0.00e+00 0.00e+00 monocarboxylic acid transport 0.00e+00 0.00e+00 carboxylic acid transport 0.00e+00 0.00e+00 lipid localization 0.00e+00 0.00e+00 anion transport 0.00e+00 0.00e+00 organic anion transport 0.00e+00 0.00e+00 bile acid and bile salt transport 0.00e+00 0.00e+00 lipid transporter activity 0.00e+00 0.00e+00 bile acid transmembrane transporter activity 0.00e+00 0.00e+00 organic anion transmembrane transporter activity 0.00e+00 0.00e+00 monocarboxylic acid transmembrane transporter activity 2.95e-12 2.01e-09 bile acid:sodium symporter activity 7.22e-11 4.46e-08 anion transmembrane transporter activity 2.07e-09 1.48e-06 sodium-independent organic anion transport 3.64e-09 1.77e-06 carboxylic acid transmembrane transporter activity 3.70e-09 1.80e-06 secondary active transmembrane transporter activity 2.78e-08 1.18e-05 organic acid:sodium symporter activity 3.53e-07 1.22e-04 solute:sodium symporter activity 1.33e-06 6.17e-04 metal ion transport 9.79e-06 2.56e-03 symporter 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 RECYCLING OF BILE ACIDS AND SALTS 0.00e+00 0.00e+00 RECYCLING OF BILE ACIDS AND SALTS 4.53e-11 1.28e-08 TRANSPORT OF ORGANIC ANIONS 5.72e-11 2.12e-08 TRANSPORT OF ORGANIC ANIONS 5.89e-11 2.17e-08 BILE ACID AND BILE SALT METABOLISM 3.08e-10 8.00e-08 BILE ACID AND BILE SALT METABOLISM 8.32e-10 2.77e-07 SLC MEDIATED TRANSMEMBRANE TRANSPORT 1.08e-08 2.36e-06 SLC MEDIATED TRANSMEMBRANE TRANSPORT 1.62e-08 4.61e-06 TRANSPORT OF VITAMINS NUCLEOSIDES AND RELATED MOLECULES 3.52e-08 9.61e-06 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 8.49e-08 1.67e-05 TRANSPORT OF VITAMINS NUCLEOSIDES AND RELATED MOLECULES 8.20e-05 1.30e-02 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 1.72e-04 2.07e-02 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 1.18e-03 1.36e-01 IRON UPTAKE AND TRANSPORT 2.16e-03 2.28e-01 METAL ION SLC TRANSPORTERS 2.55e-03 2.62e-01 STEROID HORMONES 4.18e-03 3.95e-01 METABOLISM OF STEROID HORMONES AND VITAMINS A AND D 4.46e-03 3.73e-01 METAL ION SLC TRANSPORTERS 5.35e-03 4.34e-01 STEROID HORMONES 6.28e-03 4.98e-01 METABOLISM OF STEROID HORMONES AND VITAMINS A AND D

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.77e-05 6.96e-02 increased circulating unsaturated transferrin level 8.44e-05 2.03e-01 abnormal brain iron level 1.37e-04 2.80e-01 increased circulating ferritin level 1.66e-04 3.13e-01 hemochromatosis 5.49e-04 6.42e-01 increased spleen iron level 5.94e-04 6.72e-01 abnormal liver physiology 6.17e-04 6.83e-01 abnormal bile salt homeostasis 6.86e-04 7.28e-01 decreased circulating iron level 7.48e-04 7.62e-01 increased liver iron level 1.68e-03 1.00e+00 abnormal iron homeostasis 1.92e-03 1.00e+00 abnormal cerebellar granule layer morphology 2.16e-03 1.00e+00 abnormal lipid homeostasis 3.80e-03 1.00e+00 abnormal circulating protein level 7.48e-03 1.00e+00 small alveolar lamellar bodies 7.49e-03 1.00e+00 pulmonary alveolar proteinosis 7.51e-03 1.00e+00 seminal vesicle hypoplasia 7.51e-03 1.00e+00 abnormal circulating serum albumin level 9.34e-03 1.00e+00 abnormal liver copper level 9.34e-03 1.00e+00 abnormal intestinal iron level 9.34e-03 1.00e+00 abnormal heart iron level

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

²FDR corrected p-value (Benjamini-Hochberg)