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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod375

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod375 Module size 69 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 116236 ABHD15 abhydrolase domain containing 15 10965 ACOT2 acyl-CoA thioesterase 2 53 ACP2 acid phosphatase 2, lysosomal 81794 ADAMTS10 ADAM metallopeptidase with thrombospondin type 1 motif 10 118 ADD1 adducin 1 119 ADD2 adducin 2 298646 AGTRAP angiotensin II receptor-associated protein 80210 ARMC9 armadillo repeat containing 9 140683 BPIFA2 BPI fold containing family A member 2 10380 BPNT1 3'(2'), 5'-bisphosphate nucleotidase 1 80017 C14orf159 D-glutamate cyclase 27141 CIDEB cell death-inducing DFFA-like effector b 1182 CLCN3 chloride voltage-gated channel 3 1183 CLCN4 chloride voltage-gated channel 4 81037 CLPTM1L CLPTM1 like 23242 COBL cordon-bleu WH2 repeat protein 22837 COBLL1 cordon-bleu WH2 repeat protein like 1 1414 CRYBB1 crystallin beta B1 1525 CXADR CXADR, Ig-like cell adhesion molecule 57628 DPP10 dipeptidyl peptidase like 10 1804 DPP6 dipeptidyl peptidase like 6 54878 DPP8 dipeptidyl peptidase 8 91039 DPP9 dipeptidyl peptidase 9 57488 ESYT2 extended synaptotagmin 2 83723 FAM57B family with sequence similarity 57 member B 1056 FAP carboxyl ester lipase 252995 FNDC5 fibronectin type III domain containing 5 341640 FREM2 FRAS1 related extracellular matrix protein 2 87769 GGACT gamma-glutamylamine cyclotransferase 80318 GKAP1 G kinase anchoring protein 1 2717 GLA galactosidase alpha 283383 GPR133 adhesion G protein-coupled receptor D1 4935 GPR143 G protein-coupled receptor 143 2848 GPR25 G protein-coupled receptor 25 113802 HENMT1 HEN methyltransferase 1 57594 HOMEZ homeobox and leucine zipper encoding 126119 JOSD2 Josephin domain containing 2 57670 KIAA1549 KIAA1549 64175 LEPRE1 prolyl 3-hydroxylase 1 147719 LYPD4 LY6/PLAUR domain containing 4 4163 MCC MCC, WNT signaling pathway regulator 6945 MLX MLX, MAX dimerization protein 51085 MLXIPL MLX interacting protein like 360630 NAGLU N-acetyl-alpha-glucosaminidase 57446 NDRG3 NDRG family member 3 4864 NPC1 NPC intracellular cholesterol transporter 1 8993 PGLYRP1 peptidoglycan recognition protein 1 54858 PGPEP1 pyroglutamyl-peptidase I 9780 PIEZO1 piezo type mechanosensitive ion channel component 1 5955 RCN2 reticulocalbin 2 9805 SCRN1 secernin 1 10955 SERINC3 serine incorporator 3 83699 SH3BGRL2 SH3 domain binding glutamate rich protein like 2 83442 SH3BGRL3 SH3 domain binding glutamate rich protein like 3 6566 SLC16A1 solute carrier family 16 member 1 23539 SLC16A8 solute carrier family 16 member 8 10478 SLC25A17 solute carrier family 25 member 17 140679 SLC32A1 solute carrier family 32 member 1 10568 SLC34A2 solute carrier family 34 member 2 51324 SPG21 SPG21, maspardin 55617 TASP1 taspase 1 57146 TMEM159 transmembrane protein 159 252839 TMEM9 transmembrane protein 9 9168 TMSB10 thymosin beta 10 51075 TMX2 thioredoxin related transmembrane protein 2 54863 TOR4A torsin family 4 member A 55293 UEVLD UEV and lactate/malate dehyrogenase domains 150223 YDJC YdjC chitooligosaccharide deacetylase homolog 55906 ZC4H2 zinc finger C4H2-type containing

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 1.21e-01 1.67e-07 GO dipeptidyl-peptidase activity molecular_function 1.10e-01 1.72e-04 Reactome Proton-coupled monocarboxylate transport Transport of small molecules 5.85e-02 3.21e-04 GO F-actin capping protein complex cellular_component 5.85e-02 3.21e-04 Reactome ChREBP activates metabolic gene expression Metabolism 2.73e-02 1.03e-02 Reactome Type II Na+/Pi cotransporters Transport of small molecules 1.79e-02 6.25e-04 GO antiporter activity molecular_function 5.19e-03 7.49e-04 GO voltage-gated chloride channel activity molecular_function

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 1.11e-07 4.24e-05 dipeptidyl-peptidase activity 2.42e-07 8.67e-05 exopeptidase activity 1.79e-06 5.41e-04 aminopeptidase activity 1.30e-05 4.90e-03 anion transmembrane transport 2.71e-05 6.51e-03 anion transmembrane transporter activity 1.38e-04 2.73e-02 peptidase activity 1.83e-04 3.50e-02 actin monomer binding 1.86e-04 4.93e-02 lactate transport 1.86e-04 4.93e-02 lactate transmembrane transport 1.94e-04 3.68e-02 secondary active transmembrane transporter activity 2.11e-04 5.48e-02 anion transport 2.32e-04 5.94e-02 actin filament network formation 2.46e-04 4.54e-02 lactate transmembrane transporter activity 2.52e-04 6.37e-02 actin filament organization 3.82e-04 6.64e-02 monocarboxylic acid transmembrane transporter activity 4.33e-04 7.14e-02 F-actin capping protein complex 5.67e-04 9.39e-02 serine-type peptidase activity 6.00e-04 1.30e-01 regulation of actin filament depolymerization 6.09e-04 1.00e-01 serine hydrolase activity 6.52e-04 1.39e-01 monocarboxylic acid transport

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 4.55e-05 7.68e-03 BILE SALT AND ORGANIC ANION SLC TRANSPORTERS 3.40e-04 4.58e-02 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 3.41e-04 3.84e-02 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 5.03e-04 5.46e-02 BILE SALT AND ORGANIC ANION SLC TRANSPORTERS 6.08e-04 7.64e-02 SLC MEDIATED TRANSMEMBRANE TRANSPORT 6.96e-04 7.26e-02 SLC MEDIATED TRANSMEMBRANE TRANSPORT 7.17e-04 7.45e-02 BASIGIN INTERACTIONS 8.04e-04 9.72e-02 PYRUVATE METABOLISM 1.05e-03 1.05e-01 PYRUVATE METABOLISM 2.66e-03 2.39e-01 PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE 2.84e-03 2.87e-01 BASIGIN INTERACTIONS 3.74e-03 3.59e-01 PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE 4.36e-03 4.09e-01 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 6.76e-03 5.85e-01 INTEGRATION OF ENERGY METABOLISM 1.18e-02 9.09e-01 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 1.65e-02 1.00e+00 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 1.69e-02 1.00e+00 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 1.83e-02 1.00e+00 CYTOSOLIC SULFONATION OF SMALL MOLECULES 1.88e-02 1.00e+00 CASPASE MEDIATED CLEAVAGE OF CYTOSKELETAL PROTEINS 1.89e-02 1.00e+00 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.52e-03 1e+00 spherocytosis 2.70e-03 1e+00 kyphoscoliosis 2.80e-03 1e+00 astrocytosis 3.48e-03 1e+00 abnormal pons morphology 5.08e-03 1e+00 abnormal CNS glial cell morphology 5.45e-03 1e+00 increased mean corpuscular hemoglobin concentration 6.01e-03 1e+00 abnormal lysosome morphology 6.01e-03 1e+00 abnormal macrophage morphology 7.34e-03 1e+00 abnormal heart valve morphology 7.80e-03 1e+00 abnormal microglial cell physiology 8.67e-03 1e+00 impaired synaptic plasticity 1.08e-02 1e+00 decreased mean corpuscular hemoglobin 1.11e-02 1e+00 abnormal hepatocyte morphology 1.17e-02 1e+00 abnormal eye electrophysiology 1.25e-02 1e+00 abnormal Purkinje cell dendrite morphology 1.30e-02 1e+00 increased post-tetanic potentiation 1.31e-02 1e+00 pulmonary alveolar proteinosis 1.31e-02 1e+00 abnormal suprachiasmatic nucleus morphology 1.49e-02 1e+00 abnormal ciliary body pigmentation 1.49e-02 1e+00 decreased mean platelet volume

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

²FDR corrected p-value (Benjamini-Hochberg)