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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod108

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod108 Module size 49 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 80332 ADAM33 ADAM metallopeptidase domain 33 23786 BCL2L13 BCL2 like 13 140923 BNIP3 BCL2 interacting protein 3 like 665 BNIP3L BCL2 interacting protein 3 like 283870 BRICD5 BRICHOS domain containing 5 56935 C11orf75 single-pass membrane protein with coiled-coil domains 4 79415 C17orf62 cytochrome b-245 chaperone 1 147872 CCDC155 coiled-coil domain containing 155 55231 CCDC87 coiled-coil domain containing 87 969 CD69 CD69 molecule 64581 CLEC7A C-type lectin domain containing 7A 2055 CLN8 CLN8, transmembrane ER and ERGIC protein 245934 DEFB121 defensin beta 121 64184 EDDM3B epididymal protein 3B 60343 FAM3A family with sequence similarity 3 member A 89885 FATE1 fetal and adult testis expressed 1 55340 GIMAP5 GTPase, IMAP family member 5 84873 GPR128 adhesion G protein-coupled receptor G7 146395 GSG1L GSG1 like 3895 KTN1 kinectin 1 388633 LDLRAD1 low density lipoprotein receptor class A domain containing 1 56925 LXN latexin 7851 MALL mal, T cell differentiation protein like 84975 MFSD5 major facilitator superfamily domain containing 5 54860 MS4A12 membrane spanning 4-domains A12 4815 NINJ2 ninjurin 2 116154 PHACTR3 phosphatase and actin regulator 3 51090 PLLP plasmolipin 754 PTTG1IP PTTG1 interacting protein 344892 RTP2 receptor transporter protein 2 84102 SLC41A2 solute carrier family 41 member 2 163183 SYNE4 spectrin repeat containing nuclear envelope family member 4 84314 TMEM107 transmembrane protein 107 8834 TMEM11 transmembrane protein 11 85013 TMEM128 transmembrane protein 128 80194 TMEM134 transmembrane protein 134 28978 TMEM14A transmembrane protein 14A 130827 TMEM182 transmembrane protein 182 219854 TMEM218 transmembrane protein 218 157753 TMEM74 transmembrane protein 74 144110 TMEM86A transmembrane protein 86A 255043 TMEM86B transmembrane protein 86B 79089 TMUB2 transmembrane and ubiquitin like domain containing 2 11045 UPK1A uroplakin 1A 7348 UPK1B uroplakin 1B 7379 UPK2 uroplakin 2 7380 UPK3A uroplakin 3A 105375355 UPK3B uroplakin 3B 221302 ZUFSP zinc finger containing ubiquitin peptidase 1

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 3.05e-02 1.41e-04 GO structural constituent of myelin sheath molecular_function 2.09e-02 1.72e-04 GO meiotic nuclear membrane microtubule tethering complex cellular_component

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 1.64e-05 3.85e-03 outer membrane 3.41e-05 1.15e-02 mitochondrial protein catabolic process 9.95e-05 2.91e-02 membrane raft polarization 1.02e-04 2.97e-02 membrane raft localization 1.03e-04 2.99e-02 negative regulation of mitochondrial membrane potential 1.06e-04 3.07e-02 negative regulation of membrane potential 1.07e-04 3.09e-02 mitochondrial outer membrane permeabilization 1.36e-04 3.79e-02 positive regulation of mitochondrial membrane permeability involved in apoptotic process 1.70e-04 4.57e-02 positive regulation of mitochondrial membrane permeability 2.14e-04 5.54e-02 mitochondrial membrane organization 2.20e-04 4.09e-02 structural constituent of myelin sheath 3.35e-04 8.05e-02 regulation of mitochondrial membrane permeability involved in apoptotic process 3.85e-04 9.05e-02 membrane raft organization 6.47e-04 1.38e-01 defense response to other organism 8.07e-04 1.21e-01 nuclear outer membrane 8.70e-04 1.76e-01 epithelial cell differentiation 1.59e-03 2.88e-01 mitochondrion organization 1.59e-03 2.16e-01 apical plasma membrane 1.78e-03 3.15e-01 apoptotic mitochondrial changes 1.78e-03 3.15e-01 positive regulation of macroautophagy

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.63e-03 3.50e-01 METAL ION SLC TRANSPORTERS 5.02e-03 4.12e-01 METAL ION SLC TRANSPORTERS 8.56e-03 7.08e-01 BETA DEFENSINS 1.33e-02 9.24e-01 BETA DEFENSINS 1.33e-02 9.24e-01 DEFENSINS 1.41e-02 1.00e+00 DEFENSINS 4.24e-02 1.00e+00 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 4.50e-02 1.00e+00 INNATE IMMUNE SYSTEM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.82e-06 2.86e-02 abnormal urothelium morphology 9.49e-05 2.18e-01 abnormal urinary bladder physiology 1.20e-04 2.54e-01 increased blood urea nitrogen level 1.79e-03 1.00e+00 increased circulating creatinine level 1.87e-03 1.00e+00 vesicoureteral reflux 2.23e-03 1.00e+00 hydronephrosis 3.09e-03 1.00e+00 thin retinal outer nuclear layer 3.52e-03 1.00e+00 retinal degeneration 3.74e-03 1.00e+00 broad limb buds 5.61e-03 1.00e+00 increased urination frequency 5.61e-03 1.00e+00 abnormal hypoglossal nerve morphology 5.64e-03 1.00e+00 decreased urine uric acid level 7.47e-03 1.00e+00 ectopic digits 7.47e-03 1.00e+00 basisphenoid bone foramen 7.47e-03 1.00e+00 camptomelia 7.48e-03 1.00e+00 absent presphenoid bone 7.48e-03 1.00e+00 delayed intramembranous bone ossification 7.48e-03 1.00e+00 small basisphenoid bone 7.50e-03 1.00e+00 decreased cardiomyocyte apoptosis 9.33e-03 1.00e+00 ureter obstruction

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

²FDR corrected p-value (Benjamini-Hochberg)