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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod263

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod263 Module size 57 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 89978 ATPBD4 diphthamine biosynthesis 6 8315 BRAP BRCA1 associated protein 79624 C6orf211 acidic residue methyltransferase 1 57003 CCDC47 coiled-coil domain containing 47 114757 CYGB cytoglobin 83850 ESYT3 extended synaptotagmin 3 152273 FGD5 FYVE, RhoGEF and PH domain containing 5 57655 GRAMD1A GRAM domain containing 1A 57476 GRAMD1B GRAM domain containing 1B 54762 GRAMD1C GRAM domain containing 1C 3416 IDE insulin degrading enzyme 723961 INS-IGF2 INS-IGF2 readthrough 9636 ISG15 ISG15 ubiquitin-like modifier 23277 KIAA0664 clustered mitochondria homolog 57189 KIAA1147 KIAA1147 55728 N4BP2 NEDD4 binding protein 2 90634 N4BP2L1 NEDD4 binding protein 2 like 1 10443 N4BP2L2 NEDD4 binding protein 2 like 2 10641 NPRL2 NPR2 like, GATOR1 complex subunit 4898 NRD1 nardilysin convertase 4938 OAS1 2'-5'-oligoadenylate synthetase 1 4939 OAS2 2'-5'-oligoadenylate synthetase 2 4940 OAS3 2'-5'-oligoadenylate synthetase 3 8638 OASL 2'-5'-oligoadenylate synthetase like 79156 PLEKHF1 pleckstrin homology and FYVE domain containing 1 79666 PLEKHF2 pleckstrin homology and FYVE domain containing 2 553158 PRR5-ARHGAP8 PRR5-ARHGAP8 readthrough 55005 RMND1 required for meiotic nuclear division 1 homolog 285180 RUFY4 RUN and FYVE domain containing 4 57147 SCYL3 SCY1 like pseudokinase 3 6561 SLC13A1 solute carrier family 13 member 1 9058 SLC13A2 solute carrier family 13 member 2 64849 SLC13A3 solute carrier family 13 member 3 26266 SLC13A4 solute carrier family 13 member 4 284111 SLC13A5 solute carrier family 13 member 5 6564 SLC15A1 solute carrier family 15 member 1 6565 SLC15A2 solute carrier family 15 member 2 51296 SLC15A3 solute carrier family 15 member 3 121260 SLC15A4 solute carrier family 15 member 4 729025 SLC15A5 solute carrier family 15 member 5 6567 SLC16A2 solute carrier family 16 member 2 285672 SREK1IP1 SREK1 interacting protein 1 55852 TEX2 testis expressed 2 9375 TM9SF2 transmembrane 9 superfamily member 2 55858 TMEM165 transmembrane protein 165 9725 TMEM63A transmembrane protein 63A 55362 TMEM63B transmembrane protein 63B 57156 TMEM63C transmembrane protein 63C 22996 TTC39A tetratricopeptide repeat domain 39A 158219 TTC39B tetratricopeptide repeat domain 39B 125488 TTC39C tetratricopeptide repeat domain 39C 337867 UBAC2 UBA domain containing 2 23666 UBBP4 ubiquitin B pseudogene 4 10537 UBD ubiquitin D 8266 UBL4A ubiquitin like 4A 164153 UBL4B ubiquitin like 4B 93550 ZFAND4 zinc finger AN1-type containing 4

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 7.07e-01 5.29e-14 Reactome Sodium-coupled sulphate, di- and tri-carboxylate transporters Transport of small molecules 6.41e-01 5.29e-14 GO peptide:proton symporter activity molecular_function 8.94e-02 2.52e-11 Reactome Proton/oligopeptide cotransporters Transport of small molecules 2.82e-02 6.97e-03 GO BAT3 complex cellular_component 2.82e-02 6.97e-03 Reactome Intracellular oxygen transport Transport of small molecules 9.59e-03 2.65e-06 GO negative regulation of viral genome replication biological_process 6.95e-03 4.26e-07 GO type I interferon signaling pathway 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 symporter activity 3.41e-11 2.16e-08 secondary active transmembrane transporter activity 1.63e-10 9.72e-08 2'-5'-oligoadenylate synthetase activity 2.41e-10 1.41e-07 peptide:proton symporter activity 8.72e-08 3.39e-05 sodium:dicarboxylate symporter activity 3.27e-07 1.70e-04 monovalent inorganic cation transport 3.93e-07 2.01e-04 type I interferon signaling pathway 3.93e-07 2.01e-04 cellular response to type I interferon 3.96e-07 2.02e-04 response to type I interferon 4.49e-07 2.28e-04 negative regulation of viral genome replication 6.90e-07 3.39e-04 oligopeptide transport 1.40e-06 4.33e-04 solute:proton symporter activity 1.87e-06 8.44e-04 response to interferon-gamma 4.33e-06 1.81e-03 regulation of viral genome replication 5.68e-06 2.32e-03 defense response to virus 1.02e-05 2.66e-03 double-stranded RNA binding 1.08e-05 4.15e-03 interferon-gamma-mediated signaling pathway 1.63e-05 4.08e-03 cation transmembrane transporter activity 1.93e-05 6.96e-03 response to virus 1.97e-05 7.08e-03 succinate transmembrane transport

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 5.89e-08 1.18e-05 SLC MEDIATED TRANSMEMBRANE TRANSPORT 1.64e-07 3.12e-05 BILE SALT AND ORGANIC ANION SLC TRANSPORTERS 2.49e-07 6.12e-05 INTERFERON ALPHA BETA SIGNALING 3.08e-07 7.47e-05 SLC MEDIATED TRANSMEMBRANE TRANSPORT 1.13e-06 2.54e-04 INTERFERON SIGNALING 1.87e-06 3.12e-04 INTERFERON ALPHA BETA SIGNALING 2.18e-06 4.63e-04 CYTOKINE SIGNALING IN IMMUNE SYSTEM 2.69e-06 5.61e-04 BILE SALT AND ORGANIC ANION SLC TRANSPORTERS 3.86e-06 7.87e-04 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 5.35e-06 1.07e-03 INTERFERON GAMMA SIGNALING 1.04e-05 1.99e-03 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 1.64e-05 2.37e-03 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 2.21e-05 3.13e-03 INTERFERON GAMMA SIGNALING 2.72e-05 3.79e-03 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 4.05e-05 6.93e-03 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 4.14e-05 5.63e-03 INTERFERON SIGNALING 1.51e-04 1.84e-02 CYTOKINE SIGNALING IN IMMUNE SYSTEM 4.96e-04 5.39e-02 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 1.05e-03 1.23e-01 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 4.77e-02 1.00e+00 NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.00e-04 4.47e-01 abnormal renal reabsorbtion 1.87e-03 1.00e+00 abnormal glycerol level 3.06e-03 1.00e+00 abnormal liver physiology 3.74e-03 1.00e+00 abnormal thyroxine level 3.75e-03 1.00e+00 increased thyroid-stimulating hormone level 5.61e-03 1.00e+00 decreased circulating lactate level 5.61e-03 1.00e+00 decreased susceptibility to age related obesity 5.61e-03 1.00e+00 abnormal circulating interferon level 5.61e-03 1.00e+00 increased triiodothyronine level 7.48e-03 1.00e+00 abnormal miscarriage rate 9.33e-03 1.00e+00 altered tumor pathology 9.46e-03 1.00e+00 decreased triiodothyronine level 1.12e-02 1.00e+00 clonic seizures 1.12e-02 1.00e+00 abnormal triiodothyronine level 1.12e-02 1.00e+00 increased circulating triiodothyronine level 1.24e-02 1.00e+00 decreased circulating glucose level 1.30e-02 1.00e+00 abnormal interferon secretion 1.31e-02 1.00e+00 increased bile salt level 1.47e-02 1.00e+00 abnormal enzyme/coenzyme activity 1.62e-02 1.00e+00 amyloid beta deposits

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

²FDR corrected p-value (Benjamini-Hochberg)