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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod274

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod274 Module size 59 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 155465 AGR3 anterior gradient 3, protein disulphide isomerase family member 200316 APOBEC3F apolipoprotein B mRNA editing enzyme catalytic subunit 3F 60489 APOBEC3G apolipoprotein B mRNA editing enzyme catalytic subunit 3G 26580 BSCL2 BSCL2, seipin lipid droplet biogenesis associated 219738 C10orf35 family with sequence similarity 241 member B 29035 C16orf72 chromosome 16 open reading frame 72 79025 C20orf195 fibronectin type III domain containing 11 375791 C9orf169 cysteine rich tail 1 203228 C9orf72 chromosome 9 open reading frame 72 55013 CCDC109B mitochondrial calcium uniporter dominant negative beta subunit 374355 CCDC172 coiled-coil domain containing 172 374969 CCDC23 small vasohibin binding protein 55246 CCDC25 coiled-coil domain containing 25 54520 CCDC93 coiled-coil domain containing 93 388512 CLEC17A C-type lectin domain containing 17A 144402 CPNE8 copine 8 1421 CRYGD crystallin gamma D 1667 DEFA1 defensin alpha 1 414918 DENND6B DENN domain containing 6B 29952 DPP7 dipeptidyl peptidase 7 55211 DPPA4 developmental pluripotency associated 4 55068 ENOX1 ecto-NOX disulfide-thiol exchanger 1 55007 FAM118A family with sequence similarity 118 member A 79072 FASTKD3 FAST kinase domains 3 55783 FTSJD1 cap methyltransferase 2 54332 GDAP1 ganglioside induced differentiation associated protein 1 26157 GIMAP2 GTPase, IMAP family member 2 23593 HEBP2 heme binding protein 2 117283 IP6K3 inositol hexakisphosphate kinase 3 83986 ITFG3 family with sequence similarity 234 member A 57614 KIAA1468 RAB11 binding and LisH domain, coiled-coil and HEAT repeat containing 100431172 KLRF2 killer cell lectin like receptor F2 11133 KPTN kaptin, actin binding protein 23185 LARP4B La ribonucleoprotein domain family member 4B 79609 METTL21D valosin containing protein lysine methyltransferase 9848 MFAP3L microfibril associated protein 3 like 10227 MFSD10 major facilitator superfamily domain containing 10 10361 NPM2 nucleophosmin/nucleoplasmin 2 4884 NPTX1 neuronal pentraxin 1 4885 NPTX2 neuronal pentraxin 2 11163 NUDT4 nudix hydrolase 4 220064 ORAOV1 LTO1, ABCE1 maturation factor 5026 P2RX5 purinergic receptor P2X 5 55041 PLEKHB2 pleckstrin homology domain containing B2 170680 PSORS1C2 psoriasis susceptibility 1 candidate 2 134701 RIPPLY2 ripply transcriptional repressor 2 143686 SESN3 sestrin 3 9194 SLC16A7 solute carrier family 16 member 7 116843 SLC18B1 solute carrier family 18 member B1 90843 TCEAL8 transcription elongation factor A like 8 79022 TMEM106C transmembrane protein 106C 54958 TMEM160 transmembrane protein 160 55069 TMEM248 transmembrane protein 248 55787 TXLNG taxilin gamma 201294 UNC13D unc-13 homolog D 54532 USP53 ubiquitin specific peptidase 53 51186 WBP5 transcription elongation factor A like 9 9502 XAGE2 X antigen family member 2 84858 ZNF503 zinc finger protein 503

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 3.04e-02 2.35e-04 Reactome Synthesis of pyrophosphates in the cytosol Metabolism 2.66e-02 1.88e-04 GO DNA cytosine deamination biological_process 2.63e-02 1.88e-04 GO negative regulation of single stranded viral RNA replication via double stranded DNA intermediate 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 6.14e-06 2.49e-03 natural killer cell degranulation 2.04e-05 4.70e-03 apolipoprotein B mRNA editing enzyme complex 4.41e-05 1.44e-02 natural killer cell activation involved in immune response 5.63e-05 1.26e-02 cytidine deaminase activity 8.05e-05 1.63e-02 azurophil granule lumen 8.56e-05 2.56e-02 defense response to virus 1.11e-04 3.19e-02 DNA cytosine deamination 1.23e-04 3.49e-02 negative regulation of single stranded viral RNA replication via double stranded DNA intermediate 1.25e-04 3.53e-02 cell killing 1.40e-04 3.88e-02 positive regulation of defense response to virus by host 1.52e-04 2.83e-02 azurophil granule 1.56e-04 4.26e-02 cytidine deamination 1.56e-04 4.26e-02 regulation of single stranded viral RNA replication via double stranded DNA intermediate 1.60e-04 4.35e-02 DNA deamination 2.36e-04 6.02e-02 base conversion or substitution editing 2.53e-04 6.39e-02 regulation of defense response to virus by host 3.36e-04 8.07e-02 pyrimidine nucleoside catabolic process 3.67e-04 8.70e-02 response to virus 5.15e-04 1.15e-01 natural killer cell activation 5.32e-04 1.18e-01 negative regulation of transposition

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.61e-03 1.54e-01 APOBEC3G MEDIATED RESISTANCE TO HIV1 INFECTION 1.63e-03 1.55e-01 VIF MEDIATED DEGRADATION OF APOBEC3G 2.42e-03 2.51e-01 APOBEC3G MEDIATED RESISTANCE TO HIV1 INFECTION 2.43e-03 2.52e-01 VIF MEDIATED DEGRADATION OF APOBEC3G 2.45e-03 2.53e-01 HOST INTERACTIONS OF HIV FACTORS 4.94e-03 4.53e-01 HIV INFECTION 6.67e-03 5.26e-01 BILE SALT AND ORGANIC ANION SLC TRANSPORTERS 9.06e-03 6.78e-01 HOST INTERACTIONS OF HIV FACTORS 1.08e-02 7.78e-01 HIV INFECTION 1.12e-02 8.71e-01 DEFENSINS 1.31e-02 9.12e-01 DEFENSINS 1.92e-02 1.00e+00 BILE SALT AND ORGANIC ANION SLC TRANSPORTERS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.35e-03 1e+00 abnormal innervation 3.74e-03 1e+00 chromatolysis 5.62e-03 1e+00 abnormal myotome morphology 5.62e-03 1e+00 absent vertebral pedicles 5.63e-03 1e+00 abnormal vertebral pedicle morphology 5.63e-03 1e+00 abnormal white adipose tissue amount 6.22e-03 1e+00 increased lean body mass 7.47e-03 1e+00 absent proximal rib 8.75e-03 1e+00 decreased response to stress-induced hyperthermia 9.35e-03 1e+00 abnormal adipose tissue development 9.37e-03 1e+00 absent lymph node germinal center 1.12e-02 1e+00 decreased interscapular fat pad weight 1.12e-02 1e+00 decreased renal fat pad weight 1.12e-02 1e+00 abnormal white fat cell morphology 1.31e-02 1e+00 lipodystrophy 1.31e-02 1e+00 decreased white fat cell number 1.31e-02 1e+00 abnormal fat cell differentiation 1.49e-02 1e+00 failure of somite differentiation 1.49e-02 1e+00 decreased mesenteric fat pad weight 1.50e-02 1e+00 abnormal rostral-caudal patterning of the somites

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

²FDR corrected p-value (Benjamini-Hochberg)