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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod148

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod148 Module size 81 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 5826 ABCD4 ATP binding cassette subfamily D member 4 52 ACP1 acid phosphatase 1 29028 ATAD2 ATPase family, AAA domain containing 2 54454 ATAD2B ATPase family, AAA domain containing 2B 84529 C15orf41 chromosome 15 open reading frame 41 64149 C17orf75 chromosome 17 open reading frame 75 55352 C17orf79 coordinator of PRMT5 and differentiation stimulator 200844 C3orf67 chromosome 3 open reading frame 67 54969 C4orf27 histone PARylation factor 1 79741 CCDC7 coiled-coil domain containing 7 64925 CCDC71 coiled-coil domain containing 71 1043 CD52 CD52 molecule 146059 CDAN1 codanin 1 27439 CECR6 transmembrane protein 121B 79094 CHAC1 ChaC glutathione specific gamma-glutamylcyclotransferase 1 494143 CHAC2 ChaC cation transport regulator homolog 2 8208 CHAF1B chromatin assembly factor 1 subunit B 9391 CIAO1 cytosolic iron-sulfur assembly component 1 1466 CSRP2 cysteine and glycine rich protein 2 56259 CTNNBL1 catenin beta like 1 7913 DEK DEK proto-oncogene 1677 DFFB DNA fragmentation factor subunit beta 373863 DND1 DND microRNA-mediated repression inhibitor 1 23741 EID1 EP300 interacting inhibitor of differentiation 1 9917 FAM20B FAM20B, glycosaminoglycan xylosylkinase 84293 FAM213A peroxiredoxin like 2A 163479 FNDC7 fibronectin type III domain containing 7 391059 FRRS1 ferric chelate reductase 1 60558 GUF1 GUF1 homolog, GTPase 3068 HDGF heparin binding growth factor 81932 HDHD3 haloacid dehalogenase like hydrolase domain containing 3 7290 HIRA histone cell cycle regulator 10075 HUWE1 HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase 90865 IL33 interleukin 33 3638 INSIG1 insulin induced gene 1 51141 INSIG2 insulin induced gene 2 79768 KATNBL1 katanin regulatory subunit B1 like 1 5927 KDM5A lysine demethylase 5A 10765 KDM5B lysine demethylase 5B 7403 KDM6A lysine demethylase 6A 23135 KDM6B lysine demethylase 6B 83746 L3MBTL2 L3MBTL2, polycomb repressive complex 1 subunit 8930 MBD4 methyl-CpG binding domain 4, DNA glycosylase 55669 MFN1 mitofusin 1 9927 MFN2 mitofusin 2 4528 MTIF2 mitochondrial translational initiation factor 2 79829 NAA40 N(alpha)-acetyltransferase 40, NatD catalytic subunit 340719 NANOS1 nanos C2HC-type zinc finger 1 339345 NANOS2 nanos C2HC-type zinc finger 2 342977 NANOS3 nanos C2HC-type zinc finger 3 91754 NEK8 NIMA related kinase 9 9480 ONECUT2 one cut homeobox 2 84875 PARP10 poly(ADP-ribose) polymerase family member 10 10016 PDCD6 programmed cell death 6 8682 PEA15 proliferation and apoptosis adaptor protein 15 553115 PEF1 penta-EF-hand domain containing 1 51105 PHF20L1 PHD finger protein 20 like 1 129285 PPP1R21 protein phosphatase 1 regulatory subunit 21 80209 PROSER1 proline and serine rich 1 84795 PYROXD2 pyridine nucleotide-disulphide oxidoreductase domain 2 84600 RAG1 recombination activating 1 23504 RIMBP2 RIMS binding protein 2 79048 SECISBP2 SECIS binding protein 2 55244 SLC47A1 solute carrier family 47 member 1 146802 SLC47A2 solute carrier family 47 member 2 22865 SLITRK3 SLIT and NTRK like family member 3 316013 SRI SET domain containing 2 6737 TRIM21 tripartite motif containing 21 54765 TRIM44 tripartite motif containing 44 298692 TTL tubulin tyrosine ligase like 10 83887 TTLL2 tubulin tyrosine ligase like 2 254173 TTLL5 tubulin tyrosine ligase like 10 164714 TTLL8 tubulin tyrosine ligase like 8 7328 UBE2H ubiquitin conjugating enzyme E2 H 9960 USP3 ubiquitin specific peptidase 3 7404 UTY ubiquitously transcribed tetratricopeptide repeat containing, Y-linked 389136 VGLL3 vestigial like family member 3 79968 WDR76 WD repeat domain 76 114991 ZNF618 zinc finger protein 618 51123 ZNF706 zinc finger protein 706 741 ZNHIT2 zinc finger HIT-type containing 2

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 2.95e-01 4.91e-07 GO histone demethylase activity (H3-K27 specific) molecular_function 7.47e-02 9.10e-09 GO dioxygenase activity molecular_function 6.74e-02 1.74e-05 GO positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay biological_process 5.86e-02 3.77e-04 GO mitochondrion localization biological_process 2.73e-02 1.11e-02 Reactome Interleukin-33 signaling Immune System 2.01e-02 7.36e-04 GO glutathione catabolic process biological_process 2.01e-02 7.36e-04 GO drug transmembrane transporter activity molecular_function 2.00e-02 7.29e-10 GO histone binding molecular_function 1.81e-02 1.06e-05 Reactome Carboxyterminal post-translational modifications of tubulin Metabolism of proteins 1.66e-02 3.77e-04 GO histone H3-K4 demethylation biological_process 1.06e-02 8.81e-04 GO negative regulation of fatty acid biosynthetic process biological_process 7.36e-03 7.97e-06 GO MLL3/4 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 2.55e-08 1.57e-05 chromatin organization 7.11e-08 4.12e-05 histone lysine demethylation 1.54e-07 8.42e-05 histone demethylation 1.97e-07 1.06e-04 protein demethylation 2.25e-07 1.20e-04 histone H3-K27 demethylation 2.42e-07 8.67e-05 histone demethylase activity 2.60e-07 1.37e-04 covalent chromatin modification 3.34e-07 1.16e-04 histone demethylase activity (H3-K27 specific) 8.30e-07 2.68e-04 demethylase activity 1.98e-06 5.93e-04 histone binding 4.72e-06 1.96e-03 demethylation 9.58e-06 3.72e-03 histone modification 1.27e-05 3.25e-03 chromatin binding 2.66e-05 9.23e-03 regulation of chromatin organization 3.83e-05 8.91e-03 dioxygenase activity 4.26e-05 1.40e-02 positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay 4.78e-05 1.54e-02 regulation of gene silencing 6.65e-05 2.05e-02 regulation of chromatin silencing 6.82e-05 1.41e-02 SREBP-SCAP-Insig complex 7.96e-05 1.70e-02 calcium-dependent cysteine-type endopeptidase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.60e-04 2.36e-02 BILE SALT AND ORGANIC ANION SLC TRANSPORTERS 2.89e-04 3.32e-02 BILE SALT AND ORGANIC ANION SLC TRANSPORTERS 3.18e-03 2.80e-01 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 3.43e-03 3.35e-01 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 4.41e-03 3.69e-01 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 4.94e-03 4.53e-01 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 7.73e-03 5.94e-01 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 9.06e-03 7.40e-01 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 1.19e-02 9.15e-01 RESOLUTION OF AP SITES VIA THE MULTIPLE NUCLEOTIDE PATCH REPLACEMENT PATHWAY 1.19e-02 9.15e-01 BASE FREE SUGAR PHOSPHATE REMOVAL VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 1.60e-02 1.00e+00 RESOLUTION OF AP SITES VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 1.60e-02 1.00e+00 BASE EXCISION REPAIR 1.80e-02 1.00e+00 RESOLUTION OF AP SITES VIA THE MULTIPLE NUCLEOTIDE PATCH REPLACEMENT PATHWAY 1.80e-02 1.00e+00 BASE FREE SUGAR PHOSPHATE REMOVAL VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 1.92e-02 1.00e+00 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 2.09e-02 1.00e+00 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 2.45e-02 1.00e+00 RESOLUTION OF AP SITES VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 2.45e-02 1.00e+00 BASE EXCISION REPAIR 2.97e-02 1.00e+00 APOPTOSIS INDUCED DNA FRAGMENTATION 3.03e-02 1.00e+00 APOPTOSIS INDUCED DNA FRAGMENTATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.73e-04 7.2e-01 partial embryonic lethality during organogenesis 1.37e-03 1.0e+00 abnormal developmental patterning 1.44e-03 1.0e+00 decreased somite size 2.42e-03 1.0e+00 abnormal notochord morphology 3.96e-03 1.0e+00 small heart 4.08e-03 1.0e+00 autoimmune response 4.60e-03 1.0e+00 failure of heart looping 5.65e-03 1.0e+00 abnormal inguinal lymph node morphology 6.39e-03 1.0e+00 caudal body truncation 6.62e-03 1.0e+00 kinked neural tube 8.30e-03 1.0e+00 dermatitis 9.34e-03 1.0e+00 decreased respiratory mucosa goblet cell number 9.38e-03 1.0e+00 absent immature B cells 9.64e-03 1.0e+00 abnormal rostral-caudal axis patterning 9.89e-03 1.0e+00 abnormal forebrain development 1.12e-02 1.0e+00 abnormal prechordal plate morphology 1.12e-02 1.0e+00 increased testicular teratoma incidence 1.25e-02 1.0e+00 abnormal mitochondrial physiology 1.31e-02 1.0e+00 abnormal T cell receptor beta chain V(D)J recombination 1.43e-02 1.0e+00 increased circulating creatinine level

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

²FDR corrected p-value (Benjamini-Hochberg)