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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod150

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod150 Module size 77 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 84519 ACRBP acrosin binding protein 126549 ANKLE1 ankyrin repeat and LEM domain containing 1 56987 BBX BBX, HMG-box containing 57673 BEND3 BEN domain containing 3 221927 BRAT1 BRCA1 associated ATM activator 1 144097 C11orf84 spindlin interactor and repressor of chromatin binding 400506 C16orf88 lysine rich nucleolar protein 1 147339 C18orf25 chromosome 18 open reading frame 25 56941 C3orf37 5-hydroxymethylcytosine binding, ES cell specific 65250 C5orf42 ciliogenesis and planar polarity effector 1 126075 CCDC159 coiled-coil domain containing 159 55038 CDCA4 cell division cycle associated 4 8161 COIL coilin 1382 CRABP2 cellular retinoic acid binding protein 2 117159 DCD dermcidin 23116 FAM179B TOG array regulator of axonemal microtubules 1 54865 GPATCH4 G-patch domain containing 4 389524 GTF2IRD2B GTF2I repeat domain containing 2B 54919 HEATR2 dynein axonemal assembly factor 5 388697 HRNR hornerin 11077 HSF2BP heat shock transcription factor 2 binding protein 23379 KIAA0947 interactor of little elongation complex ELL subunit 1 23608 MKRN1 makorin ring finger protein 1 22880 MORC2 MORC family CW-type zinc finger 2 23515 MORC3 MORC family CW-type zinc finger 3 84437 MSANTD4 Myb/SANT DNA binding domain containing 4 with coiled-coils 84901 NFATC2IP nuclear factor of activated T cells 2 interacting protein 51199 NIN ninein 139135 PASD1 PAS domain containing repressor 1 100169851 PATE3 prostate and testis expressed 3 57661 PHRF1 PHD and ring finger domains 1 8554 PIAS1 protein inhibitor of activated STAT 1 9063 PIAS2 protein inhibitor of activated STAT 2 51588 PIAS4 protein inhibitor of activated STAT 4 333926 PPM1J protein phosphatase, Mg2+/Mn2+ dependent 1J 79832 QSER1 glutamine and serine rich 1 10180 RBM6 RNA binding motif protein 6 9921 RNF10 ring finger protein 10 254225 RNF169 ring finger protein 169 81790 RNF170 ring finger protein 170 6047 RNF4 ring finger protein 4 25950 RWDD3 RWD domain containing 3 10055 SAE1 SUMO1 activating enzyme subunit 1 29843 SENP1 SUMO specific peptidase 1 59343 SENP2 SUMO specific peptidase 2 205564 SENP5 SUMO specific peptidase 5 26054 SENP6 SUMO specific peptidase 6 57337 SENP7 SUMO specific peptidase 7 375484 SIMC1 SUMO interacting motifs containing 1 100506736 SLFN5 schlafen family member 12 like 23347 SMCHD1 structural maintenance of chromosomes flexible hinge domain containing 1 55084 SOBP sine oculis binding protein homolog 55553 SOX6 SRY-box 6 728695 SPANXB2 SPANX family member B1 7341 SUMO1 small ubiquitin-like modifier 1 6613 SUMO2 small ubiquitin-like modifier 2 6612 SUMO3 small ubiquitin-like modifier 3 387082 SUMO4 small ubiquitin-like modifier 4 9338 TCEAL1 transcription elongation factor A like 1 140597 TCEAL2 transcription elongation factor A like 2 11070 TMEM115 transmembrane protein 115 199953 TMEM201 transmembrane protein 201 10210 TOPORS TOP1 binding arginine/serine rich protein 63970 TP53AIP1 tumor protein p53 regulated apoptosis inducing protein 1 10054 UBA2 ubiquitin like modifier activating enzyme 2 7326 UBE2G1 ubiquitin conjugating enzyme E2 G1 7329 UBE2I ubiquitin conjugating enzyme E2 I 65264 UBE2Z ubiquitin conjugating enzyme E2 Z 25130 UBN2 syntaxin 2 8237 USP11 ubiquitin specific peptidase 11 10208 USPL1 ubiquitin specific peptidase like 1 84186 ZCCHC7 zinc finger CCHC-type containing 7 11244 ZHX1 zinc fingers and homeoboxes 1 79830 ZMYM1 zinc finger MYM-type containing 1 9205 ZMYM5 zinc finger MYM-type containing 5 24149 ZNF318 zinc finger protein 318 26036 ZNF451 zinc finger protein 451

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 4.47e-01 1.78e-23 Reactome Processing and activation of SUMO Metabolism of proteins 2.14e-01 5.84e-12 GO protein desumoylation biological_process 1.61e-01 1.34e-31 GO protein sumoylation biological_process 1.31e-01 8.14e-16 Reactome SUMO is transferred from E1 to E2 (UBE2I, UBC9) Metabolism of proteins 3.52e-02 3.67e-06 GO positive regulation of protein sumoylation biological_process 2.50e-02 1.74e-13 Reactome SUMOylation of transcription factors Metabolism of proteins 2.40e-02 1.27e-10 Reactome SUMOylation of immune response proteins Metabolism of proteins 1.06e-02 2.13e-16 GO PML body 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 0.00e+00 0.00e+00 protein sumoylation 0.00e+00 0.00e+00 nuclear body 0.00e+00 0.00e+00 PML body 0.00e+00 0.00e+00 SUMO transferase activity 7.14e-21 6.91e-18 peptidyl-lysine modification 5.59e-17 5.30e-14 protein modification by small protein conjugation 5.40e-11 4.60e-08 protein desumoylation 1.18e-10 7.15e-08 SUMO-specific protease activity 1.89e-10 1.11e-07 protein tag 1.02e-09 5.41e-07 ubiquitin-like protein transferase activity 1.65e-09 8.45e-07 SUMO ligase activity 9.44e-08 5.35e-05 positive regulation of protein sumoylation 1.26e-07 4.77e-05 SUMO binding 3.49e-07 1.21e-04 SUMO polymer binding 3.65e-07 1.26e-04 SUMO-specific endopeptidase activity 5.04e-07 2.54e-04 regulation of protein sumoylation 1.44e-06 6.65e-04 global genome nucleotide-excision repair 3.08e-06 8.90e-04 cysteine-type peptidase activity 5.24e-06 1.45e-03 ubiquitin protein ligase binding 5.48e-06 1.51e-03 ubiquitin-like protein ligase binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.64e-06 3.56e-04 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 4.76e-06 9.57e-04 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 1.80e-05 2.59e-03 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 2.18e-05 3.10e-03 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 4.65e-05 7.81e-03 REGULATION OF IFNG SIGNALING 1.55e-04 1.88e-02 REGULATION OF IFNG SIGNALING 1.52e-03 1.46e-01 INTERFERON GAMMA SIGNALING 2.41e-03 2.50e-01 INTERFERON GAMMA SIGNALING 4.85e-03 4.00e-01 INTERFERON SIGNALING 8.71e-03 6.57e-01 CYTOKINE SIGNALING IN IMMUNE SYSTEM 1.18e-02 8.41e-01 MEIOTIC SYNAPSIS 2.04e-02 1.00e+00 INTERFERON SIGNALING 3.66e-02 1.00e+00 CYTOKINE SIGNALING IN IMMUNE SYSTEM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.58e-03 1e+00 abnormal DNA methylation 1.66e-03 1e+00 abnormal sternum morphology 1.87e-03 1e+00 abnormal hemoglobin content 2.68e-03 1e+00 partial perinatal lethality 3.27e-03 1e+00 abnormal trophoblast giant cells 3.68e-03 1e+00 polydactyly 3.75e-03 1e+00 abnormal monocyte differentiation 4.55e-03 1e+00 abnormal trophoblast layer morphology 5.42e-03 1e+00 decreased body length 5.61e-03 1e+00 decreased IgD level 5.61e-03 1e+00 decreased interleukin-3 secretion 5.68e-03 1e+00 postaxial polydactyly 7.48e-03 1e+00 short scala media 7.48e-03 1e+00 pulmonary artery hypoplasia 9.34e-03 1e+00 decreased threshold for auditory brainstem response 9.34e-03 1e+00 pulmonary valve atresia 1.12e-02 1e+00 abnormal marginal zone B cell physiology 1.12e-02 1e+00 abnormal atrioventricular cushion morphology 1.12e-02 1e+00 delayed chorioallantoic fusion 1.31e-02 1e+00 duplex kidney

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

²FDR corrected p-value (Benjamini-Hochberg)