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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod343

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod343 Module size 94 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 29974 A1CF APOBEC1 complementation factor 141 ADPRH ADP-ribosylarginine hydrolase 26993 AKAP8L A-kinase anchoring protein 8 like 11199 ANXA10 annexin A10 339 APOBEC1 apolipoprotein B mRNA editing enzyme catalytic subunit 1 64860 ARMCX5 armadillo repeat containing X-linked 5 8815 BANF1 barrier to autointegration factor 1 26005 C2CD3 C2 calcium dependent domain containing 3 25871 C3orf17 nucleolus and neural progenitor protein 57662 CAMSAP3 calmodulin regulated spectrin associated protein family member 3 284001 CCDC57 coiled-coil domain containing 57 253635 CCDC75 G-patch domain containing 11 23580 CDC42EP4 CDC42 effector protein 4 51265 CDKL3 cyclin dependent kinase like 3 9541 CIR1 corepressor interacting with RBPJ, 1 55313 CPPED1 calcineurin like phosphoesterase domain containing 1 441521 CT45A5 cancer/testis antigen family 45 member A5 199221 DZIP1L DAZ interacting zinc finger protein 1 like 84285 EIF1AD eukaryotic translation initiation factor 1A domain containing 2010 EMD emerin 132884 EVC2 EvC ciliary complex subunit 2 220108 FAM124A family with sequence similarity 124 member A 199870 FAM76A family with sequence similarity 76 member A 23360 FNBP4 formin binding protein 4 23070 FTSJD2 cap methyltransferase 1 8939 FUBP3 far upstream element binding protein 3 27238 GPKOW G-patch domain and KOW motifs 121355 GTSF1 gametocyte specific factor 1 149699 GTSF1L gametocyte specific factor 1 like 221092 HNRNPUL2 heterogeneous nuclear ribonucleoprotein U like 2 3617 IMPG1 interphotoreceptor matrix proteoglycan 1 10657 KHDRBS1 KH RNA binding domain containing, signal transduction associated 1 55425 KIAA1704 GPALPP motifs containing 1 57805 KIAA1967 cell cycle and apoptosis regulator 2 3920 LAMP2 lysosomal associated membrane protein 2 118426 LOH12CR1 BLOC-1 related complex subunit 5 10586 MAB21L2 mab-21 like 2 4135 MAP6 microtubule associated protein 6 79091 METTL22 methyltransferase like 22 4253 MIA2 MIA SH3 domain ER export factor 2 4277 MICB MHC class I polypeptide-related sequence B 8079 MLF2 myeloid leukemia factor 2 136647 MPLKIP M-phase specific PLK1 interacting protein 23040 MYT1L myelin transcription factor 1 like 81614 NIPA2 NIPA magnesium transporter 2 64710 NUCKS1 nuclear casein kinase and cyclin dependent kinase substrate 1 84955 NUDCD1 NudC domain containing 1 79629 OCEL1 occludin/ELL domain containing 1 114771 PGLYRP3 peptidoglycan recognition protein 3 57115 PGLYRP4 peptidoglycan recognition protein 4 285848 PNPLA1 patatin like phospholipase domain containing 1 11168 PSIP1 PC4 and SFRS1 interacting protein 1 54899 PXK PX domain containing serine/threonine kinase like 54814 QPCTL glutaminyl-peptide cyclotransferase like 64901 RANBP17 RAN binding protein 17 54033 RBM11 RNA binding motif protein 11 79171 RBM42 RNA binding motif protein 42 5937 RBMS1 RNA binding motif single stranded interacting protein 1 27288 RBMXL2 RBMX like 2 1381 RBP5 cellular retinoic acid binding protein 1 149603 RNF187 ring finger protein 187 26015 RPAP1 RNA polymerase II associated protein 1 6238 RRBP1 ribosome binding protein 1 6248 RS1 regulator of solute carriers 1 65117 RSRC2 arginine and serine rich coiled-coil 2 27111 SDCBP2 syndecan binding protein 2 90525 SHF Src homology 2 domain containing F 64094 SMOC2 SPARC related modular calcium binding 2 54937 SOHLH2 spermatogenesis and oogenesis specific basic helix-loop-helix 2 246329 STAC3 SH3 and cysteine rich domain 3 8859 STK19 serine/threonine kinase 19 10923 SUB1 SUB1 homolog, transcriptional regulator 10147 SUGP2 SURP and G-patch domain containing 2 51224 TCEB3B elongin A2 7070 THY1 Thy-1 cell surface antigen 100113407 TMEM170B transmembrane protein 170B 29767 TMOD2 tropomodulin 2 29766 TMOD3 tropomodulin 3 7112 TMPO thymopoietin 160335 TMTC2 transmembrane and tetratricopeptide repeat containing 2 84675 TRIM55 tripartite motif containing 55 7286 TUFT1 tuftelin 1 9898 UBAP2L ubiquitin associated protein 2 like 84747 UNC119B unc-119 lipid binding chaperone B 84669 USP32 ubiquitin specific peptidase 32 7375 USP4 ubiquitin specific peptidase 4 85015 USP45 ubiquitin specific peptidase 45 8409 UXT ubiquitously expressed prefoldin like chaperone 54521 WDR44 WD repeat domain 44 116143 WDR92 WD repeat domain 92 100381270 ZBED6 zinc finger BED-type containing 6 9877 ZC3H11A zinc finger CCCH-type containing 11A 126299 ZNF428 zinc finger protein 428 27332 ZNF638 zinc finger protein 638

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 2.09e-01 2.05e-06 Reactome Clearance of Nuclear Envelope Membranes from Chromatin Cell Cycle 5.82e-02 4.26e-04 GO detection of bacterium biological_process 3.58e-02 4.26e-04 Reactome Formation of the Editosome Metabolism of RNA 2.97e-02 4.26e-04 GO establishment of integrated proviral latency biological_process 2.45e-02 4.26e-04 Reactome mRNA Editing: C to U Conversion Metabolism of RNA 1.96e-02 8.30e-04 GO myofibril assembly biological_process 6.58e-03 5.46e-04 Reactome Autointegration results in viral DNA circles Disease 4.71e-03 5.46e-04 Reactome Integration of viral DNA into host genomic DNA Disease 4.62e-03 1.81e-04 GO poly(U) RNA binding molecular_function

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 5.10e-06 2.11e-03 mRNA processing 5.10e-05 1.63e-02 mRNA metabolic process 1.39e-04 3.86e-02 cytidine to uridine editing 1.40e-04 2.76e-02 N-acetylmuramoyl-L-alanine amidase activity 2.56e-04 4.70e-02 peptidoglycan receptor activity 3.26e-04 7.88e-02 mitotic nuclear envelope reassembly 3.75e-04 8.85e-02 nuclear envelope disassembly 4.04e-04 9.40e-02 pointed-end actin filament capping 4.24e-04 9.79e-02 base conversion or substitution editing 4.25e-04 9.81e-02 peptidoglycan catabolic process 4.99e-04 1.12e-01 RNA splicing 6.02e-04 1.30e-01 regulation of RNA export from nucleus 7.06e-04 1.49e-01 establishment of integrated proviral latency 7.33e-04 1.17e-01 peptidoglycan binding 7.86e-04 1.62e-01 establishment of viral latency 8.04e-04 1.65e-01 mRNA modification 8.22e-04 1.68e-01 lipoprotein transport 9.63e-04 1.91e-01 detection of bacterium 1.16e-03 2.23e-01 nuclear envelope reassembly 1.52e-03 2.22e-01 poly(U) RNA binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 9.91e-06 1.90e-03 APOBEC3G MEDIATED RESISTANCE TO HIV1 INFECTION 3.01e-05 5.28e-03 INTEGRATION OF PROVIRUS 3.18e-05 5.56e-03 EARLY PHASE OF HIV LIFE CYCLE 3.35e-05 5.82e-03 INTERACTIONS OF VPR WITH HOST CELLULAR PROTEINS 3.75e-05 5.13e-03 APOBEC3G MEDIATED RESISTANCE TO HIV1 INFECTION 4.10e-05 5.58e-03 INTEGRATION OF PROVIRUS 4.58e-05 6.16e-03 INTERACTIONS OF VPR WITH HOST CELLULAR PROTEINS 1.20e-04 1.50e-02 EARLY PHASE OF HIV LIFE CYCLE 1.68e-04 2.46e-02 HOST INTERACTIONS OF HIV FACTORS 1.17e-03 1.16e-01 HOST INTERACTIONS OF HIV FACTORS 1.84e-03 1.98e-01 HIV LIFE CYCLE 2.52e-03 2.59e-01 HIV INFECTION 3.83e-03 3.66e-01 MRNA PROCESSING 5.47e-03 4.41e-01 MRNA PROCESSING 6.00e-03 4.78e-01 HIV LIFE CYCLE 9.97e-03 7.31e-01 HIV INFECTION 4.86e-02 1.00e+00 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.42e-04 4.86e-01 abnormal gut flora balance 5.74e-04 6.58e-01 intestinal ulcer 1.08e-03 9.40e-01 gastrointestinal hemorrhage 1.95e-03 1.00e+00 decreased circulating HDL cholesterol level 3.04e-03 1.00e+00 abnormal crypts of Lieberkuhn morphology 3.75e-03 1.00e+00 small exoccipital bone 3.75e-03 1.00e+00 small supraoccipital bone 3.75e-03 1.00e+00 broad nasal bone 4.22e-03 1.00e+00 abnormal intestinal goblet cell morphology 4.24e-03 1.00e+00 abnormal intestinal epithelium morphology 4.89e-03 1.00e+00 abnormal intestinal mucosa morphology 5.62e-03 1.00e+00 abnormal behavioral response to amphetamine 6.95e-03 1.00e+00 abnormal chemokine secretion 7.49e-03 1.00e+00 broad head 9.34e-03 1.00e+00 absent lens vesicle 9.34e-03 1.00e+00 abnormal erythroblast morphology 9.35e-03 1.00e+00 disorganized retinal inner nuclear layer 1.12e-02 1.00e+00 disorganized retinal outer nuclear layer 1.12e-02 1.00e+00 abnormal basicranium morphology 1.12e-02 1.00e+00 abnormal occipital bone morphology

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

²FDR corrected p-value (Benjamini-Hochberg)