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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod269

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod269 Module size 50 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 4059 BCAM basal cell adhesion molecule (Lutheran blood group) 79656 BEND5 BEN domain containing 5 631 BFSP1 beaded filament structural protein 1 8548 BLZF1 basic leucine zipper nuclear factor 1 497661 C18orf32 chromosome 18 open reading frame 32 84645 C22orf23 chromosome 22 open reading frame 23 84688 C9orf24 chromosome 9 open reading frame 24 285782 CAGE1 cancer antigen 1 51134 CCDC41 centrosomal protein 83 51019 CCDC53 WASH complex subunit 3 51622 CCZ1 CCZ1 homolog, vacuolar protein trafficking and biogenesis associated 23406 COTL1 coactosin like F-actin binding protein 1 27132 CPNE7 copine 7 85359 DGCR6L DiGeorge syndrome critical region gene 6 like 286499 FAM133A family with sequence similarity 133 member A 253725 FAM21A WASH complex subunit 2C 387680 FAM21B WASH complex subunit 2A NA FAM21D 23307 FKBP15 FK506 binding protein 15 652968 GATSL3 cytosolic arginine sensor for mTORC1 subunit 1 2803 GOLGA4 golgin A4 2824 GPM6B glycoprotein M6B 25900 IFFO1 intermediate filament family orphan 1 23288 IQCE IQ motif containing E 9897 KIAA0196 WASH complex subunit 5 9729 KIAA0408 KIAA0408 23325 KIAA1033 WASH complex subunit 4 201255 LRRC45 leucine rich repeat containing 45 8581 LY6D lymphocyte antigen 6 family member D 55700 MAP7D1 MAP7 domain containing 1 26509 MYOF myoferlin 145781 MYZAP GRINL1A complex locus 1 54550 NECAB2 N-terminal EF-hand calcium binding protein 2 55247 NEIL3 nei like DNA glycosylase 3 399909 PCNXL3 pecanex 3 9883 POM121 POM121 transmembrane nucleoporin 57148 RALGAPB Ral GTPase activating protein non-catalytic beta subunit 201299 RDM1 RAD52 motif containing 1 6273 S100A2 S100 calcium binding protein A2 113174 SAAL1 serum amyloid A like 1 63898 SH2D4A SH2 domain containing 4A 8406 SRPX sushi repeat containing protein X-linked 93081 TEX30 testis expressed 30 25880 TMEM186 transmembrane protein 186 57217 TTC7A tetratricopeptide repeat domain 7A 55591 VEZT vezatin, adherens junctions transmembrane protein NA WASH4P 653440 WASH6P WAS protein family homolog 6, pseudogene 84272 YIPF4 Yip1 domain family member 4 51101 ZC2HC1A zinc finger C2HC-type containing 1A

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).

No specific annotations were found for this module

All enriched annotations

Gene Ontology

P-value1 FDR2 Term 0.00e+00 0.00e+00 WASH complex 6.03e-08 2.15e-05 early endosome 2.14e-06 9.54e-04 endosomal transport 6.08e-06 2.47e-03 retrograde transport, endosome to Golgi 3.36e-05 1.13e-02 endomembrane system organization 4.22e-05 1.39e-02 plasma membrane organization 4.45e-05 1.45e-02 establishment of protein localization to plasma membrane 5.05e-05 1.62e-02 cytosolic transport 8.29e-05 1.67e-02 endosome 1.43e-04 2.82e-02 alpha-tubulin binding 2.94e-04 7.23e-02 Golgi to plasma membrane protein transport 4.23e-04 9.77e-02 protein localization to plasma membrane 4.78e-04 7.77e-02 early endosome membrane 9.70e-04 1.93e-01 Arp2/3 complex-mediated actin nucleation 9.90e-04 1.96e-01 actin nucleation 1.48e-03 2.72e-01 establishment of protein localization to membrane 1.53e-03 2.09e-01 recycling endosome membrane 1.56e-03 2.83e-01 Golgi to plasma membrane transport 1.60e-03 2.89e-01 regulation of actin cytoskeleton organization 1.85e-03 3.25e-01 regulation of actin filament-based process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 4.20e-02 1e+00 REGULATION OF GLUCOKINASE BY GLUCOKINASE REGULATORY PROTEIN 4.20e-02 1e+00 INTERACTIONS OF VPR WITH HOST CELLULAR PROTEINS 4.20e-02 1e+00 TRANSPORT OF RIBONUCLEOPROTEINS INTO THE HOST NUCLEUS 4.32e-02 1e+00 GLUCOSE TRANSPORT 4.36e-02 1e+00 NEP NS2 INTERACTS WITH THE CELLULAR EXPORT MACHINERY 4.81e-02 1e+00 TRANSPORT OF MATURE MRNA DERIVED FROM AN INTRONLESS TRANSCRIPT 4.82e-02 1e+00 TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.88e-03 1e+00 colorless urine 3.76e-03 1e+00 abnormal tail pigmentation 3.76e-03 1e+00 epidermal necrosis 5.64e-03 1e+00 hypergranulosis 7.50e-03 1e+00 abnormal stomach non-glandular epithelium morphology 7.50e-03 1e+00 abnormal mineral level 7.51e-03 1e+00 erythroblastosis 7.51e-03 1e+00 abnormal erythrocyte cell number 7.52e-03 1e+00 acanthocytosis 9.39e-03 1e+00 orthokeratosis 1.12e-02 1e+00 decreased skeletal muscle fiber density 1.12e-02 1e+00 decreased megakaryocyte cell number 1.13e-02 1e+00 flaky skin 1.30e-02 1e+00 delayed blastocyst hatching from the zona pellucida 1.31e-02 1e+00 skeletal muscle fiber degeneration 1.31e-02 1e+00 deformed nails 1.31e-02 1e+00 parakeratosis 1.49e-02 1e+00 abnormal deltoid tuberosity morphology 1.49e-02 1e+00 increased body mass index 1.49e-02 1e+00 abnormal iron level

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

²FDR corrected p-value (Benjamini-Hochberg)