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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod299

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod299 Module size 59 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 5624 APC protein C, inactivator of coagulation factors Va and VIIIa 296558 APC2 anaphase promoting complex subunit 2 149478 BTBD19 BTB domain containing 19 54494 C11orf71 chromosome 11 open reading frame 71 29919 C18orf8 regulator of MON1-CCZ1 255057 C19orf26 CACN subunit beta associated regulatory protein 154743 C7orf60 base methyltransferase of 25S rRNA 2 homolog 138162 C9orf116 chromosome 9 open reading frame 116 54897 CASZ1 castor zinc finger 1 114800 CCDC85A coiled-coil domain containing 85A 440193 CCDC88C coiled-coil domain containing 88C 50937 CDON cell adhesion associated, oncogene regulated 51550 CINP cyclin dependent kinase 2 interacting protein 1455 CSNK1G2 casein kinase 1 gamma 2 1499 CTNNB1 catenin beta 1 56998 CTNNBIP1 catenin beta interacting protein 1 51339 DACT1 dishevelled binding antagonist of beta catenin 1 168002 DACT2 dishevelled binding antagonist of beta catenin 2 147906 DACT3 dishevelled binding antagonist of beta catenin 3 27121 DKK4 dickkopf WNT signaling pathway inhibitor 4 65989 DLK2 delta like non-canonical Notch ligand 2 90288 EFCAB12 EF-hand calcium binding domain 12 161436 EML5 echinoderm microtubule associated protein like 5 219287 FAM123A APC membrane recruitment protein 2 139285 FAM123B APC membrane recruitment protein 1 205147 FAM123C APC membrane recruitment protein 3 201294 FHL3 unc-13 homolog D 9457 FHL5 four and a half LIM domains 5 24147 FJX1 four jointed box 1 10023 FRAT1 FRAT1, WNT signaling pathway regulator 23401 FRAT2 FRAT2, WNT signaling pathway regulator 54810 GIPC2 GIPC PDZ domain containing family member 2 126326 GIPC3 GIPC PDZ domain containing family member 3 57120 GOPC golgi associated PDZ and coiled-coil motif containing 51704 GPRC5B G protein-coupled receptor class C group 5 member B 29923 HILPDA hypoxia inducible lipid droplet associated 57536 KIAA1328 KIAA1328 313498 LMBR1 Cd72 molecule 4008 LMO7 LIM domain 7 9175 MAP3K13 mitogen-activated protein kinase kinase kinase 13 23184 MESDC2 mesoderm development LRP chaperone 57701 NCKAP5L NCK associated protein 5 like 85409 NKD2 naked cuticle homolog 2 729330 OC90 otoconin 90 5017 OVOL1 ovo like transcriptional repressor 1 58495 OVOL2 ovo like zinc finger 2 7849 PAX8 paired box 8 130271 PLEKHH2 pleckstrin homology, MyTH4 and FERM domain containing H2 29964 PRICKLE4 prickle planar cell polarity protein 4 26575 RGS17 regulator of G protein signaling 17 5998 RGS3 regulator of G protein signaling 3 340419 RSPO2 R-spondin 2 6358 SCYL2 C-C motif chemokine ligand 14 6477 SIAH1 siah E3 ubiquitin protein ligase 1 132851 SPATA4 spermatogenesis associated 4 23075 SWAP70 switching B cell complex subunit SWAP70 83591 THAP2 THAP domain containing 2 128025 WDR64 WD repeat domain 64 7739 ZNF185 zinc finger protein 185 with LIM domain

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 2.55e-01 1.83e-13 GO beta-catenin destruction complex cellular_component 2.24e-01 2.33e-07 GO delta-catenin binding molecular_function 1.89e-01 2.33e-03 Reactome APC truncation mutants are not K63 polyubiquitinated Disease 2.80e-02 6.97e-03 Reactome RHO GTPases regulate CFTR trafficking Signal Transduction 1.70e-02 8.59e-09 Reactome Disassembly of the destruction complex and recruitment of AXIN to the membrane Signal Transduction 8.11e-04 9.35e-08 GO negative regulation of Wnt signaling pathway 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 0.00e+00 0.00e+00 Wnt signaling pathway 1.71e-10 8.56e-08 beta-catenin destruction complex 1.47e-08 9.37e-06 regulation of Wnt signaling pathway 1.85e-08 8.09e-06 beta-catenin binding 2.64e-07 1.39e-04 regulation of canonical Wnt signaling pathway 4.07e-07 1.39e-04 delta-catenin binding 9.45e-07 4.52e-04 beta-catenin destruction complex disassembly 1.16e-06 5.45e-04 negative regulation of Wnt signaling pathway 4.95e-06 2.05e-03 negative regulation of canonical Wnt signaling pathway 6.10e-06 1.56e-03 catenin complex 1.54e-05 5.69e-03 canonical Wnt signaling pathway 4.42e-05 1.44e-02 protein complex disassembly 1.06e-04 2.18e-02 protein kinase A binding 1.18e-04 3.37e-02 regulation of catenin import into nucleus 1.44e-04 2.70e-02 lamellipodium 1.51e-04 2.96e-02 protein kinase binding 2.05e-04 3.85e-02 protein kinase C binding 2.73e-04 6.81e-02 regulation of nodal signaling pathway 3.35e-04 5.94e-02 kinase binding 4.83e-04 1.09e-01 branching involved in ureteric bud morphogenesis

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 4.09e-11 1.16e-08 CTNNB1 PHOSPHORYLATION CASCADE 3.91e-10 1.34e-07 CTNNB1 PHOSPHORYLATION CASCADE 3.97e-08 8.16e-06 SIGNALING BY WNT 1.32e-06 2.93e-04 SIGNALING BY WNT 3.50e-04 3.94e-02 APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS 8.78e-04 8.96e-02 APOPTOTIC EXECUTION PHASE 2.00e-03 1.86e-01 MYOGENESIS 3.01e-03 3.02e-01 MYOGENESIS 3.41e-03 3.34e-01 APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS 6.99e-03 6.00e-01 APOPTOTIC EXECUTION PHASE 7.23e-03 5.62e-01 APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS 1.03e-02 8.15e-01 ADHERENS JUNCTIONS INTERACTIONS 1.08e-02 7.78e-01 SYNTHESIS SECRETION AND INACTIVATION OF GLP1 1.26e-02 8.86e-01 INCRETIN SYNTHESIS SECRETION AND INACTIVATION 1.26e-02 8.86e-01 ADHERENS JUNCTIONS INTERACTIONS 1.63e-02 1.00e+00 CELL CELL JUNCTION ORGANIZATION 1.71e-02 1.00e+00 APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS 1.71e-02 1.00e+00 SYNTHESIS SECRETION AND INACTIVATION OF GLP1 1.71e-02 1.00e+00 INCRETIN SYNTHESIS SECRETION AND INACTIVATION 1.82e-02 1.00e+00 APOPTOSIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.02e-04 2.29e-01 dilated uterine cervix 3.22e-04 4.70e-01 growth retardation of incisors 6.07e-04 6.78e-01 detached acrosome 8.51e-04 8.22e-01 single kidney 1.13e-03 9.65e-01 abnormal maxillary shelf morphology 1.13e-03 9.65e-01 abnormal sperm nucleus morphology 1.16e-03 9.82e-01 small pharyngeal arch 1.58e-03 1.00e+00 absent kidney 1.60e-03 1.00e+00 abnormal hindgut morphology 1.88e-03 1.00e+00 abnormal maxillary prominence morphology 1.92e-03 1.00e+00 abnormal maxilla morphology 2.02e-03 1.00e+00 abnormal acrosome morphology 2.21e-03 1.00e+00 increased intestinal adenoma incidence 3.05e-03 1.00e+00 cardia bifida 3.07e-03 1.00e+00 increased gastrointestinal tumor incidence 3.33e-03 1.00e+00 increased intestinal adenocarcinoma incidence 3.34e-03 1.00e+00 abnormal digestive system development 3.44e-03 1.00e+00 vagina atresia 4.84e-03 1.00e+00 delayed kidney development 5.61e-03 1.00e+00 abnormal neural crest cell delamination

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

²FDR corrected p-value (Benjamini-Hochberg)