Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod371

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod371 Module size 47 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10863 ADAM23 ADAM metallopeptidase domain 28 10551 AGR2 anterior gradient 2, protein disulphide isomerase family member 57463 AMIGO1 adhesion molecule with Ig like domain 1 347902 AMIGO2 adhesion molecule with Ig like domain 2 386724 AMIGO3 adhesion molecule with Ig like domain 3 339201 ASB16-AS1 ASB16 antisense RNA 1 8938 BAIAP3 BAI1 associated protein 3 8419 BFSP2 beaded filament structural protein 2 819 CAMLG calcium modulating ligand 912 CD1D CD1d molecule 976 CD97 adhesion G protein-coupled receptor E5 84518 CNFN cornifelin 8292 COLQ collagen like tail subunit of asymmetric acetylcholinesterase 102724652 CRYAA crystallin alpha A2 1411 CRYBA1 crystallin beta A1 1412 CRYBA2 crystallin beta A2 1417 CRYBB3 crystallin beta B3 1420 CRYGC crystallin gamma C 1485 CTAG1B cancer/testis antigen 1B 1509 CTSD cathepsin D 30817 EMR2 adhesion G protein-coupled receptor E2 54845 ESRP1 epithelial splicing regulatory protein 1 80004 ESRP2 epithelial splicing regulatory protein 2 2125 EVPL envoplakin 2350 FOLR2 folate receptor beta 27190 IL17B interleukin 17B 79070 KDELC1 KDEL motif containing 1 387264 KRTAP5-1 keratin associated protein 5-1 10314 LANCL1 LanC like 1 10609 LEPREL4 prolyl 3-hydroxylase family member 4 (non-enzymatic) 4014 LOR loricrin 26020 LRP10 LDL receptor related protein 10 4241 MFI2 melanotransferrin 23154 NCDN neurochondrin 9796 PHYHIP phytanoyl-CoA 2-hydroxylase interacting protein 5304 PIP prolactin induced protein 51535 PPHLN1 periphilin 1 79170 PRR15L proline rich 15 like 5660 PSAP prosaposin 9783 RIMS3 regulating synaptic membrane exocytosis 3 138065 RNF183 ring finger protein 183 8796 SCEL sciellin 6440 SFTPC surfactant protein C 9368 SLC9A3R1 SLC9A3 regulator 1 6699 SPRR1B small proline rich protein 1B 6707 SPRR3 small proline rich protein 3 326340 ZAR1 zygote arrest 1

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 1.57e-01 3.46e-12 GO structural constituent of eye lens molecular_function 1.19e-01 4.30e-03 Reactome Defective pro-SFTPC causes pulmonary surfactant metabolism dysfunction 2 (SMDP2) and respiratory distress syndrome (RDS) Disease 2.39e-02 4.92e-09 GO cornified envelope cellular_component 1.19e-03 2.94e-04 GO negative regulation of phosphatidylinositol 3-kinase signaling 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 1.49e-11 9.76e-09 structural constituent of eye lens 3.38e-09 2.34e-06 epithelial cell differentiation 3.65e-09 1.53e-06 cornified envelope 3.32e-08 2.01e-05 epidermal cell differentiation 2.24e-07 1.19e-04 epidermis development 3.33e-07 1.73e-04 keratinocyte differentiation 9.28e-07 2.96e-04 structural molecule activity 1.56e-06 7.16e-04 skin development 2.92e-06 1.27e-03 keratinization 3.43e-06 1.47e-03 peptide cross-linking 5.79e-06 2.36e-03 regulation of synapse assembly 3.72e-05 1.24e-02 regulation of synapse organization 3.89e-05 1.29e-02 regulation of synapse structure or activity 8.41e-05 2.52e-02 negative regulation of phosphatidylinositol 3-kinase signaling 1.10e-04 3.17e-02 visual perception 1.12e-04 3.22e-02 sensory perception of light stimulus 1.21e-04 3.44e-02 positive regulation of synapse assembly 1.31e-04 3.67e-02 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules 2.88e-04 5.20e-02 aspartic-type endopeptidase activity 3.05e-04 7.46e-02 lens development in camera-type eye

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.46e-03 1.63e-01 CLASS B 2 SECRETIN FAMILY RECEPTORS 1.10e-02 7.90e-01 CLASS B 2 SECRETIN FAMILY RECEPTORS 1.28e-02 8.97e-01 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2 2.33e-02 1.00e+00 GLYCOSPHINGOLIPID METABOLISM 2.53e-02 1.00e+00 SPHINGOLIPID METABOLISM 3.53e-02 1.00e+00 GLYCOSPHINGOLIPID METABOLISM 3.85e-02 1.00e+00 PLATELET ACTIVATION SIGNALING AND AGGREGATION 4.42e-02 1.00e+00 GPCR LIGAND BINDING 4.71e-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 6.20e-05 1.64e-01 small lens 9.66e-05 2.21e-01 abnormal lens fiber morphology 1.46e-04 2.92e-01 abnormal intestinal mucosa morphology 3.44e-04 4.86e-01 abnormal antigen presentation 5.99e-04 6.74e-01 total cataracts 6.76e-04 7.22e-01 nuclear cataracts 1.06e-03 9.29e-01 tonic seizures 1.93e-03 1.00e+00 colitis 2.65e-03 1.00e+00 cataract 3.05e-03 1.00e+00 microphthalmia 3.43e-03 1.00e+00 abnormal intestinal goblet cell morphology 3.61e-03 1.00e+00 kidney inflammation 5.16e-03 1.00e+00 abnormal liver morphology 5.61e-03 1.00e+00 subcapsular cataracts 5.62e-03 1.00e+00 increased spinal cord size 5.63e-03 1.00e+00 abnormal interleukin-4 secretion 5.64e-03 1.00e+00 straub tail 6.32e-03 1.00e+00 increased cell proliferation 7.30e-03 1.00e+00 ataxia 7.49e-03 1.00e+00 abnormal NK T cell morphology

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

²FDR corrected p-value (Benjamini-Hochberg)