Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod204

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod204 Module size 14 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 51668 HSPB11 heat shock protein family B (small) member 11 9742 IFT140 intraflagellar transport 140 90410 IFT20 intraflagellar transport 20 112752 IFT43 intraflagellar transport 43 56912 IFT46 intraflagellar transport 46 51098 IFT52 intraflagellar transport 52 117028 IFT57 bridging integrator 1 80173 IFT74 intraflagellar transport 74 28981 IFT81 intraflagellar transport 81 8100 IFT88 intraflagellar transport 88 55171 TBCCD1 TBCC domain containing 1 79809 TTC21B tetratricopeptide repeat domain 21B 57728 WDR19 WD repeat domain 19 57539 WDR35 WD repeat domain 35

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 3.58e-01 3.37e-15 GO intraciliary transport particle A cellular_component 1.44e-01 3.24e-21 GO intraciliary transport particle B cellular_component 5.81e-02 9.29e-35 GO intraciliary transport involved in cilium assembly biological_process 3.68e-02 7.86e-34 GO ciliary tip cellular_component 3.24e-02 1.36e-34 Reactome Intraflagellar transport Organelle biogenesis and maintenance

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 organelle assembly 0.00e+00 0.00e+00 cilium assembly 0.00e+00 0.00e+00 cell projection assembly 0.00e+00 0.00e+00 smoothened signaling pathway 0.00e+00 0.00e+00 microtubule-based movement 0.00e+00 0.00e+00 microtubule-based process 0.00e+00 0.00e+00 protein complex localization 0.00e+00 0.00e+00 intraciliary transport 0.00e+00 0.00e+00 cytoskeleton-dependent intracellular transport 0.00e+00 0.00e+00 cilium organization 0.00e+00 0.00e+00 intraciliary transport involved in cilium assembly 0.00e+00 0.00e+00 transport along microtubule 0.00e+00 0.00e+00 microtubule organizing center 0.00e+00 0.00e+00 ciliary tip 0.00e+00 0.00e+00 intraciliary transport particle 0.00e+00 0.00e+00 cilium 0.00e+00 0.00e+00 intraciliary transport particle B 3.06e-12 1.75e-09 intraciliary transport particle A 3.56e-11 1.90e-08 centrosome 8.29e-11 6.93e-08 intraciliary retrograde transport

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.50e-09 1.27e-04 polydactyly 6.49e-06 3.43e-02 absent embryonic cilia 7.17e-06 3.69e-02 abnormal neural tube morphology/development 3.92e-05 1.22e-01 abnormal direction of heart looping 1.43e-04 2.88e-01 abnormal maxilla morphology 1.58e-04 3.05e-01 atrioventricular septal defect 1.61e-04 3.09e-01 abnormal cranial flexure morphology 4.04e-04 5.35e-01 exencephaly 5.08e-04 6.10e-01 abnormal direction of embryo turning 5.78e-04 6.61e-01 common atrium 6.92e-04 7.31e-01 delayed embryo turning 6.97e-04 7.33e-01 absent floor plate 1.21e-03 1.00e+00 abnormal craniofacial morphology 1.22e-03 1.00e+00 left pulmonary isomerism 1.48e-03 1.00e+00 short ribs 1.68e-03 1.00e+00 preaxial polydactyly 1.68e-03 1.00e+00 rib bifurcation 1.80e-03 1.00e+00 cleft palate 2.43e-03 1.00e+00 abnormal limb bud morphology 2.94e-03 1.00e+00 polycystic kidney

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

²FDR corrected p-value (Benjamini-Hochberg)