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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod285

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod285 Module size 10 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 54806 AHI1 Abelson helper integration site 1 27077 B9D1 B9 domain containing 1 57545 CC2D2A coiled-coil and C2 domain containing 2A 54903 MKS1 Meckel syndrome, type 1 79600 TCTN1 tectonic family member 1 79867 TCTN2 tectonic family member 2 200728 TMEM17 transmembrane protein 17 51259 TMEM216 transmembrane protein 216 79583 TMEM231 transmembrane protein 231 91147 TMEM67 transmembrane protein 67

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 5.36e-01 4.66e-34 GO MKS complex cellular_component

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 membrane docking 0.00e+00 0.00e+00 cell projection assembly 0.00e+00 0.00e+00 cilium organization 0.00e+00 0.00e+00 ciliary basal body docking 0.00e+00 0.00e+00 cilium 0.00e+00 0.00e+00 ciliary transition zone 0.00e+00 0.00e+00 MKS complex 6.77e-09 4.49e-06 smoothened signaling pathway 5.27e-07 1.61e-04 ciliary membrane 1.15e-05 4.40e-03 protein localization to ciliary transition zone 2.13e-05 7.59e-03 non-motile cilium assembly 2.93e-05 1.01e-02 embryonic morphogenesis 3.65e-05 1.22e-02 epithelial tube morphogenesis 6.07e-05 1.89e-02 tube morphogenesis 7.48e-05 2.27e-02 neural tube formation 8.87e-05 1.77e-02 cell projection membrane 9.11e-05 2.70e-02 embryonic epithelial tube formation 1.03e-04 2.99e-02 epithelial tube formation

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.02e-09 3.80e-05 preaxial polydactyly 3.95e-09 1.13e-04 holoprosencephaly 3.60e-08 6.47e-04 abnormal embryonic neuroepithelium morphology 9.00e-07 8.06e-03 polycystic kidney 1.98e-06 1.46e-02 absent embryonic cilia 2.18e-06 1.56e-02 abnormal renal tubule epithelial cell primary cilium morphology 3.54e-06 2.24e-02 microphthalmia 2.94e-05 1.01e-01 heterotaxia 7.10e-05 1.80e-01 cleft palate 1.10e-04 2.40e-01 decreased embryonic cilium length 1.52e-04 2.97e-01 abnormal rostral-caudal axis patterning 1.59e-04 3.06e-01 cerebellum vermis hypoplasia 2.29e-04 3.79e-01 exencephaly 2.75e-04 4.28e-01 abnormal bile duct development 2.77e-04 4.29e-01 complete lethality throughout fetal growth and development 3.19e-04 4.68e-01 abnormal cell morphology 4.02e-04 5.34e-01 duplex kidney 4.14e-04 5.42e-01 polydactyly 4.62e-04 5.79e-01 absent floor plate 5.15e-04 6.17e-01 kidney cysts

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

²FDR corrected p-value (Benjamini-Hochberg)