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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod254

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod254 Module size 26 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 55198 APPL2 adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 2 10139 ARFRP1 ADP ribosylation factor related protein 1 200894 ARL13B ADP ribosylation factor like GTPase 13B 339231 ARL16 ADP ribosylation factor like GTPase 16 50807 ASAP1 ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 157807 CLVS1 clavesin 1 134829 CLVS2 clavesin 2 57589 KIAA1432 RIC1 homolog, RAB6A GEF complex partner 1 23041 MON2 MON2 homolog, regulator of endosome-to-Golgi trafficking 158747 MOSPD2 motile sperm domain containing 2 114884 OSBPL10 oxysterol binding protein like 10 114885 OSBPL11 oxysterol binding protein like 11 114879 OSBPL5 oxysterol binding protein like 5 114882 OSBPL8 oxysterol binding protein like 8 114883 OSBPL9 oxysterol binding protein like 9 6017 RLBP1 retinaldehyde binding protein 1 6397 SEC14L1 SEC14 like lipid binding 1 23541 SEC14L2 SEC14 like lipid binding 2 266629 SEC14L3 SEC14 like lipid binding 3 284904 SEC14L4 SEC14 like lipid binding 4 9717 SEC14L5 SEC14 like lipid binding 5 730005 SEC14L6 SEC14 like lipid binding 6 685079 SYS1 Sys1 golgi trafficking protein 373 TRIM23 tripartite motif containing 23 7274 TTPA alpha tocopherol transfer protein 79183 TTPAL alpha tocopherol transfer protein like

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 4.29e-01 1.22e-03 Reactome Vitamin E Metabolism 2.01e-01 1.29e-12 GO sterol binding molecular_function 3.47e-02 3.25e-12 GO sterol transporter activity molecular_function 2.81e-02 3.66e-03 Reactome ARL13B-mediated ciliary trafficking of INPP5E Organelle biogenesis and maintenance 2.77e-02 4.47e-07 GO phospholipid transporter activity molecular_function

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 lipid binding 1.81e-08 7.92e-06 phospholipid binding 3.30e-08 1.37e-05 phosphatidylinositol phosphate binding 5.42e-07 1.80e-04 phosphatidylinositol binding 1.54e-06 4.72e-04 phosphatidylserine binding 2.04e-06 5.66e-04 trans-Golgi network membrane 2.36e-06 6.98e-04 vitamin E binding 3.66e-06 1.56e-03 phosphatidylserine acyl-chain remodeling 3.79e-06 1.08e-03 alcohol binding 4.02e-06 1.70e-03 post-Golgi vesicle-mediated transport 8.13e-06 2.16e-03 phosphatidylinositol bisphosphate binding 8.62e-06 3.39e-03 phosphatidylserine metabolic process 8.68e-06 3.41e-03 lipid transport 1.22e-05 4.63e-03 lipid localization 1.33e-05 3.38e-03 modified amino acid binding 1.87e-05 4.63e-03 lipid transporter activity 2.36e-05 8.31e-03 phospholipid transport 3.17e-05 7.51e-03 cholesterol binding 3.39e-05 1.14e-02 Golgi to plasma membrane transport 4.36e-05 1.00e-02 sterol binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.76e-04 6.6e-01 retinal degeneration 1.87e-03 1.0e+00 abnormal vitamin E level 1.87e-03 1.0e+00 abnormal somatosensory cortex physiology 1.88e-03 1.0e+00 head shaking 3.74e-03 1.0e+00 absent extraembryonic coelom 3.74e-03 1.0e+00 increased circulating phospholipid level 3.75e-03 1.0e+00 skeletal muscle fiber atrophy 5.61e-03 1.0e+00 paresis 5.61e-03 1.0e+00 abnormal spinal cord ventral horn morphology 5.61e-03 1.0e+00 absent ectoplacental cavity 5.63e-03 1.0e+00 spina bifida 5.64e-03 1.0e+00 delayed dark adaptation 7.48e-03 1.0e+00 disorganized retinal layers 7.48e-03 1.0e+00 dystonia 7.49e-03 1.0e+00 abnormal egg cylinder morphology 7.51e-03 1.0e+00 placental labyrinth hypoplasia 1.12e-02 1.0e+00 decreased retinal photoreceptor cell number 1.12e-02 1.0e+00 increased variability of skeletal muscle fiber size 1.12e-02 1.0e+00 decreased trophoblast giant cell number 1.12e-02 1.0e+00 decreased circulating VLDL cholesterol level

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

²FDR corrected p-value (Benjamini-Hochberg)