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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod130

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod130 Module size 21 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 403 ARL3 ADP ribosylation factor like GTPase 3 8915 BCL10 B cell CLL/lymphoma 10 7809 BSND barttin CLCNK type accessory beta subunit 84270 C9orf89 caspase recruitment domain family member 19 11092 C9orf9 sperm acrosome associated 9 79827 CLMP CXADR like membrane protein 51181 DCXR dicarbonyl and L-xylulose reductase 84080 ENKD1 enkurin domain containing 1 65983 GRAMD3 GRAM domain containing 2B 51512 GTSE1 G2 and S-phase expressed 1 283987 HID1 HID1 domain containing 22832 KIAA1009 centrosomal protein 162 54627 KIAA1383 microtubule associated protein 10 284451 ODF3L2 outer dense fiber of sperm tails 3 like 2 51308 REEP2 receptor accessory protein 2 6102 RP2 RP2, ARL3 GTPase activating protein 27230 SERP1 stress associated endoplasmic reticulum protein 1 9751 SNPH syntaphilin 727837 SSX2B SSX family member 2B 54867 TMEM214 transmembrane protein 214 55829 VIMP selenoprotein S

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 1.40e-01 1.05e-29 GO cytoplasmic microtubule cellular_component 1.22e-01 6.16e-06 Reactome Trafficking of myristoylated proteins to the cilium 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 cytoplasmic microtubule 0.00e+00 0.00e+00 microtubule 0.00e+00 0.00e+00 supramolecular fiber 1.95e-03 3.34e-01 protein transport into membrane raft 2.56e-03 4.16e-01 glucose metabolic process 3.15e-03 4.91e-01 post-Golgi vesicle-mediated transport 3.47e-03 4.15e-01 periciliary membrane compartment 3.89e-03 5.71e-01 post-chaperonin tubulin folding pathway 3.89e-03 5.71e-01 D-xylose metabolic process 3.89e-03 5.71e-01 glucuronate catabolic process to xylulose 5-phosphate 3.94e-03 5.76e-01 protein localization to membrane raft 5.15e-03 7.11e-01 hexose metabolic process 5.84e-03 7.72e-01 endoplasmic reticulum tubular network organization 5.98e-03 7.83e-01 positive regulation of mast cell cytokine production 7.12e-03 7.30e-01 lipopolysaccharide receptor complex 7.77e-03 9.47e-01 xylulose metabolic process 7.87e-03 9.51e-01 interleukin-6 production 7.87e-03 9.51e-01 regulation of microtubule binding 7.97e-03 9.58e-01 negative regulation of mature B cell apoptotic process 8.15e-03 9.75e-01 monosaccharide metabolic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.44e-03 3.35e-01 DOWNSTREAM TCR SIGNALING 5.18e-03 4.70e-01 ACTIVATION OF NF KAPPAB IN B CELLS 5.44e-03 4.40e-01 DOWNSTREAM TCR SIGNALING 6.92e-03 5.95e-01 DOWNSTREAM SIGNALING EVENTS OF B CELL RECEPTOR BCR 8.95e-03 6.71e-01 ACTIVATION OF NF KAPPAB IN B CELLS 9.01e-03 6.75e-01 DOWNSTREAM SIGNALING EVENTS OF B CELL RECEPTOR BCR 9.90e-03 7.27e-01 TCR SIGNALING 1.03e-02 8.15e-01 TCR SIGNALING 1.21e-02 9.26e-01 SIGNALING BY THE B CELL RECEPTOR BCR 1.90e-02 1.00e+00 SIGNALING BY THE B CELL RECEPTOR BCR 2.32e-02 1.00e+00 ACTIVATION OF CHAPERONE GENES BY XBP1S 3.74e-02 1.00e+00 ACTIVATION OF CHAPERONE GENES BY XBP1S

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.74e-03 1e+00 increased circulating bicarbonate level 3.74e-03 1e+00 bile duct inflammation 5.60e-03 1e+00 abnormal extrahepatic bile duct morphology 5.61e-03 1e+00 dilated gallbladder 5.61e-03 1e+00 pancreas cysts 5.61e-03 1e+00 increased hindbrain apoptosis 5.61e-03 1e+00 decreased activated T cell number 5.61e-03 1e+00 abnormal immune cell physiology 7.47e-03 1e+00 hypokalemia 7.47e-03 1e+00 alkalosis 7.48e-03 1e+00 decreased circulating growth hormone level 9.33e-03 1e+00 small thyroid gland 9.33e-03 1e+00 small pituitary gland 9.37e-03 1e+00 absent vibrissae 1.12e-02 1e+00 abnormal synaptic bouton morphology 1.12e-02 1e+00 abnormal neural fold elevation formation 1.12e-02 1e+00 small adenohypophysis 1.30e-02 1e+00 abnormal bile duct morphology 1.30e-02 1e+00 abnormal marginal zone B cell physiology 1.30e-02 1e+00 small adrenal glands

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

²FDR corrected p-value (Benjamini-Hochberg)