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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod185

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod185 Module size 26 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 869 CBLN1 cerebellin 1 precursor 147381 CBLN2 cerebellin 2 precursor 643866 CBLN3 cerebellin 3 precursor 140689 CBLN4 cerebellin 4 precursor 1080 CFTR cystic fibrosis transmembrane conductance regulator 1193 CLIC2 chloride intracellular channel 2 25932 CLIC4 chloride intracellular channel 4 53405 CLIC5 chloride intracellular channel 5 54102 CLIC6 chloride intracellular channel 6 286464 CXorf22 cilia and flagella associated protein 47 10243 GPHN gephyrin 374918 IGFL1 IGF like family member 1 388555 IGFL3 IGF like family member 3 81689 ISCA1 iron-sulfur cluster assembly 1 122961 ISCA2 iron-sulfur cluster assembly 2 55034 MOCOS molybdenum cofactor sulfurase 4810 NHS NHS actin remodeling regulator 5023 P2RX1 purinergic receptor P2X 1 22953 P2RX2 purinergic receptor P2X 2 5024 P2RX3 purinergic receptor P2X 3 5334 PLCL1 phospholipase C like 1 (inactive) 54870 QRICH1 glutamine rich 1 92400 RBM18 RNA binding motif protein 18 221409 SPATS1 spermatogenesis associated serine rich 1 56674 TMEM9B TMEM9 domain family member B 4308 TRPM1 transient receptor potential cation channel subfamily M member 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 1.09e-01 4.71e-08 GO purinergic nucleotide receptor activity molecular_function 1.09e-01 4.71e-08 GO extracellularly ATP-gated cation channel activity molecular_function 5.79e-02 1.93e-05 GO Mo-molybdopterin cofactor biosynthetic process biological_process 5.44e-02 1.93e-05 Reactome Molybdenum cofactor biosynthesis Metabolism 2.39e-02 2.07e-09 GO chloride channel complex cellular_component 2.10e-02 3.49e-03 Reactome RHO GTPases regulate CFTR trafficking Signal Transduction 5.43e-03 1.93e-07 GO voltage-gated ion channel activity molecular_function 5.31e-03 8.44e-05 Reactome Mitochondrial iron-sulfur cluster biogenesis Metabolism

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 2.60e-09 1.30e-06 ion channel activity 5.33e-09 2.53e-06 channel activity 5.33e-09 2.53e-06 passive transmembrane transporter activity 2.51e-08 9.44e-06 chloride channel complex 9.12e-08 3.53e-05 chloride channel activity 1.02e-07 3.92e-05 anion channel activity 1.04e-07 5.86e-05 chloride transmembrane transport 1.13e-07 6.33e-05 chloride transport 1.17e-07 4.44e-05 chloride transmembrane transporter activity 1.05e-06 4.97e-04 regulation of ion transport 1.20e-06 5.61e-04 inorganic anion transport 5.16e-06 2.13e-03 purinergic nucleotide receptor signaling pathway 8.16e-06 3.23e-03 anion transmembrane transport 1.08e-05 2.80e-03 extracellular ATP-gated cation channel activity 1.15e-05 2.79e-03 integral component of nuclear inner membrane 1.35e-05 5.06e-03 Mo-molybdopterin cofactor biosynthetic process 2.00e-05 4.93e-03 purinergic nucleotide receptor activity 2.25e-05 7.97e-03 response to ATP 2.40e-05 8.43e-03 protein maturation by iron-sulfur cluster transfer 2.47e-05 8.65e-03 molybdopterin cofactor metabolic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 8.37e-04 8.58e-02 ELEVATION OF CYTOSOLIC CA2 LEVELS 8.38e-04 8.58e-02 PLATELET CALCIUM HOMEOSTASIS 2.78e-03 2.81e-01 METABOLISM OF VITAMINS AND COFACTORS 3.29e-03 3.25e-01 ELEVATION OF CYTOSOLIC CA2 LEVELS 3.30e-03 3.25e-01 PLATELET CALCIUM HOMEOSTASIS 7.60e-03 5.86e-01 PLATELET HOMEOSTASIS 8.07e-03 6.16e-01 METABOLISM OF VITAMINS AND COFACTORS 1.32e-02 9.91e-01 PLATELET HOMEOSTASIS 2.93e-02 1.00e+00 ABC FAMILY PROTEINS MEDIATED TRANSPORT

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.17e-04 2.5e-01 abnormal vas deferens morphology 4.59e-03 1.0e+00 decreased litter size 5.61e-03 1.0e+00 decreased keratinocyte migration 5.64e-03 1.0e+00 dilated gallbladder 5.64e-03 1.0e+00 abnormal lacrimal gland morphology 5.64e-03 1.0e+00 coiled cecum 5.64e-03 1.0e+00 increased respiratory mucosa goblet cell number 6.79e-03 1.0e+00 abnormal nervous system electrophysiology 7.48e-03 1.0e+00 pancreatic acinar cell zymogen granule accumulation 7.49e-03 1.0e+00 abnormal uterine cervix morphology 7.51e-03 1.0e+00 abnormal nasal mucosa morphology 7.51e-03 1.0e+00 small cecum 9.12e-03 1.0e+00 abnormal pulmonary alveolus morphology 9.33e-03 1.0e+00 abnormal chemical nociception 9.35e-03 1.0e+00 abnormal lens capsule morphology 9.36e-03 1.0e+00 enlarged gallbladder 9.36e-03 1.0e+00 pancreatic acinar cell atrophy 9.37e-03 1.0e+00 crypts of Lieberkuhn abscesses 9.38e-03 1.0e+00 dilated pancreatic duct 9.39e-03 1.0e+00 pulmonary interstitial fibrosis

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

²FDR corrected p-value (Benjamini-Hochberg)