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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod296

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod296 Module size 42 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 41 ASIC1 acid sensing ion channel subunit 1 40 ASIC2 acid sensing ion channel subunit 2 682 BSG basigin (Ok blood group) 54836 BSPRY B-box and SPRY domain containing 10462 CLEC10A C-type lectin domain containing 10A 1260 CNGA2 cyclic nucleotide gated channel alpha 2 1368 CPM carboxypeptidase M 160518 DENND5B DENN domain containing 5B 50506 DUOX2 dual oxidase 2 151651 EFHB EF-hand domain family member B 166752 FREM3 FRAS1 related extracellular matrix 3 2596 GAP43 growth associated protein 43 2993 GYPA glycophorin A (MNS blood group) 8689 KRT36 keratin 36 3964 LGALS8 galectin 8 23324 MAN2B2 mannosidase alpha class 2B member 2 375056 MIA3 MIA SH3 domain ER export factor 3 84073 MYCBPAP MYCBP associated protein 401 NCAM2 paired like homeobox 2A 57502 NLGN4X neuroligin 4 X-linked 115677 NOSTRIN nitric oxide synthase trafficking 9381 OTOF otoferlin 23022 PALLD palladin, cytoskeletal associated protein 51248 PDZD11 PDZ domain containing 11 145814 PGPEP1L pyroglutamyl-peptidase I like 219348 PLAC9 placenta specific 9 5354 PLP1 proteolipid protein 1 5420 PODXL podocalyxin like 5630 PRPH peripherin 57127 RHBG Rh family B glycoprotein (gene/pseudogene) 6006 RHCE Rh blood group CcEe antigens 6274 S100A3 S100 calcium binding protein A3 29970 SCHIP1 schwannomin interacting protein 1 256987 SERINC5 serine incorporator 5 201232 SLC16A13 solute carrier family 16 member 13 9123 SLC16A3 solute carrier family 16 member 3 81609 SNX27 sorting nexin family member 27 8128 ST8SIA2 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2 55576 STAB2 stabilin 2 113277 TMEM106A transmembrane protein 106A 23585 TMEM50A transmembrane protein 50A 162514 TRPV3 transient receptor potential cation channel subfamily V member 3

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 8.40e-02 6.02e-05 Reactome Proton-coupled monocarboxylate transport Transport of small molecules 5.86e-02 1.12e-04 GO ammonium transmembrane transporter activity molecular_function 3.26e-02 3.47e-06 GO monocarboxylic acid transport biological_process 1.31e-02 2.63e-04 GO response to acidic pH biological_process 1.49e-03 3.61e-04 GO glial cell differentiation biological_process

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 9.94e-05 2.06e-02 cation transmembrane transporter activity 1.20e-04 3.41e-02 cation transmembrane transport 1.39e-04 2.75e-02 acid-sensing ion channel activity 1.65e-04 4.46e-02 sensory perception of sour taste 3.32e-04 8.00e-02 neuron cell-cell adhesion 3.40e-04 8.15e-02 calcium ion transport 3.83e-04 6.66e-02 cation channel activity 6.85e-04 1.45e-01 response to acidic pH 6.87e-04 1.45e-01 divalent metal ion transport 7.08e-04 1.49e-01 leukocyte migration 7.15e-04 1.15e-01 ligand-gated sodium channel activity 8.21e-04 1.68e-01 ammonium transmembrane transport 9.02e-04 1.82e-01 organic cation transport 9.09e-04 1.83e-01 metal ion transport 1.12e-03 2.16e-01 chemical synaptic transmission 1.18e-03 2.26e-01 detection of mechanical stimulus 1.46e-03 2.69e-01 neuron recognition 1.49e-03 2.73e-01 calcium ion transmembrane transport 1.58e-03 2.86e-01 negative regulation of synaptic transmission 1.69e-03 2.43e-01 ion channel activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.83e-04 3.89e-02 BASIGIN INTERACTIONS 4.29e-04 4.73e-02 PYRUVATE METABOLISM 5.08e-04 6.52e-02 PYRUVATE METABOLISM 6.24e-04 6.59e-02 BASIGIN INTERACTIONS 9.95e-04 1.00e-01 PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE 1.40e-03 1.36e-01 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 1.51e-03 1.68e-01 PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE 2.07e-03 2.20e-01 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 2.21e-03 2.03e-01 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 2.42e-03 2.51e-01 HYALURONAN UPTAKE AND DEGRADATION 2.42e-03 2.51e-01 HYALURONAN METABOLISM 1.08e-02 7.78e-01 BILE SALT AND ORGANIC ANION SLC TRANSPORTERS 1.09e-02 8.53e-01 TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 1.36e-02 9.40e-01 HYALURONAN UPTAKE AND DEGRADATION 1.52e-02 1.00e+00 HYALURONAN METABOLISM 1.54e-02 1.00e+00 N GLYCAN ANTENNAE ELONGATION 1.54e-02 1.00e+00 N GLYCAN ANTENNAE ELONGATION IN THE MEDIAL TRANS GOLGI 1.74e-02 1.00e+00 ENOS ACTIVATION AND REGULATION 1.81e-02 1.00e+00 BILE SALT AND ORGANIC ANION SLC TRANSPORTERS 2.14e-02 1.00e+00 ENOS ACTIVATION AND REGULATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.03e-03 9.16e-01 abnormal olfactory system physiology 1.47e-03 1.00e+00 decreased fibroblast cell migration 1.58e-03 1.00e+00 abnormal axon morphology 2.19e-03 1.00e+00 abnormal olfactory bulb morphology 2.53e-03 1.00e+00 abnormal startle reflex 3.76e-03 1.00e+00 absent bone trabeculae 5.61e-03 1.00e+00 absent optic tract 5.62e-03 1.00e+00 abnormal cerebellum white matter morphology 7.49e-03 1.00e+00 abnormal optic chiasm morphology 7.50e-03 1.00e+00 erythroderma 7.75e-03 1.00e+00 complete postnatal lethality 8.20e-03 1.00e+00 small liver 9.04e-03 1.00e+00 abnormal corneocyte envelope morphology 9.34e-03 1.00e+00 anosmia 1.12e-02 1.00e+00 abnormal sensory neuron physiology 1.12e-02 1.00e+00 abnormal inner hair cell synaptic ribbon morphology 1.12e-02 1.00e+00 thyroid gland hyperplasia 1.31e-02 1.00e+00 axonal spheroids 1.49e-02 1.00e+00 delayed inner ear development 1.68e-02 1.00e+00 partial embryonic lethality at implantation

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

²FDR corrected p-value (Benjamini-Hochberg)