Search of phenotype related candidate genes using gene ontology-based semantic similarity and protein interaction information: application to Brugada syndrome.
This work presents a methodology for finding phenotype candidate genes starting from a set of known related genes. This is accomplished by automatically mining and organizing the available scientific literature using Gene Ontology-based semantic similarity. As a case study, Brugada syndrome related genes have been used as input in order to obtain a list of other possible candidate genes related with this disease. Brugada anomaly produces a typical alteration in the Electrocardiogram and carriers of the disease show an increased probability of sudden death. Results show a set of semantically coherent proteins that are shown to be related with synaptic transmission and muscle contraction physiological processes.
Massanet
Raimon
R
Biomedical Engineering Research Center (CREB), Technical University of Catalonia (UPC). raimon.massanet@upc.edu
Gallardo-Chacon
Joan-Josep
JJ
Caminal
Pere
P
Perera
Alexandre
A
D001698:Biomedical Engineering; D053840:Brugada Syndrome / Q000235:genetics* / Q000503:physiopathology; D020746:Calcium Channels, L-Type / Q000235:genetics; D057225:Data Mining; D030541:Databases, Genetic; D030562:Databases, Protein; D005796:Genes; D056726:Genetic Association Studies; D006801:Humans; D009124:Muscle Proteins / Q000235:genetics; D009200:Myocardial Contraction / Q000235:genetics; D062554:NAV1.5 Voltage-Gated Sodium Channel; D025941:Protein Interaction Mapping; D012660:Semantics; D015222:Sodium Channels / Q000235:genetics; D009435:Synaptic Transmission / Q000235:genetics
C079146:CACNA1C protein, human; D020746:Calcium Channels, L-Type; D009124:Muscle Proteins; D062554:NAV1.5 Voltage-Gated Sodium Channel; C568320:SCN5A protein, human; D015222:Sodium Channels