GeneDB4PCa: Developing and Curating a Comprehensive Gene Database for Prostate Cancer Single Nucleotide Polymorphisms

Disease-specific databases have been established as an efficient approach to facilitating the sharing, annotation, integration, and analysis, of variations in all genes across all diseases. Genetic information on prostate cancer is still scattered around in numerous resources, with none successfully having all of it. GeneDB4PCa integrates all the single nucleotide polymorphisms associated with prostate cancer, their corresponding genes, and gene level annotation in a one-stop interface for the benefit of physicians and researchers.SNPs and their corresponding genes were curated from the literature and further annotated with basic information, domain function, molecular function, gene ontology, disease and phenotype information, and drug-gene interaction. Annotation metadata were retrieved from existing databases such as HGNC, InterPro, OMIM, GO database, and DGID via their APIs using R scripts, and manually retrieved from UniProtKB and InterPro. The GeneDB4PCa is a three-tier architectural system with a presentation layer, logic layer, and server and database layer. The presentation layer consists of the application user interface developed using HTML, CSS, and JavaScript while the logic layer was developed using PHP, and the data is stored and organised using MySQL. Annotation revealed that prostate cancer-associated genes are involved in regulating DNA transcription factor activity, and gland development. They perform molecular functions such as DNA binding transcription activator activity and are associated with cellular components such as cell-cell junction, nuclear spec, ciliary plasm, ciliary basal body, axoneme, actin filament, and actomyosin. These genes further interact as agonists, inhibitors, modulators, antagonists, antibodies, or a combination of these with certain drugs, and additionally influence phenotypes and diseases such as androgen insensitivity, Budd-Chiari syndrome, Microvascular complications of diabetes, Myelofibrosis, Nephronophthisis, Thrombocythemia, Hypospadias. GeneDB4PCa can be found at https://gene.comnavig.com/.