dbPepVar: A novel cancer proteogenomics database

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dc.contributor.authorCunha, Lucas Marques da
dc.contributor.authorTerrematte, Patrick Cesar Alves
dc.contributor.authorFiúza, Tayná da Silva
dc.contributor.authorSilva, Vandeclecio Lira da
dc.contributor.authorKroll, José Eduardo
dc.contributor.authorSouza, Sandro José de
dc.contributor.authorSouza, Gustavo Antonio de
dc.date.accessioned2022-11-29T12:55:44Z
dc.date.available2022-11-29T12:55:44Z
dc.date.issued2022-08
dc.description.resumoCancers arise from the acquisition of DNA mutations, such as substitutions, deletions, amplifications, and rearrangements. Understanding the distribution and correlation of such mutations in cancer may aid the characterization of the disease and subsequent identification of biomarkers for diagnosis and treatment. The proteogenomics database (dbPepVar) created here combines genetic variation information from dbSNP with protein sequences from NCBI’s RefSeq. Public mass spectrometry datasets (Ovarian, Colorectal, Breast, and Prostate) were used to perform a pan-cancer analysis, allowing the identification of unique genetic variations. As a result, 3,726 variant peptides were identified in samples from patients with ovarian cancer, 2,543 in prostate, 2,661 in breast and 2,411 in colon-rectal cancer patients. Data resulting from the proteogenomics approach employed and connected to other biological databases is now available in an intuitive and dynamic web portal where novice users can explore general aspects of the dataset in graph or table format, or dive in to filter the data with click and select options or using more advanced queries with regex. All data can be downloaded in csv or pdf format. In perspective, the web portal developed may direct studies to identify new therapeutic targets for different cancers, and one can also use our database for characterization of variants in samples of unknown genetic background, such as archived samplespt_BR
dc.identifier.citationCUNHA, Lucas Marques da; TERREMATTE, Patrick; FIUZA, Tayna da Silva; SILVA, Vandeclecio Lira da; KROLL, Jose Eduardo; SOUZA, Sandro Jose de; SOUZA, Gustavo Antonio de. DbPepVar: a novel cancer proteogenomics database. Ieee Access, [S. l.], v. 10, p. 90982-90994, ago. 2022. Doi: http://dx.doi.org/10.1109/access.2022.3201897. Disponível em: https://ieeexplore.ieee.org/document/9867999. Acesso em: 29 nov. 2022.pt_BR
dc.identifier.doi10.1109/ACCESS.2022.3201897
dc.identifier.urihttps://repositorio.ufrn.br/handle/123456789/49920
dc.languageenpt_BR
dc.publisherInstitute of Electrical and Electronics Engineers (IEEE)pt_BR
dc.rightsAttribution 3.0 Brazil*
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/br/*
dc.subjectProteogenomicspt_BR
dc.subjectProteogenomics databasept_BR
dc.subjectNeoplasms - Geneticspt_BR
dc.subjectGenetic variationpt_BR
dc.titledbPepVar: A novel cancer proteogenomics databasept_BR
dc.typearticlept_BR

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