dbPepVar: A novel cancer proteogenomics database

Cancers 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...

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Principais autores: Cunha, Lucas Marques da, Terrematte, Patrick Cesar Alves, Fiúza, Tayná da Silva, Silva, Vandeclecio Lira da, Kroll, José Eduardo, Souza, Sandro José de, Souza, Gustavo Antonio de
Formato: article
Idioma:English
Publicado em: Institute of Electrical and Electronics Engineers (IEEE)
Assuntos:
Proteogenomics
Proteogenomics database
Neoplasms - Genetics
Genetic variation
Endereço do item:https://repositorio.ufrn.br/handle/123456789/49920
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spelling ri-123456789-499202022-11-29T12:55:44Z dbPepVar: A novel cancer proteogenomics database Cunha, Lucas Marques da Terrematte, Patrick Cesar Alves Fiúza, Tayná da Silva Silva, Vandeclecio Lira da Kroll, José Eduardo Souza, Sandro José de Souza, Gustavo Antonio de Proteogenomics Proteogenomics database Neoplasms - Genetics Genetic variation Cancers 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 samples 2022-11-29T12:55:44Z 2022-11-29T12:55:44Z 2022-08 article CUNHA, 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. https://repositorio.ufrn.br/handle/123456789/49920 10.1109/ACCESS.2022.3201897 en Attribution 3.0 Brazil http://creativecommons.org/licenses/by/3.0/br/ application/pdf Institute of Electrical and Electronics Engineers (IEEE)
institution Repositório Institucional
collection RI - UFRN
language English
topic Proteogenomics
Proteogenomics database
Neoplasms - Genetics
Genetic variation
spellingShingle Proteogenomics
Proteogenomics database
Neoplasms - Genetics
Genetic variation
Cunha, Lucas Marques da
Terrematte, Patrick Cesar Alves
Fiúza, Tayná da Silva
Silva, Vandeclecio Lira da
Kroll, José Eduardo
Souza, Sandro José de
Souza, Gustavo Antonio de
dbPepVar: A novel cancer proteogenomics database
description Cancers 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 samples
format article
author Cunha, Lucas Marques da
Terrematte, Patrick Cesar Alves
Fiúza, Tayná da Silva
Silva, Vandeclecio Lira da
Kroll, José Eduardo
Souza, Sandro José de
Souza, Gustavo Antonio de
author_facet Cunha, Lucas Marques da
Terrematte, Patrick Cesar Alves
Fiúza, Tayná da Silva
Silva, Vandeclecio Lira da
Kroll, José Eduardo
Souza, Sandro José de
Souza, Gustavo Antonio de
author_sort Cunha, Lucas Marques da
title dbPepVar: A novel cancer proteogenomics database
title_short dbPepVar: A novel cancer proteogenomics database
title_full dbPepVar: A novel cancer proteogenomics database
title_fullStr dbPepVar: A novel cancer proteogenomics database
title_full_unstemmed dbPepVar: A novel cancer proteogenomics database
title_sort dbpepvar: a novel cancer proteogenomics database
publisher Institute of Electrical and Electronics Engineers (IEEE)
publishDate 2022
url https://repositorio.ufrn.br/handle/123456789/49920
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AT fiuzataynadasilva dbpepvaranovelcancerproteogenomicsdatabase
AT silvavandecleciolirada dbpepvaranovelcancerproteogenomicsdatabase
AT krolljoseeduardo dbpepvaranovelcancerproteogenomicsdatabase
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