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ChiTaRS-3.1—the enhanced chimeric transcripts and RNA-seq database matched with protein–protein interactions
Discovery of chimeric RNAs, which are produced by chromosomal translocations as well as the joining of exons from different genes by trans-splicing, has added a new level of complexity to our study and understanding of the transcriptome. The enhanced ChiTaRS-3.1 database (http://chitars.md.biu.ac.il...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210585/ https://www.ncbi.nlm.nih.gov/pubmed/27899596 http://dx.doi.org/10.1093/nar/gkw1127 |
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author | Gorohovski, Alessandro Tagore, Somnath Palande, Vikrant Malka, Assaf Raviv-Shay, Dorith Frenkel-Morgenstern, Milana |
author_facet | Gorohovski, Alessandro Tagore, Somnath Palande, Vikrant Malka, Assaf Raviv-Shay, Dorith Frenkel-Morgenstern, Milana |
author_sort | Gorohovski, Alessandro |
collection | PubMed |
description | Discovery of chimeric RNAs, which are produced by chromosomal translocations as well as the joining of exons from different genes by trans-splicing, has added a new level of complexity to our study and understanding of the transcriptome. The enhanced ChiTaRS-3.1 database (http://chitars.md.biu.ac.il) is designed to make widely accessible a wealth of mined data on chimeric RNAs, with easy-to-use analytical tools built-in. The database comprises 34 922 chimeric transcripts along with 11 714 cancer breakpoints. In this latest version, we have included multiple cross-references to GeneCards, iHop, PubMed, NCBI, Ensembl, OMIM, RefSeq and the Mitelman collection for every entry in the ‘Full Collection’. In addition, for every chimera, we have added a predicted chimeric protein–protein interaction (ChiPPI) network, which allows for easy visualization of protein partners of both parental and fusion proteins for all human chimeras. The database contains a comprehensive annotation for 34 922 chimeric transcripts from eight organisms, and includes the manual annotation of 200 sense-antiSense (SaS) chimeras. The current improvements in the content and functionality to the ChiTaRS database make it a central resource for the study of chimeric transcripts and fusion proteins. |
format | Online Article Text |
id | pubmed-5210585 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-52105852017-01-05 ChiTaRS-3.1—the enhanced chimeric transcripts and RNA-seq database matched with protein–protein interactions Gorohovski, Alessandro Tagore, Somnath Palande, Vikrant Malka, Assaf Raviv-Shay, Dorith Frenkel-Morgenstern, Milana Nucleic Acids Res Database Issue Discovery of chimeric RNAs, which are produced by chromosomal translocations as well as the joining of exons from different genes by trans-splicing, has added a new level of complexity to our study and understanding of the transcriptome. The enhanced ChiTaRS-3.1 database (http://chitars.md.biu.ac.il) is designed to make widely accessible a wealth of mined data on chimeric RNAs, with easy-to-use analytical tools built-in. The database comprises 34 922 chimeric transcripts along with 11 714 cancer breakpoints. In this latest version, we have included multiple cross-references to GeneCards, iHop, PubMed, NCBI, Ensembl, OMIM, RefSeq and the Mitelman collection for every entry in the ‘Full Collection’. In addition, for every chimera, we have added a predicted chimeric protein–protein interaction (ChiPPI) network, which allows for easy visualization of protein partners of both parental and fusion proteins for all human chimeras. The database contains a comprehensive annotation for 34 922 chimeric transcripts from eight organisms, and includes the manual annotation of 200 sense-antiSense (SaS) chimeras. The current improvements in the content and functionality to the ChiTaRS database make it a central resource for the study of chimeric transcripts and fusion proteins. Oxford University Press 2017-01-04 2016-11-28 /pmc/articles/PMC5210585/ /pubmed/27899596 http://dx.doi.org/10.1093/nar/gkw1127 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Gorohovski, Alessandro Tagore, Somnath Palande, Vikrant Malka, Assaf Raviv-Shay, Dorith Frenkel-Morgenstern, Milana ChiTaRS-3.1—the enhanced chimeric transcripts and RNA-seq database matched with protein–protein interactions |
title | ChiTaRS-3.1—the enhanced chimeric transcripts and RNA-seq database matched with protein–protein interactions |
title_full | ChiTaRS-3.1—the enhanced chimeric transcripts and RNA-seq database matched with protein–protein interactions |
title_fullStr | ChiTaRS-3.1—the enhanced chimeric transcripts and RNA-seq database matched with protein–protein interactions |
title_full_unstemmed | ChiTaRS-3.1—the enhanced chimeric transcripts and RNA-seq database matched with protein–protein interactions |
title_short | ChiTaRS-3.1—the enhanced chimeric transcripts and RNA-seq database matched with protein–protein interactions |
title_sort | chitars-3.1—the enhanced chimeric transcripts and rna-seq database matched with protein–protein interactions |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210585/ https://www.ncbi.nlm.nih.gov/pubmed/27899596 http://dx.doi.org/10.1093/nar/gkw1127 |
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