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IsopiRBank: a research resource for tracking piRNA isoforms
PIWI-interacting RNAs (piRNAs) are essential for transcriptional and post-transcriptional regulation of transposons and coding genes in germline. With the development of sequencing technologies, length variations of piRNAs have been identified in several species. However, the extent to which, piRNA...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6025188/ https://www.ncbi.nlm.nih.gov/pubmed/29961820 http://dx.doi.org/10.1093/database/bay059 |
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author | Zhang, Huan Ali, Asim Gao, Jianing Ban, Rongjun Jiang, Xiaohua Zhang, Yuanwei Shi, Qinghua |
author_facet | Zhang, Huan Ali, Asim Gao, Jianing Ban, Rongjun Jiang, Xiaohua Zhang, Yuanwei Shi, Qinghua |
author_sort | Zhang, Huan |
collection | PubMed |
description | PIWI-interacting RNAs (piRNAs) are essential for transcriptional and post-transcriptional regulation of transposons and coding genes in germline. With the development of sequencing technologies, length variations of piRNAs have been identified in several species. However, the extent to which, piRNA isoforms exist, and whether these isoforms are functionally distinct from canonical piRNAs remain uncharacterized. Through data mining from 2154 datasets of small RNA sequencing data from four species (Homo sapiens, Mus musculus, Danio rerio and Drosophila melanogaster), we have identified 8 749 139 piRNA isoforms from 175 454 canonical piRNAs, and classified them on the basis of variations on 5′ or 3′ end via the alignment of isoforms with canonical sequence. We thus established a database named IsopiRBank. Each isoforms has detailed annotation as follows: normalized expression data, classification, spatiotemporal expression data and genome origin. Users can also select interested isoforms for further analysis, including target prediction and Enrichment analysis. Taken together, IsopiRBank is an interactive database that aims to present the first integrated resource of piRNA isoforms, and broaden the research of piRNA biology. IsopiRBank can be accessed at http://mcg.ustc.edu.cn/bsc/isopir/index.html without any registration or log in requirement. Database URL: http://mcg.ustc.edu.cn/bsc/isopir/index.html |
format | Online Article Text |
id | pubmed-6025188 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-60251882018-07-30 IsopiRBank: a research resource for tracking piRNA isoforms Zhang, Huan Ali, Asim Gao, Jianing Ban, Rongjun Jiang, Xiaohua Zhang, Yuanwei Shi, Qinghua Database (Oxford) Database Tool PIWI-interacting RNAs (piRNAs) are essential for transcriptional and post-transcriptional regulation of transposons and coding genes in germline. With the development of sequencing technologies, length variations of piRNAs have been identified in several species. However, the extent to which, piRNA isoforms exist, and whether these isoforms are functionally distinct from canonical piRNAs remain uncharacterized. Through data mining from 2154 datasets of small RNA sequencing data from four species (Homo sapiens, Mus musculus, Danio rerio and Drosophila melanogaster), we have identified 8 749 139 piRNA isoforms from 175 454 canonical piRNAs, and classified them on the basis of variations on 5′ or 3′ end via the alignment of isoforms with canonical sequence. We thus established a database named IsopiRBank. Each isoforms has detailed annotation as follows: normalized expression data, classification, spatiotemporal expression data and genome origin. Users can also select interested isoforms for further analysis, including target prediction and Enrichment analysis. Taken together, IsopiRBank is an interactive database that aims to present the first integrated resource of piRNA isoforms, and broaden the research of piRNA biology. IsopiRBank can be accessed at http://mcg.ustc.edu.cn/bsc/isopir/index.html without any registration or log in requirement. Database URL: http://mcg.ustc.edu.cn/bsc/isopir/index.html Oxford University Press 2018-06-28 /pmc/articles/PMC6025188/ /pubmed/29961820 http://dx.doi.org/10.1093/database/bay059 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database Tool Zhang, Huan Ali, Asim Gao, Jianing Ban, Rongjun Jiang, Xiaohua Zhang, Yuanwei Shi, Qinghua IsopiRBank: a research resource for tracking piRNA isoforms |
title | IsopiRBank: a research resource for tracking piRNA isoforms |
title_full | IsopiRBank: a research resource for tracking piRNA isoforms |
title_fullStr | IsopiRBank: a research resource for tracking piRNA isoforms |
title_full_unstemmed | IsopiRBank: a research resource for tracking piRNA isoforms |
title_short | IsopiRBank: a research resource for tracking piRNA isoforms |
title_sort | isopirbank: a research resource for tracking pirna isoforms |
topic | Database Tool |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6025188/ https://www.ncbi.nlm.nih.gov/pubmed/29961820 http://dx.doi.org/10.1093/database/bay059 |
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