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piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species

PIWI interacting RNAs (piRNAs) have emerged as important gene regulators in recent times. Since the release of our first version of piRNAQuest in 2014, lots of novel piRNAs have been annotated in different species other than human, mouse and rat. Such new developments in piRNA research have led us t...

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Autores principales: Ghosh, Byapti, Sarkar, Arijita, Mondal, Sudip, Bhattacharya, Namrata, Khatua, Sunirmal, Ghosh, Zhumur
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Taylor & Francis 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8786328/
https://www.ncbi.nlm.nih.gov/pubmed/34965192
http://dx.doi.org/10.1080/15476286.2021.2010960
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author Ghosh, Byapti
Sarkar, Arijita
Mondal, Sudip
Bhattacharya, Namrata
Khatua, Sunirmal
Ghosh, Zhumur
author_facet Ghosh, Byapti
Sarkar, Arijita
Mondal, Sudip
Bhattacharya, Namrata
Khatua, Sunirmal
Ghosh, Zhumur
author_sort Ghosh, Byapti
collection PubMed
description PIWI interacting RNAs (piRNAs) have emerged as important gene regulators in recent times. Since the release of our first version of piRNAQuest in 2014, lots of novel piRNAs have been annotated in different species other than human, mouse and rat. Such new developments in piRNA research have led us to develop an updated database piRNAQuest V.2. It consists of 92,77,689 piRNA entries for 25 new species of different phylum along with human, mouse and rat. Besides providing primary piRNA features which include their genomic location, with further information on piRNAs overlapping with repeat elements, pseudogenes and syntenic regions, etc., the novel features of this version includes (i) density based cluster prediction, (ii) piRNA expression profile across various healthy and disease systems and (iii) piRNA target prediction. The concept of density-based piRNA cluster identification is robust as it does not consider parametric distribution in its model. The piRNA expression profile for 21 disease systems including cancer have been hosted in addition to 32 tissue specific piRNA expression profile for various species. Further, the piRNA target prediction section includes both predicted and curated piRNA targets within eight disease systems and developmental stages of mouse testis. Further, users can visualize the piRNA-target duplex structure and the ping-pong signature pattern for all the ping-pong piRNA partners in different species. Overall, piRNAQuest V.2 is an updated user-friendly database which will serve as a useful resource to survey, search and retrieve information on piRNAs for multiple species. This freely accessible database is available at http://dibresources.jcbose.ac.in/zhumur/pirnaquest2.
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spelling pubmed-87863282022-01-25 piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species Ghosh, Byapti Sarkar, Arijita Mondal, Sudip Bhattacharya, Namrata Khatua, Sunirmal Ghosh, Zhumur RNA Biol Research Paper PIWI interacting RNAs (piRNAs) have emerged as important gene regulators in recent times. Since the release of our first version of piRNAQuest in 2014, lots of novel piRNAs have been annotated in different species other than human, mouse and rat. Such new developments in piRNA research have led us to develop an updated database piRNAQuest V.2. It consists of 92,77,689 piRNA entries for 25 new species of different phylum along with human, mouse and rat. Besides providing primary piRNA features which include their genomic location, with further information on piRNAs overlapping with repeat elements, pseudogenes and syntenic regions, etc., the novel features of this version includes (i) density based cluster prediction, (ii) piRNA expression profile across various healthy and disease systems and (iii) piRNA target prediction. The concept of density-based piRNA cluster identification is robust as it does not consider parametric distribution in its model. The piRNA expression profile for 21 disease systems including cancer have been hosted in addition to 32 tissue specific piRNA expression profile for various species. Further, the piRNA target prediction section includes both predicted and curated piRNA targets within eight disease systems and developmental stages of mouse testis. Further, users can visualize the piRNA-target duplex structure and the ping-pong signature pattern for all the ping-pong piRNA partners in different species. Overall, piRNAQuest V.2 is an updated user-friendly database which will serve as a useful resource to survey, search and retrieve information on piRNAs for multiple species. This freely accessible database is available at http://dibresources.jcbose.ac.in/zhumur/pirnaquest2. Taylor & Francis 2021-12-29 /pmc/articles/PMC8786328/ /pubmed/34965192 http://dx.doi.org/10.1080/15476286.2021.2010960 Text en © 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. https://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/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Paper
Ghosh, Byapti
Sarkar, Arijita
Mondal, Sudip
Bhattacharya, Namrata
Khatua, Sunirmal
Ghosh, Zhumur
piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species
title piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species
title_full piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species
title_fullStr piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species
title_full_unstemmed piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species
title_short piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species
title_sort pirnaquest v.2: an updated resource for searching through the pirnaome of multiple species
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8786328/
https://www.ncbi.nlm.nih.gov/pubmed/34965192
http://dx.doi.org/10.1080/15476286.2021.2010960
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