REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments

Author:

Mansi Luigi1,Tangaro Marco Antonio2,Lo Giudice Claudio1,Flati Tiziano3,Kopel Eli4,Schaffer Amos Avraham4ORCID,Castrignanò Tiziana5,Chillemi Giovanni6,Pesole Graziano127ORCID,Picardi Ernesto127ORCID

Affiliation:

1. Department of Biosciences, Biotechnologies and Biopharmaceutics (DBBB), University of Bari, Via Orabona 4, 70125 Bari, Italy

2. Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Amendola 122/O, 70126 Bari, Italy

3. SCAI-Super Computing Applications and Innovation Department, CINECA, Via dei Tizii 6B, 00185 Rome, Italy

4. Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 52900 Ramat Gan, Israel

5. Department of Ecological and Biological Sciences (DEB), University of Tuscia, Via S. Camillo de Lellis 44, 01100 Viterbo, Italy

6. Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis 44, 01100 Viterbo, Italy

7. National Institute of Biostructures and Biosystems (INBB), 00136 Roma, Italy

Abstract

Abstract RNA editing is a relevant epitranscriptome phenomenon able to increase the transcriptome and proteome diversity of eukaryotic organisms. ADAR mediated RNA editing is widespread in humans in which millions of A-to-I changes modify thousands of primary transcripts. RNA editing has pivotal roles in the regulation of gene expression or modulation of the innate immune response or functioning of several neurotransmitter receptors. Massive transcriptome sequencing has fostered the research in this field. Nonetheless, different aspects of the RNA editing biology are still unknown and need to be elucidated. To support the study of A-to-I RNA editing we have updated our REDIportal catalogue raising its content to about 16 millions of events detected in 9642 human RNAseq samples from the GTEx project by using a dedicated pipeline based on the HPC version of the REDItools software. REDIportal now allows searches at sample level, provides overviews of RNA editing profiles per each RNAseq experiment, implements a Gene View module to look at individual events in their genic context and hosts the CLAIRE database. Starting from this novel version, REDIportal will start collecting non-human RNA editing changes for comparative genomics investigations. The database is freely available at http://srv00.recas.ba.infn.it/atlas/index.html.

Funder

Elixir ITA

PRACE call 15

PRACE call 18

Publisher

Oxford University Press (OUP)

Subject

Genetics

Cited by 103 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3