MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs).
MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs).
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MINRbase：一个核和核糖体RNA衍生片段（rRF）的综合数据库。
DOI：
10.1093/nar/gkad833
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发表时间：
2024-01-05
影响因子：
14.9
通讯作者：
中科院分区：
文献类型：
--
作者：
我们描述了线粒体和核RRNA碎片数据库（MinRbase），这是一个旨在开发核糖体RNA衍生片段的研究（RRFS）的知识存储库（RRFS）。 （18s，5.8s，28s，5s），两个线粒体RRNA（12s，16s）或45 s Pre-RRNA的四个垫片，我们通过分析11个632个数据集，包括Geuvadis和癌症基因组（TCGA）RepoSitories， Minrbase提供了一个用户友好的界面，使研究人员可以根据一个或多个标准发出复杂的查询，例如父母RRNA身份，核苷酸序列，RRF最低丰度和元数据关键词（例如，组织类型，疾病）。 RRF通过组织类型，疾病，性别，血统和其他变量提供了颗粒状的崩溃； ：45s的内部垫片是丰富的RRF的产物，许多丰富的RRF跨越了RRF的已知边界； ，疾病）。
We describe the Mitochondrial and Nuclear rRNA fragment database (MINRbase), a knowledge repository aimed at facilitating the study of ribosomal RNA-derived fragments (rRFs). MINRbase provides interactive access to the profiles of 130 238 expressed rRFs arising from the four human nuclear rRNAs (18S, 5.8S, 28S, 5S), two mitochondrial rRNAs (12S, 16S) or four spacers of 45S pre-rRNA. We compiled these profiles by analyzing 11 632 datasets, including the GEUVADIS and The Cancer Genome Atlas (TCGA) repositories. MINRbase offers a user-friendly interface that lets researchers issue complex queries based on one or more criteria, such as parental rRNA identity, nucleotide sequence, rRF minimum abundance and metadata keywords (e.g. tissue type, disease). A ‘summary’ page for each rRF provides a granular breakdown of its expression by tissue type, disease, sex, ancestry and other variables; it also allows users to create publication-ready plots at the click of a button. MINRbase has already allowed us to generate support for three novel observations: the internal spacers of 45S are prolific producers of abundant rRFs; many abundant rRFs straddle the known boundaries of rRNAs; rRF production is regimented and depends on ‘personal attributes’ (sex, ancestry) and ‘context’ (tissue type, tissue state, disease). MINRbase is available at https://cm.jefferson.edu/MINRbase/.
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