MINRbase

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/.本研究介绍了线粒体与核核糖体RNA片段数据库（Mitochondrial and Nuclear rRNA fragment database, MINRbase）——一款旨在推动核糖体RNA衍生片段（ribosomal RNA-derived fragments, rRFs）研究的专业知识库。该数据库支持交互式检索130238个已表达rRF的表达谱，这些片段均源自人类的4种核核糖体RNA（18S、5.8S、28S、5S）、2种线粒体核糖体RNA（12S、16S），或45S前体核糖体RNA的四个内部间隔区。本研究通过分析11632组数据集构建了上述表达谱，数据集来源涵盖GEUVADIS项目与癌症基因组图谱（The Cancer Genome Atlas, TCGA）数据库。MINRbase配备了友好易用的用户界面，支持研究人员基于一项或多项条件开展复杂查询，例如母源核糖体RNA标识、核苷酸序列、rRF最低表达量，以及元数据关键词（如组织类型、疾病类型）。每个rRF均配有专属“概览”页面，可按组织类型、疾病、性别、祖先背景及其他变量对其表达情况进行精细化拆解；同时支持用户一键生成可直接用于发表的可视化图表。目前，MINRbase已助力我们为三项全新研究发现提供了实证支撑：45S前体核糖体RNA的内部间隔区可高效产生大量高丰度rRF；众多高丰度rRF跨越核糖体RNA已知的边界区域；rRF的生成具有严格调控规律，且受“个体属性”（性别、祖先背景）与“环境背景”（组织类型、组织状态、疾病）影响。用户可通过以下网址访问MINRbase：https://cm.jefferson.edu/MINRbase/

搜集汇总

背景与挑战

背景概述

MINRbase是一个专注于核糖体RNA衍生片段（rRFs）的数据库，涵盖人类核糖体和线粒体RNA来源的130,238个表达片段，基于11,632个数据集分析构建。该数据库提供交互式查询功能，允许用户根据rRNA类型、序列、表达量等条件进行检索，并支持通过可视化工具生成表达摘要。MINRbase旨在帮助研究人员探索rRFs的表达模式及其与组织类型、疾病等变量的关联。