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miRNATissueAtlas 2025: an update to the uniformly processed and annotated human and mouse non-coding RNA tissue atlas
Nucleic Acids Research ( IF 16.6 ) Pub Date : 2024-11-14 , DOI: 10.1093/nar/gkae1036
Shusruto Rishik, Pascal Hirsch, Friederike Grandke, Tobias Fehlmann, Andreas Keller

MiRNAs represent a non-coding RNA class that regulate gene expression and pathways. While miRNAs are evolutionary conserved most data stems from Homo sapiens and Mus musculus. As miRNA expression is highly tissue specific, we developed miRNATissueAtlas to comprehensively explore this landscape in H. sapiens. We expanded the H. sapiens tissue repertoire and included M. musculus. In past years, the number of public miRNA expression datasets has grown substantially. Our previous releases of the miRNATissueAtlas represent a great framework for a uniformly pre-processed and label-harmonized resource containing information on these datasets. We incorporate the respective data in the newest release, miRNATissueAtlas 2025, which contains expressions from 9 classes of ncRNA from 799 billion reads across 61 593 samples for H. sapiens and M. musculus. The number of organs and tissues has increased from 28 and 54 to 74 and 373, respectively. This number includes physiological tissues, cell lines and extracellular vesicles. New tissue specificity index calculations build atop the knowledge of previous iterations. Calculations from cell lines enable comparison with physiological tissues, providing a valuable resource for translational research. Finally, between H. sapiens and M. musculus, 35 organs overlap, allowing cross-species comparisons. The updated miRNATissueAtlas 2025 is available at https://www.ccb.uni-saarland.de/tissueatlas2025.

中文翻译:


miRNATissueAtlas 2025:对均匀加工和注释的人和小鼠非编码 RNA 组织图谱的更新



MiRNA 代表一类调节基因表达和通路的非编码 RNA。虽然 miRNA 是进化上保守的,但大多数数据来自智人和肌肉动物。由于 miRNA 表达具有高度的组织特异性,我们开发了 miRNATissueAtlas 来全面探索 H. sapiens 中的这一景观。我们扩展了 H. sapiens 组织库并包括 M. musculus。在过去几年中,公开的 miRNA 表达数据集的数量大幅增长。我们之前版本的 miRNATissueAtlas 代表了一个很棒的框架,用于统一预处理和标签协调的资源,其中包含有关这些数据集的信息。我们将相应的数据整合到最新版本的 miRNATissueAtlas 2025 中,其中包含 61 593 个样本中 7990 亿个读数的 9 类 ncRNA 的表达,用于智人和肌肉分枝杆菌。器官和组织的数量分别从 28 个和 54 个增加到 74 个和 373 个。这个数字包括生理组织、细胞系和细胞外囊泡。新的组织特异性指数计算建立在以前迭代的知识之上。细胞系的计算结果可以与生理组织进行比较,为转化研究提供宝贵的资源。最后,在 H. sapiens 和 M. musculus 之间,有 35 个器官重叠,允许跨物种比较。更新后的 miRNATissueAtlas 2025 可在 https://www.ccb.uni-saarland.de/tissueatlas2025 获取。
更新日期:2024-11-14
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