Abstract
For many research aspects on small non-coding RNAs, especially microRNAs, computational tools and databases are developed. This includes quantification of miRNAs, piRNAs, tRNAs and tRNA fragments, circRNAs and others. Furthermore, the prediction of new miRNAs, isomiRs, arm switch events, target and target pathway prediction and miRNA pathway enrichment are common tasks. Additionally, databases and resources containing expression profiles, e.g., from different tissues, organs or cell types, are generated. This information in turn leads to improved miRNA repositories. While most of the respective tools are implemented in a species-independent manner, we focused on tools for human small non-coding RNAs. This includes four aspects: (1) miRNA analysis tools (2) databases on miRNAs and variations thereof (3) databases on expression profiles (4) miRNA helper tools facilitating frequent tasks such as naming conversion or reporter assay design. Although dependencies between the tools exist and several tools are jointly used in studies, the interoperability is limited. We present HumiR, a joint web presence for our tools. HumiR facilitates an entry in the world of miRNA research, supports the selection of the right tool for a research task and represents the very first step towards a fully integrated knowledge-base for human small non-coding RNA research. We demonstrate the utility of HumiR by performing a very comprehensive analysis of Alzheimer’s miRNAs.
Highlights
In almost all organisms, bacteria, viruses, plants, animals and mammals, research on small non-coding RNA is performed
The current state-of-the-art on miRNA research has been published by Bartel in 2018 [1]
115 TB of sequencing data on small RNAs are deposited in sequence read archive (SRA), covering 2 × 1012 reads
Summary
Bacteria, viruses, plants, animals and mammals, research on small non-coding RNA is performed. Many of the tools are independent of the organism or support several organisms, a certain focus on Homo Sapiens can be recognized This is motivated by the fact that most and the largest data sets are available for humans as sketched above. In addition to respective databases, data warehouses have been generated as resources for miRNA expression patterns, including expression profiles for different organs, tissues, cell types and other specimen types. The joint paradigm of all solutions is in that they must be available as a web service and not require any installation of client-side software For these tools, the focus has been on Homo sapiens. We will provide an outlook on how we will further improve and automate the iBniotemroolepcuelresa2b0i2li0t,y10o, fxtFhOeRtPoEoElsRvRiEaVAIEPWIs towards a fully integrated knowledge base
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