Abstract
MicroRNAs (miRNAs) are functional RNA molecules which play important roles in the post-transcriptional regulation. miRNAs regulate their target genes by repressing translation or inducing degradation of the target genes’ mRNAs. Many databases have been constructed to provide computationally predicted miRNA targets. However, they cannot provide the miRNA targets expressed in a specific tissue and related to a specific disease at the same time. Moreover, they cannot provide the common targets of multiple miRNAs and the common miRNAs of multiple genes at the same time. To solve these two problems, we construct a database called CSmiRTar (Condition-Specific miRNA Targets). CSmiRTar collects computationally predicted targets of 2588 human miRNAs and 1945 mouse miRNAs from four most widely used miRNA target prediction databases (miRDB, TargetScan, microRNA.org and DIANA-microT) and implements functional filters which allows users to search (i) a miRNA’s targets expressed in a specific tissue or/and related to a specific disease, (ii) multiple miRNAs’ common targets expressed in a specific tissue or/and related to a specific disease, (iii) a gene’s miRNAs related to a specific disease, and (iv) multiple genes’ common miRNAs related to a specific disease. We believe that CSmiRTar will be a useful database for biologists to study the molecular mechanisms of post-transcriptional regulation in human or mouse. CSmiRTar is available at http://cosbi.ee.ncku.edu.tw/CSmiRTar/ or http://cosbi4.ee.ncku.edu.tw/CSmiRTar/.
Highlights
MicroRNAs, 20–25 nucleotides non-coding RNAs, play important roles in the post-transcriptional regulation of gene expression [1,2,3]
CSmiRTar implements (i) a tissue filter for users to search the miRNA targets expressed in a specific tissue, (ii) a disease filter for users to search the miRNA targets related to a specific disease, and (iii) a database filter for users to search the miRNA targets supported by multiple existing miRNA target prediction databases
CSmiRTar allows users to search the common targets of a set of input miRNAs under a specific physiological condition and the common miRNAs of a set of input genes under a specific physiological condition
Summary
MicroRNAs (miRNAs), 20–25 nucleotides non-coding RNAs, play important roles in the post-transcriptional regulation of gene expression [1,2,3]. Manually curated miRNA targets with experimental evidence from the literature but they are far from complete The other databases such as TargetScan [10], miRDB [13], microRNA.org [14], DIANA-microT [15], miRecords [16], MAGIA [17], mirDIP [18], miRSystem [19] and miRGator [20] collect computationally predicted miRNA targets generated from various algorithms. CSmiRTar collects computationally predicted targets of 2588 human miRNAs and 1945 mouse miRNAs from four most widely used miRNA target prediction databases (miRDB, TargetScan, microRNA.org and DIANA-microT). Five data sources were used to construct CSmiRTar. First, the experimentally validated human and mouse miRNA targets were retrieved from miRTarBase [12], which manually collected miRNA-target interactions with experimental evidence from the literature.
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