Bioinformatics Resources for MicroRNA Discovery

Biomarker identification is often associated with the diagnosis and evaluation of various diseases. Recently, the role of microRNA (miRNA) has been implicated in the development of diseases, particularly cancer. With the advent of next-generation sequencing, the amount of data on miRNA has increased tremendously in the last decade, requiring new bioinformatics approaches for processing and storing new information. New strategies have been developed in mining these sequencing datasets to allow better understanding toward the actions of miRNAs. As a result, many databases have also been established to disseminate these findings.  Several databases are discussed below. The inclusion of databases reviewed here must meet the following criteria:

  1. clear documentation of updates and history,
  2. recent updates in the past 12 months,
  3. not a simple derivative on data from another database.
DATABASE MAIN FEATURE ANNOTATION DOWNLOAD OPTIONS INTEGRATED TOOLS, API AND VISUALIZATION DATA SOURCE
mirBase Nomenclature assignment Manual, automated (text mining) EMBL, fasta, gff3 Stem-loop, deep-sequencing SRA, GEO, PubMed, community
miRDB Functional annotation Automated (machine-learning) Spreadsheet, flat file n/a PubMed, RNA-seq, miRBase
mirWalk Predicted binding sites Mutomated (multiple programs) Search tables n/a Refseq 61, miRBase
mirTarBase miRNA-target interactions Manual, automated (NLP) Spreadsheet, flat file Word cloud, expressionprofile, structure of pre-miRNA, CytoscapeWeb TCGA, GEO, CLIP-seq, CLASH-seq, Degradome-seq
mirCancer miRNA expression Manual, automated (text mining) Flat file n/a miRBase, PubMed
doRiNA RNA binding proteins (RBPs), miRNA Automated pipeline BED file UCSC Genome Browser, REST, Python API GEO, CLIP-seq, selected literature
SomamiR Somatic and germline mutations Automated, aided by KEGG Spreadsheet n/a NHGRI GWAS, TCGA
EDRN Biomarker information Manual, automated in EDRN Catalog and Archive Service (eCAS) Flat file Biomarker Summary Information, BioMuta Studies from participants

 

Moore AC, Winkjer JS, Tseng TT. (2016) Bioinformatics Resources for MicroRNA Discovery. Biomark Insights 10(Suppl 4):53-8. [article]

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