Bioinformatics Resources for MicroRNA Discovery

Posted by: RNA-Seq Blog in Databases February 8, 2016 4,079 Views

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:

clear documentation of updates and history,
recent updates in the past 12 months,
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