RNA-Seq Blog Transcriptome Research & Industry News
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 |
