Learn to use miRBase, an online resource for microRNA genomics. In miRBase users can find stem-loop miRNA precursor sequences, mature microRNA sequences, information about miRNA clusters, genomic coordinates, features flanking a microRNA gene, and references to original literature describing the miRNA. The resource also includes a database of computationally predicted microRNA targets. MicroRNA and target sequences are linked to annotated databases that provide additional biological knowledge. The entire contents of the database are available for free downloading. Learn to use this database, to facilitate all your microRNA research needs.

You will learn:

  • multiple ways to search the miRBase database, e.g. by name, keyword, genomic location, and by sequence
  • to navigate the microRNA entry pages
  • to access and use deep sequencing reports to interpret microRNA validity
  • to find genomic features marking the start and end of primary miRNA transcripts
  • to find all potential miRNA targets in a genome
TUTORIAL RELATED CONTENT

TUTORIALS

This tutorial is a part of the tutorial group Expression resources. You might find the other tutorials in the group interesting:

Functional Glycomics Gateway: The home for Functional Glycomics research

CleanEx: A Database of Heterogeneous Gene Expression Data Based on A Consistent Gene Nomenclature

Allen Mouse Brain Atlas: Mapped gene expression data in mouse brain

DBTSS: Database of Transcriptional Start Sites

Alternative Splicing and Transcript Diversity (ASTD) database: A bioinformatics resource for alternative splice events and transcripts for human, mouse, and rat

GENSAT: Provides an extensive amount of high quality images of gene expression in the central nervous system of the mouse.

Gene Expression Omnibus (GEO): A gene expression/molecular abundance repository and a curated, online resource for gene expression data

ArrayExpress: A public repository for microarray gene expression data at the EBI

CATEGORIES

Nucleotides : Tools that are primarily used in the storage, retrieval, or exploration of nucleotide-based data. Some tools may also involve protein sequence information.

BLOG POSTS

Video Tip of the Week: RNACentral, wrangling non-coding RNA for simplifying access: Non-coding RNA data can be tricky to locate in public data sources. Sometimes it is handled with other gene sets, other times it's not. Some ncRNA may be found in databases of one type or one species, ...

What's The Answer? (miRNA targets): BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that ar...

Video Tip of the Week: MapMi, automated mapping of microRNA loci: Today's video tip of the week is on MapMi. This tool is found at EBI and was developed by the Enright lab. The purpose of this tool is a computational system for mapping of miRNAs within and across sp...

Friday SNPpets: Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don't make it to a blog post. Here they are for your e...

Tip of the Week: RepTar, a database of miRNA target sites: microRNAs have become a rich source of research as they probably have a huge effect on gene expression and disease. The human genome may encode over 1,000 miRNAs that target over half of our genes. Th...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Capra E. et al., Small RNA sequencing of cryopreserved semen from single bull revealed altered miRNAs and piRNAs expression between High- and Low-motile sperm populations Non-human and non-rodent vertebrate genomics. BMC Genomics (2017) doi:10.1186/s12864-016-3394-7

Barrero A. Roberto et al., An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids. BMC Bioinformatics (2017) doi:10.1186/s12859-016-1428-4

Cumbo Fabio et al., TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas Results and data. BMC Bioinformatics (2017) doi:10.1186/s12859-016-1419-5

Rasko E.J. John et al., Nuclear microRNAs in normal hemopoiesis and cancer. Journal of Hematology Oncology (2017) doi:10.1186/s13045-016-0375-x

Guo Yan et al., Comprehensive evaluation of extracellular small RNA isolation methods from serum in high throughput sequencing Human and rodent genomics. BMC Genomics (2017) doi:10.1186/s12864-016-3470-z