miRBase

miRBase provides a repository of microRNA (miRNA) sequences and annotations and integrates short RNA deep-sequencing reads to support miRNA identification, annotation evidence, and expression analysis.

Key Features:

• Comprehensive catalog (miRBase 16): Contains over 15,000 microRNA gene loci across more than 140 species and over 17,000 distinct mature microRNA sequences.
• Integration of deep-sequencing reads: Incorporates reads from short RNA deep-sequencing experiments with existing microRNA annotations.
• Read mapping and quantitative data: Provides mapped read data associated with specific microRNA annotations to support relative expression estimates.
• Read filtering: Enables filtering of reads by experiment and by read count for focused analyses.
• Tissue- and stage-specific expression search: Supports searches for microRNAs based on tissue- and developmental stage-specific expression patterns.
• Annotation evidence and isoform insight: Supplies read-based evidence for annotations and information on alternative mature microRNA isoforms to inform annotation refinement.

Scientific Applications:

• Expression estimation: Use mapped short RNA deep-sequencing reads as a proxy for relative microRNA expression levels.
• Annotation validation and refinement: Employ read evidence to support, revisit, and refine existing microRNA annotations.
• Isoform analysis: Identify and characterize alternative mature microRNA isoforms from mapped read data.
• Developmental and disease studies: Investigate tissue- and stage-specific microRNA expression patterns relevant to developmental biology and disease pathology.

Methodology:

Integration of short RNA deep-sequencing reads with existing microRNA annotations, mapping reads to annotations, filtering read data by experiment and count, and searching by tissue- and stage-specific expression.