smirnaDB

smirnaDB provides expression profiles and sequence- and genome-level annotations for small RNAs, particularly microRNAs (miRNAs), across multiple model organisms to support comparative and functional analysis.

Key Features:

• Organism coverage: Contains data for humans, mice, rats, zebrafish, Caenorhabditis elegans (worms), and Drosophila melanogaster (fruit flies).
• Dataset composition: Aggregates data from over 250 small RNA libraries derived from 26 distinct human and rodent organ systems and cellular environments.
• Cell and tissue representation: Includes neuronal cells and a range of hematopoietic cells covering normal and malignant states.
• Expression quantification: Provides expression profiles based on clone count information from small RNA sequencing libraries.
• Sequence and structure annotations: Reports mature miRNA sequences and precursor structures.
• Genomic annotations: Supplies genome locations and inferred transcriptional units for miRNAs.
• Conservation and maturation data: Documents broad conservation patterns and maturation processes associated with miRNAs.
• Computational analysis tools: Includes analytical tools for interrogation of expression datasets and sequence/annotation data.
• miRNA subclassification: Implements a novel subclassification scheme for miRNAs to support experimental and computational studies.

Scientific Applications:

• Expression profiling: Identification and comparison of miRNA expression patterns across organ systems, cell types, and model organisms.
• Disease and cell-state studies: Analysis of miRNA expression differences between normal and malignant hematopoietic and neuronal cells.
• Comparative genomics: Investigation of conservation patterns of miRNAs across humans, mice, rats, zebrafish, worms, and fruit flies.
• Maturation and transcriptional studies: Examination of miRNA maturation processes and inferred transcriptional units using sequence and genomic annotations.
• Functional classification: Support for experimental and computational functional studies using the provided subclassification scheme and analysis tools.

Methodology:

Expression profiles are derived from sequencing of over 250 small RNA libraries and quantified using clone count information; sequence, structural, genomic location, conservation, maturation, and inferred transcriptional unit annotations are provided for the identified miRNAs.