DIANA-miRGen

DIANA-miRGen provides comprehensive maps of cell-line- and tissue-specific microRNA (miRNA) transcription start sites (TSSs) integrated with genome-wide transcription factor (TF) binding-site annotations to elucidate regulatory mechanisms of miRNA transcription.

Key Features:

• Accurate TSS Identification: Identifies cell-line- and tissue-specific miRNA gene TSSs through analysis of over 7.3 billion RNA-, ChIP-, and DNase-Seq reads combined with prediction algorithms.
• Comprehensive TF Binding Site Maps: Provides maps comprising more than 19 million TF binding sites for 202 transcription factors across nine cell lines and six tissues in Homo sapiens and Mus musculus.
• Integration with DIANA Resources: Links TSS and TF binding-site data with DIANA miRNA target prediction and pathway analysis resources.
• Extensive Genomic Annotations: Includes expression profiles, single nucleotide polymorphism (SNP) locations, miRNA target predictions on protein-coding genes, and mappings of miRNA targets within co-regulated clusters.

Scientific Applications:

• Transcriptional regulation of miRNAs: Map TSSs and TF binding sites to study regulatory mechanisms controlling miRNA transcription.
• Co-transcriptional and cluster analyses: Investigate genomic organization and co-transcriptional dynamics of miRNA clusters.
• miRNA target and pathway studies: Combine TSS/TF annotations with miRNA target predictions for pathway-level and functional analyses.
• Comparative cell-type and species analyses: Enable cross-cell-line, tissue-specific, and Homo sapiens versus Mus musculus comparisons of miRNA regulatory elements.

Methodology:

Assembles and analyzes over 7.3 billion RNA-, ChIP-, and DNase-Seq reads and applies prediction algorithms to identify miRNA TSSs and TF binding sites.