DIANA-mirExTra

DIANA-mirExTra performs integrated differential expression analysis of mRNAs and microRNAs to identify miRNAs and transcription factors that regulate differences between two biological states using RNA-Seq read count data.

Key Features:

• Comprehensive Data Integration: Combines user-uploaded RNA-Seq read count data with 350 pre-analyzed small-RNA-Seq and 65 pre-analyzed RNA-Seq libraries.
• Extensive Interaction Databases: Utilizes a repository of experimentally supported interactions, including over 450,000 validated miRNA:mRNA interactions and more than 2 million TF binding sites from specific and high-throughput experiments.
• Accurate Annotation: Incorporates miRNA transcription start site (TSS) annotations from the microTSS framework.
• Predictive miRNA:gene Interactions: Supports predicted miRNA:gene interactions for human, mouse, nematode, and fruit fly using the DIANA-microT-CDS framework.
• Motif-based miRNA Identification: Identifies deregulated miRNAs via motif analysis in 3' untranslated regions (3' UTRs) of genes.
• Functional Pathway Linking: Integrates miRNA targets with DIANA-mirPath for pathway-level functional analysis.
• Customizable Filtering: Filters results based on provided information about miRNA expression changes.

Scientific Applications:

• Differential Regulation Discovery: Identification of miRNAs and transcription factors that drive regulatory differences between two biological states (e.g., healthy versus diseased).
• miRNA Contribution to Gene Deregulation: Computational prediction and quantification of miRNA involvement in gene deregulation relevant to complex diseases such as cancer.
• Network and Pathway Analysis: Integration of miRNA/TF interactions and pathway information to elucidate developmental programs and pathological mechanisms and to support discovery of potential therapeutic targets.

Methodology:

Performs differential expression analysis of mRNAs and miRNAs from RNA-Seq read count datasets, motif analysis of 3' UTRs, integration of experimentally validated miRNA:mRNA and TF binding data (including >450,000 validated miRNA interactions and >2 million TF binding sites), incorporation of microTSS miRNA TSS annotations, and use of DIANA-microT-CDS predicted miRNA:gene interactions for human, mouse, nematode and fruit fly, while integrating pre-analyzed small-RNA-Seq (350) and RNA-Seq (65) libraries.