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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After...
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miRPathDB: a new dictionary on microRNAs and target pathways.

Christina Backes1, Tim Kehl2, Daniel Stöckel2

  • 1Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, D-66123 Saarbruecken, Germany.

Nucleic Acids Research
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Summary

The new miRNA Pathway Dictionary Database (miRPathDB) offers comprehensive insights into microRNA (miRNA) target pathways. It links thousands of miRNAs to validated and predicted targets across numerous biological pathways for improved research.

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • MicroRNAs (miRNAs) and their regulatory roles are extensively studied, with numerous analysis tools developed.
  • Previous miRNA target pathway resources have been updated due to a tripling of known miRNAs and advancements in pathway databases like KEGG.
  • Enhanced understanding of miRNA-target interactions and related pathways necessitates updated and comprehensive databases.

Purpose of the Study:

  • To introduce the miRNA Pathway Dictionary Database (miRPathDB) as a freely accessible resource.
  • To complement existing web servers by providing easy access to miRNA-regulated pathways and pathway-targeting miRNAs.
  • To detail the specificity of miRNA-pathway regulations.

Main Methods:

  • Compilation of a large-scale database integrating multiple miRNA and pathway resources.
  • Inclusion of experimentally validated and predicted miRNA target genes.
  • Incorporation of diverse functional categories including KEGG, WikiPathways, Gene Ontology (GO), and Pfam.

Main Results:

  • The miRPathDB contains 2595 human miRNAs and extensive target gene sets (14,773 validated, 19,281 predicted).
  • It encompasses 12,875 functional categories from various pathway databases and ontologies.
  • Data for Homo sapiens and Mus musculus are available, enabling cross-species comparisons.

Conclusions:

  • miRPathDB provides a valuable, updated resource for exploring miRNA-mediated pathway regulation.
  • The database facilitates research on miRNA function, target identification, and pathway analysis.
  • It supports comparative analysis between human and mouse miRNA-pathway interactions.