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C-It-Loci: a knowledge database for tissue-enriched loci.

Tyler Weirick1, David John1, Stefanie Dimmeler1

  • 1Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt and German Center for Cardiovascular Research, Partner side Rhein-Main, Frankfurt am Main, Germany.

Bioinformatics (Oxford, England)
|July 12, 2015
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Summary

Researchers developed C-It-Loci, a database for identifying tissue-specific non-coding RNAs (ncRNAs) and protein-coding genes. This tool aids in analyzing large RNA-seq datasets to discover novel gene functions across species.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • The majority of the genome is transcribed into non-coding RNAs (ncRNAs), which outnumber protein-coding genes.
  • ncRNAs exhibit higher tissue-specific expression than protein-coding genes, suggesting crucial roles in specific tissues.
  • Rapid advancements in RNA sequencing (RNA-seq) generate vast amounts of high-throughput data, posing challenges for analysis.

Purpose of the Study:

  • To develop an intuitive database for screening tissue-specific transcripts, including ncRNAs and protein-coding genes.
  • To facilitate the identification of species-conserved loci through sequence and positional conservation.
  • To provide a starting point for further biological experiments investigating ncRNA function.

Main Methods:

  • Development of the C-It-Loci knowledge database.
  • Implementation of homology definition based on sequence and positional conservation.
  • Cross-species screening capabilities for human, mouse, and zebrafish.

Main Results:

  • C-It-Loci enables users to screen for tissue-specific transcripts across three model organisms.
  • The database identifies both protein-coding genes and ncRNAs from various tissues.
  • Homology is defined through sequence and positional conservation, allowing for the extraction of conserved loci.

Conclusions:

  • C-It-Loci is a user-friendly tool for exploring tissue-specific gene expression.
  • The database aids in the discovery of novel non-coding RNAs and their potential functions.
  • C-It-Loci serves as a valuable resource for initiating new biological research endeavors.