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Expanding and Enriching the LncRNA Gene-Disease Landscape Using the GeneCaRNA Database.

Shalini Aggarwal1, Chana Rosenblum1, Marshall Gould2

  • 1Department of Molecular Genetics, Weizmann Institute of Science, Herzl 234, Rehovot 7610010, Israel.

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Summary

The GeneCaRNA database significantly expands the catalog of human non-coding RNA (ncRNA) genes, identifying ~280,000 genes, including ~100,000 novel long non-coding RNAs (lncRNAs) for future research.

Keywords:
GeneCaRNAGeneCardshuman noncoding RNAlncRNAlong non-coding RNAncRNAnon-coding RNAsubclassification

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Non-coding RNAs (ncRNAs) play crucial roles in gene regulation and cellular processes.
  • Existing databases offer limited coverage of ncRNA genes, hindering comprehensive research.
  • The GeneCards Suite aims to consolidate and expand genomic information.

Purpose of the Study:

  • To introduce GeneCaRNA, a comprehensive human non-coding RNA gene database.
  • To significantly increase the number of identified ncRNA genes compared to existing resources.
  • To provide a foundation for exploring the functional roles of ncRNAs, particularly long non-coding RNAs (lncRNAs), in health and disease.

Main Methods:

  • Algorithmic identification of ncRNA genes from ~690,000 RNAcentral transcripts.
  • Integration of data from MalaCards for disease associations.
  • Preliminary text mining for lncRNA transcript interactions.
  • Inclusion of regulatory element data from the GeneHancer database.

Main Results:

  • GeneCaRNA contains ~280,000 human ncRNA genes, a tenfold increase over other sources.
  • ~120,000 long non-coding RNAs (lncRNAs) are included, with ~100,000 novel genes.
  • 1547 lncRNA genes are linked to diseases, with ~15% having experimental evidence.
  • Interactions with target gene products (25% ncRNAs, 75% proteins) and 131 pathways for 38 lncRNA genes are identified.
  • Regulatory elements for ~110,000 lncRNA genes are available via GeneHancer.

Conclusions:

  • GeneCaRNA represents a substantial advancement in cataloging human ncRNA genes, especially lncRNAs.
  • The database provides valuable resources for investigating lncRNA functions and their links to diseases.
  • GeneCaRNA is poised to guide future research in ncRNA biology and its role in human pathology.