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CSCD: a database for cancer-specific circular RNAs.

Siyu Xia1,2,3, Jing Feng4, Ke Chen5

  • 1School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China.

Nucleic Acids Research
|October 17, 2017
PubMed
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This summary is machine-generated.

Researchers identified over 272,000 cancer-specific circular RNAs (circRNAs) using RNA sequencing data. They created the Cancer-Specific circRNA Database (CSCD) to aid cancer research and understand circRNA functions.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Circular RNAs (circRNAs) are prevalent in cells and tissues, with high-throughput sequencing enabling their study across various diseases.
  • Existing resources lack a comprehensive database for exploring cancer-specific circRNAs.

Purpose of the Study:

  • To construct the first comprehensive database of cancer-specific circRNAs.
  • To identify and characterize circRNAs associated with cancer.
  • To provide a resource for investigating circRNA function and regulation in cancer.

Main Methods:

  • Collected and analyzed 228 total RNA or polyA(-) RNA-sequencing samples from cancer and normal cell lines.
  • Identified cancer-specific, normal-specific, and shared circRNAs.
  • Predicted microRNA response element sites, RNA binding protein sites, and translatable open reading frames.

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  • Analyzed splicing events in linear transcripts.

    • Main Results:

    • Identified 272,152 cancer-specific circRNAs.
    • Identified 950,962 circRNAs in normal samples only.
    • Identified 170,909 circRNAs common to both tumor and normal samples.
    • Constructed the Cancer-Specific circRNA Database (CSCD) available at http://gb.whu.edu.cn/CSCD.

    Conclusions:

    • The CSCD is the first comprehensive database for cancer-specific circRNAs.
    • This database will significantly advance research into the function and regulation of cancer-associated circRNAs.
    • Predicted functional elements offer insights into circRNA mechanisms in cancer.