ceRNA

The software tool ceRNA is a method for constructing competing endogenous RNA (ceRNA) networks from paired RNA-seq data. It utilizes a competition regulation mechanism and pointwise mutual information to identify significant ceRNA crosstalks, which involve interactions between long noncoding RNAs (lncRNAs), miRNAs, and mRNAs. The method first derives candidate ceRNA crosstalks based on the competition regulation mechanism, then computes a competition score for each candidate using a combination of a competition rule and pointwise mutual information. Significant ceRNA crosstalks are selected to construct the final ceRNA network.

Topic

Functional, regulatory and non-coding RNA;Gene transcripts;RNA-Seq

Detail

  • Operation: Pathway or network prediction;miRNA target prediction;miRNA expression analysis

  • Software interface: Command-line user interface

  • Language: Python

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: China Scholarship Council, Australia Research Council.

  • Input: -

  • Output: -

  • Contact: Jinyan Li jinyan.li@uts.edu.au

  • Collection: -

  • Maturity: -

Publications

  • Construction of competing endogenous RNA networks from paired RNA-seq data sets by pointwise mutual information.
  • Lan C, et al. Construction of competing endogenous RNA networks from paired RNA-seq data sets by pointwise mutual information. Construction of competing endogenous RNA networks from paired RNA-seq data sets by pointwise mutual information. 2019; 20:943. doi: 10.1186/s12864-019-6321-x
  • https://doi.org/10.1186/S12864-019-6321-X
  • PMID: 31874629
  • PMC: PMC6929403

Download and documentation

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