BGSC

The Bayesian Gene Selection Criterion (BGSC) is a software tool to predict target genes regulated by specific EGFR isoforms (II-IV) in glioblastoma cells. The tool analyzes transcriptome data from nested RNAi experiments, where different EGFR isoforms are selectively knocked down, and compares gene expression under EGF stimulation and non-stimulation conditions. BGSC employs a two-step approach based on the Bayesian Information Criterion to infer the target genes of EGFR isoforms II-IV. The predicted target genes were experimentally validated using qPCR, confirming the accuracy of the BGSC tool.

Topic

RNAi experiment;RNA splicing;Functional, regulatory and non-coding RNA

Detail

  • Operation: Differential gene expression analysis

  • Software interface: Command-line user interface

  • Language: R,Perl

  • License: MIT + file LICENSE

  • Cost: Free of charge with restrictions

  • Version name: v1.2

  • Credit: German Research Foundation (DFG), German Federal Ministry of Education and Research.

  • Input: -

  • Output: -

  • Contact: Claus Weinholdt claus.weinholdt@informatik.uni-halle.de

  • Collection: -

  • Maturity: -

Publications

  • Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line.
  • Weinholdt C, et al. Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line. Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line. 2019; 20:434. doi: 10.1186/s12859-019-2944-9
  • https://doi.org/10.1186/S12859-019-2944-9
  • PMID: 31438847
  • PMC: PMC6704634

Download and documentation

< Back to DB search