iGC

The software tool "iGC" addresses challenges in integrating gene expression and copy number alteration (CNA) data by concurrently analyzing both data types from individual patients. The package supports multiple input formats and allows users to define criteria for identifying differentially expressed genes influenced by CNAs. The analysis of real microarray datasets demonstrates that iGC-identified CNA-driven genes exhibit higher correlation coefficients between gene expression levels and copy numbers than genes located in genomic regions with CNAs.

Topic

Gene expression;Oncology

Detail

  • Operation: Gene expression analysis

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 1.32.0

  • Credit: The Center of Genomic Medicine, National Taiwan University, Taiwan, the YongLin Biomedical Engineering Center, National Taiwan University, Taiwan.

  • Input: Gene expression data [Gene expression report format]

  • Output: P-value [Textual format]

  • Contact: Liang-Bo Wang r02945054@ntu.edu.tw

  • Collection: -

  • Maturity: Stable

Publications

  • iGC-an integrated analysis package of gene expression and copy number alteration.
  • Lai YP, et al. iGC-an integrated analysis package of gene expression and copy number alteration. iGC-an integrated analysis package of gene expression and copy number alteration. 2017; 18:35. doi: 10.1186/s12859-016-1438-2
  • https://doi.org/10.1186/s12859-016-1438-2
  • PMID: 28088185
  • PMC: PMC5237550

Download and documentation

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