CeTF

CeTF is a software tool to identify meaningful gene-gene associations and the primary transcription factors involved in these relationships within co-expression networks. It uses two advanced algorithms - Partial Correlation with Information Theory (PCIT) and Regulatory Impact Factor (RIF) - to analyze gene expression data from various platforms such as microarrays, RNA-seq, and single-cell RNA-seq. By doing so, it helps users understand regulatory mechanisms underlying specific biological processes, including gene pathways in tumor stromal and tumor cells.

Topic

Transcription factors and regulatory sites;RNA-Seq;Microarray experiment;Molecular interactions, pathways and networks;Workflows

Detail

  • Operation: Expression correlation analysis;Standardisation and normalisation;Differential gene expression analysis

  • Software interface: Library

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.14.0

  • Credit: The Coordination for the Improvement of Higher Education Personnel (CAPES), São Paulo Research Foundation (FAPESP), the University of Sao Paulo.

  • Input: -

  • Output: -

  • Contact: Carlos Alberto Oliveira de Biagi Jr wilsonjr@usp.br ,Wilson Araújo Silva Jr biagi@usp.br

  • Collection: -

  • Maturity: Stable

Publications

  • CeTF: an R package to Coexpression forTranscription Factors using Regulatory ImpactFactors (RIF) and Partial Correlation andInformation (PCIT) analysis
  • Oliveira de Biagi Junior, C. A.; Perecin Nociti, R.; Osvaldo Funicheli, B.; de Cassia Ruy, P.; Bianchi Ximenez, J. P.; Silva, W. A. CeTF: an R package to Coexpression forTranscription Factors using Regulatory ImpactFactors (RIF) and Partial Correlation andInformation (PCIT) analysis. bioRxiv 2020. doi: 10.1101/2020.03.30.015784
  • https://doi.org/10.1101/2020.03.30.015784
  • PMID: -
  • PMC: -

Download and documentation

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