Apr 1, 2020

CeTF: an R package to Coexpression forTranscription Factors using Regulatory ImpactFactors (RIF) and Partial Correlation andInformation (PCIT) analysis

BioRxiv : the Preprint Server for Biology
Tugce Bilgin SonayAndreas Wagner

Abstract

Find meaningful gene-gene associations and the main Transcription Factors (TFs) in co-expression networks is one of the most important challenges in gene expression data mining. CeTF is an R package that integrates the Partial Correlation with Information Theory (PCIT) and Regulatory Impact Factors (RIF) algorithms applied to gene expression data from microarray, RNA-seq, or single-cell RNA-seq platforms. This approach allows identifying the transcription factors most likely to regulate a given network in different biological systems - for example, regulation of gene pathways in tumor stromal cells and tumor cells of the same tumor. This pipeline can be easily integrated into the high-throughput analysis.

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Mentioned in this Paper

Gene Polymorphism
Genome-Wide Association Study
Pongidae
Patterns
Untranslated Regions
CD4+ CD25+ Regulatory T Cells
Nonhuman primate
Tandem Repeat Sequences
Exons
Genome

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