CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis.

ABSTRACT:

Background

Finding meaningful gene-gene interaction and the main Transcription Factors (TFs) in co-expression networks is one of the most important challenges in gene expression data mining.

Results

Here, we developed the R package "CeTF" 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. To demonstrate the CeTF packag

SUBMITTER: Oliveira de Biagi CA 

PROVIDER: S-EPMC8379792 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature