ChIPXpress-package


Takes as input predicted TF bound targets from ChIP-chip or ChIP-seq data and ranks them according to the most likely to be a TF target gene. ChIPXpress rankings are more consistent, robust, and accurate than standard ChIP-chip or ChIP-seq rankings, which prioritize genes only on the strength of the observed peaks. ChIPXpress is able to accomplish this because it searches for TF bound genes that are highly correlated in expression with the TF across a database of highly diverse gene expresison profiles collected from different diseases, tissues, and cell types.


 package

 ChIPXpress

ChIPXpress takes as input predicted TF bound genes from
ChIPx data and uses a corresponding database of gene expression
profiles downloaded from NCBI GEO to rank the TF bound targets
in order of which gene is most likely to be functional TF
target.

George Wu

ChIPXpress

ChIPXpress: enhanced transcription factor target gene
identification from ChIP-seq and ChIP-chip data using publicly
available gene expression profiles

ChIPXpress-package function

Takes as input predicted TF bound targets from ChIP-chip or ChIP-seq data and ranks them according to the most likely to be a TF target gene. ChIPXpress rankings are more consistent, robust, and accurate than standard ChIP-chip or ChIP-seq rankings, which prioritize genes only on the strength of the observed peaks. ChIPXpress is able to accomplish this because it searches for TF bound genes that are highly correlated in expression with the TF across a database of highly diverse gene expresison profiles collected from different diseases, tissues, and cell types.

ChIPXpress-package: ChIPXpress ranks TF target genes given predicted TF targets from ChIP-chip and ChIP-seq data using publicly available gene expression data

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