colorectalcancer: Results from a microarray experiment comparing colorectal...

In SPIA: Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations

Description

The colorectal dataset consists: i) an named vector DE_Colorectal , which represents the $log2$ fold changes of the genes chosen as differentially expressed between colorectal cancer and normal samples based on data from Hong et al, 2007, using a $FDR=0.1$ and the universe of all Entrez gene IDs available on the array, ALL_Colorectal. These two vectors were obtained starting from the top dataframe which is the output from the topTable function of the limma package using the RMA processed gene expression data downloaded from GEE (GSE4107). The microarray platform used was Affymetrix HGU-133PLUS2.0.

Usage

data(colorectalcancer)

Source

Yi Hong and Kok Sun Ho and Kong Weng Eu and Peh Yean Cheah, A susceptibility gene set for early onset colorectal cancer that integrates diverse signaling pathways: implication for tumorigenesis, Clin Cancer Res, 2007, 13(4),1107-14.

SPIA documentation built on Nov. 8, 2020, 5:44 p.m.