pam50: Gene signature for ER and HER2 extracted from PAM50

In a-thind/PathAnalyser: ER & HER2 Pathway Activity Analysis For Breast Cancer Transcriptomic Datasets

Gene signature for ER and HER2 extracted from PAM50

Description

A list of two data frames containing the gene names and their corresponding expression values constituting ER and HER gene signatures obtained from PAM50 gene signature (Parker et al. 2009). The ER signature was obtained by combining the list of genes for the Luminal A and B intrinsic subtypes (centroids) predicted by PAM50 classifier in "pam50" list featured in the genefu R BiocManager package. Genes that were the most informative as demonstrated by a highly deviant centroid index for either Luminal A or B (estrogen receptor positive breast cancer subtypes) were selected as part of the ER signature for PAM50. Similarly, genes that were highly deviant in their centroid index in the HER2 intrinsic subtype (centroid) from PAM50 were selected as the HER2 signature for PAM50 using pam50 from genefu.

Usage

pam50

Format

A list holding two data frames: one for ER signature, the other for HER2 signature extracted from the PAM50 gene signature:

ER

data frame containing HUGO gene symbols and their relative expression value (-1 for down-regulated genes and 1 for up-regulated genes) in the ER signature

HER2

data frame containing gene names their relative expression value (-1 for down-regulated genes and 1 for up-regulated genes) in the HER2 signature

Source

PAM50 publication: https://pubmed.ncbi.nlm.nih.gov/19204204/).

genefu: https://bioconductor.org/packages/release/bioc/html/genefu.html

References

Parker, J.S., Mullins, M., Cheang, M.C., Leung, S., Voduc, D., Vickery, T., Davies, S., Fauron, C., He, X., Hu, Z. and Quackenbush, J.F., 2009. Supervised risk predictor of breast cancer based on intrinsic subtypes. Journal of clinical oncology, 27(8), p.1160. doi: https://doi.org/10.1200/JCO.2008.18.1370

a-thind/PathAnalyser documentation built on May 6, 2022, 9:50 a.m.