get.hao.subtypes: Get ovarian cancer subtypes as defined by Hao et al., 2017

In bhklab/consensusOV: Gene expression-based subtype classification for high-grade serous ovarian cancer

Get ovarian cancer subtypes as defined by Hao et al., 2017

Description

Get ovarian cancer subtypes as defined by Hao et al., 2017

Usage

get.hao.subtypes(expression.matrix, entrez.ids)

Arguments

expression.matrix	A matrix of gene expression values with genes as rows, samples as columns.
entrez.ids	A vector of Entrez Gene IDs, corresponding to the rows of expression.matrix.

Details

Hao et al., 2017 derived a gene signature to predict the tissue of origin of ovarian tumors as either fallopian tube (FT) or ovarian surface epithelium (OSE).

The authors found that expression patterns of tissue-specific genes, prognostic genes, and molecular markers support a dualistic tissue origin of ovarian cancer, from either FT or OSE.

The subtype classifier considers 112 signature genes including 37 genes upregulated in FT and 75 genes upregulated in OSE. A score is computed that is designed to range from 0 to 1 for FT tumors, while OSE tumors have a score ranging from -1 to 0.

Value

A list with first value tissue containing a factor of subtype names (tissue of origin); and second value score containing the tissue-of-origin score.

Author(s)

Ludwig Geistlinger

References

Hao et al. (2017) Integrated analysis reveals tubal- and ovarian-originated serous ovarian cancer and predicts differential therapeutic responses. Clinical Cancer Research, 23:7400-11.

Examples

library(Biobase)
data(GSE14764.eset)
expression.matrix <- exprs(GSE14764.eset)
entrez.ids <- as.character(fData(GSE14764.eset)$EntrezGene.ID)
get.hao.subtypes(expression.matrix, entrez.ids)

bhklab/consensusOV documentation built on Feb. 13, 2024, 4:50 a.m.