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

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

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)

consensusOV documentation built on Nov. 8, 2020, 7:06 p.m.