get.hao.subtypes {consensusOV} | R Documentation

## 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)

[Package consensusOV version 1.12.0 Index]