expO.colon.ras: Gene expression, annotations, clinical data and priors for...

In predictionet: Inference for predictive networks designed for (but not limited to) genomic data

Description

This dataset contains (part of) the gene expression, annotations and clinical data as published by the expO project (http://www.intgen.org/expo/). Genes related to KRAS mutations were retrieved from Bild et al, Nature, 2006. Only genes with known gene symbols were selected resulting in a dataset of 292 human colon tumors and 259 RAS-related genes.

Usage

data(expO.colon.ras)

Format

expO.colon.ras is a dataset containing four matrices:

demo.ras

clinical information of the colon cancer patients whose tumors were hybridized.

data.ras

matrix containing expression of genes related to RAS.

annot.ras

matrix containing annotations of the genes related to RAS.

priors.ras

matrix of priors counts for all the genes related to RAS. Each value represents the number of times an interaction was observed for a specific pair of genes (parents in rows, children in columns).

Details

The microarray platform used in the expO project is the Affymetrix HG-U133PLUS2 GeneChip.

Source

https://expo.intgen.org/geo/

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2109

References

http://www.intgen.org/expo/

Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, Olson JA Jr, Marks JR, Dressman HK, West M, Nevins JR. (2006) "Oncogenic pathway signatures in human cancers as a guide to targeted therapies", Nature, 439(7074):274-275.

Examples

data(expO.colon.ras)

predictionet documentation built on Nov. 8, 2020, 7:48 p.m.