jorissen.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 Jorissen and colleagues in 2009. 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 290 human colon tumors and 259 RAS-related genes.

Usage

data(jorissen.colon.ras)

Format

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

demo2.ras

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

data2.ras

matrix containing expression of genes related to RAS.

annot2.ras

matrix containing annotations of the genes related to RAS.

priors2.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 Jorissen's dataset is the Affymetrix HG-U133PLUS2 GeneChip.

Source

http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE14333

References

Jorissen RN, Gibbs P, Christie M, Prakash S, Lipton L, Desai J, Kerr D, Aaltonen LA, Arango D, Kruhoffer M, Orntoft TF, Andersen CL, Gruidl M, Kamath VP, Eschrich S, Yeatman TJ, Sieber OM. (2009) "Metastasis-Associated Gene Expression Changes Predict Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer", Clin Cancer Res 15(24):7642-7651.

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(jorissen.colon.ras)

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