breast {TopKLists}

Sample data from breast cancer expression

Description

The example dataset comprises three lists of microarray results (differential gene expression) from three breast cancer studies:

1. Strong Time Dependence of the 76-Gene Prognostic Signature (2007) labeled TransBig

2. MicroArray Quality Control Phase II Project (2010) labeled MDCC

3. A Clinically Relevant Gene Signature in Triple-Negative and Basal-Like Breast Cancer (2011) labeled Pusztai

Only genes (unique gene symbols) common to all studies are considered, therefore each of the three lists has the length of N = 917.

Usage

data(breast)

Format

data.frame

Source

1. TransBig: GEO GSE7390

2. MDCC: GEO GSE20194

3. Pusztai: GEP GSE20271

References

TransBig: Desmedt C, Piette F, Loi S, Wang Y et al. (2007). Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clin Cancer Res, 1;13(11):3207-14. PMID: 17545524

MDACC: Shi L, Campbell G, Jones WD, Campagne F et al. (2010). The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol;28(8):827-38. PMID: 20676074

Pusztai: Tabchy A., Valero V., Vidaurre T., Lluch A. et al. (2010). Evaluation of a 30-gene paclitaxel, fluorouracil, doxorubicin, and cyclophosphamide chemotherapy response predictor in a multicenter randomized trial in breast cancer. Clin Cancer Res 1;16(21):5351-61. PMID: 20829329