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TopKLists (version 1.0.2)

breast: 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. MicroArray Quality Control Phase II Project (2010) labeled MDACC
  2. Strong Time Dependence of the 76-Gene Prognostic Signature (2007) labeled TransBig
  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

breast

Arguments

format

data.frame

source

  1. MDACC:http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20194{GEO GSE20194}
  2. TransBig:http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse7390{GEO GSE7390}
  3. Pusztai:http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20271{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 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 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