TCGA Breast Carcinoma Data Analysis

Datasets were downloaded from the TCGA breast carcinoma web site (https://tcga-data.nci.nih.gov/docs/publications/brca_2012/) [4 (link)] (Table 1). Gene expression data by Agilent 244 K arrays were available for 547 cases. DNA copy number alteration data by Affymetrix 6.0 SNP arrays were available for 466 cases. Somatic mutation data by whole exome sequencing were available on 463 cases. The TCGA PAM50 subtype classification was downloaded also from the same site. A sample list is provided in Additional file 2: (TCGA sample ID.xlsx).

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Jiang T., Shi W., Natowicz R., Ononye S.N., Wali V.B., Kluger Y., Pusztai L, & Hatzis C. (2014). Statistical measures of transcriptional diversity capture genomic heterogeneity of cancer. BMC Genomics, 15(1), 876.

Publication 2014

244 K arrays 6.0 SNP arrays

Breast carcinoma Dna arrays Gene expression Mutation Somatic

Corresponding Organization :

Other organizations : Yale University, Laboratoire d'Informatique de Paris-Nord, Paris-Est Sup

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Variable analysis

independent variables

DNA copy number alteration data by Affymetrix 6.0 SNP arrays
Somatic mutation data by whole exome sequencing

dependent variables

Gene expression data by Agilent 244 K arrays

control variables

TCGA PAM50 subtype classification

controls

No positive or negative controls were explicitly mentioned.

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