Three lung cancer microarray data sets and matched annotation

Description

The three human lung cancer microarray data sets, from Stanford (Garber et al., 2001), Harvard (Bhattacharjee et al., 2001), and Michigan (Beer et al., 2002). The 3,924 common Entrez Gene IDs are represented, matched across the three studies. The 3,649 common gene sets (GO categories and KEGG pathways) are represented, defined in Entrez Gene ID.

Usage

data(LungCancer3)

Format

A list of two sub-lists named 'data' and 'info', respectively.

Details

LungCancer3$data is a list of 3 R matrices named 'Harvard', 'Stanford', and 'Michigan', respectively. Each matrix contains 3,924 rows as the genes have been matched across three studies. Rows are named by Entrez Gene IDs.

The number of columns corresponds to the number of arrays used in each study. Columns are named Tumor1, Tumor2, ..., and Normal1, Normal2, ..., similarly for three matrices. LungCancer3$data$Harvard (Harvard study) has 156 columns of 139 tumor vs. 17 normal samples; LungCancer3$data$Stanford (Stanford study) has 46 columns of 41 tumor vs. 5 normal samples; and LungCancer3$data$Michigan (Michigan study) has 96 columns of 86 tumor vs. 10 normal samples. For tumor samples, only adenocarcinoma samples have been included for consistency.

LungCancer3$info is again a list of two objects, named GSdef and Name, respectively.

LungCancer3$info$GSdef is a list of 3,649 gene set definitions for the 3,924 genes by GO categories and KEGG pathways. This list is named by the gene set IDs such as "GO:0007169" for GO categories and "00920" for KEGG pathways. Each entry of this list is a character vector of Entrez Gene IDs, which the gene set consists of. For example, LungCancer3$info$GSdef[[147]] returns c("348", "25", "27").

LungCancer3$info$Name is a character vector of length 3,649 corresponding to the gene sets defined in LungCancer3$info$GSdef, named by the gene set IDs. GSdef and Name have the gene sets in the same order. For example, LungCancer3$info$GSdef[[123]] and LungCancer3$info$Name[123] are both "GO:0032774".

Source

Harvard data (Bhattacharjee et al.) http://www.broad.mit.edu/mpr/lung/

Stanford data (Garber et al.) http://smd.stanford.edu/cgi-bin/data/viewDetails.pl?exptid=12827&viewSet=1

Michigan data (Beer et al.) http://dot.ped.med.umich.edu:2000/ourimage/pub/Lung/index.html

References

Beer, D. G. et al. (2002) Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nature Medicine, 8, 816-824.

Bhattacharjee, A. et al. (2001) Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc. Natl Acad. Sci., 98, 13790-13795.

Garber, M. E. et al. (2001) Diversity of gene expression in adenocarcinoma of the lung. Proc. Natl Acad. Sci., 98, 13784-13789.

Examples

data(LungCancer3)
str(LungCancer3$data)
str(LungCancer3$info$GSdef[1:3])
LungCancer3$info$Name[1:3]