| NCI60 {made4} | R Documentation |
NCI60 is a dataset of gene expression profiles of 60 National Cancer Institute (NCI) cell lines. These 60 human tumour cell lines are derived from patients with leukaemia, melanoma, along with, lung, colon, central nervous system, ovarian, renal, breast and prostate cancers. This panel of cell lines have been subjected to several different DNA microarray studies using both Affymetrix and spotted cDNA array technology. This dataset contains subsets from one cDNA spotted (Ross et al., 2000) and one Affymetrix (Staunton et al., 2001) study, and are pre-processed as described by Culhane et al., 2003.
data(NCI60)
The format is: List of 3
data.frame containing 1375 rows and 60 columns.
1375 gene expression log ratio measurements of the NCI60 cell lines.data.frame containing 1517 rows and 60 columns.
1517 Affymetrix gene expression average difference measurements of the NCI60 cell lines.matrix of 60 rows and 2 columns.
The first column contains the names of the 60 cell line which were analysed.
The second column lists the 9 phenotypes of the cell lines, which are
BREAST, CNS, COLON, LEUK, MELAN, NSCLC, OVAR, PROSTATE, RENAL.The datasets were processed as described by Culhane et al., 2003.
The Ross data.frame contains gene expression profiles of each cell lines in the NCI-60 panel,
which were determined using spotted cDNA arrays containing 9,703 human cDNAs (Ross et al., 2000).
The data were downloaded from The NCI Genomics and Bioinformatics Group Datasets resource
http://discover.nci.nih.gov/datasetsNature2000.jsp. The updated version of this dataset
(updated 12/19/01) was retrieved. Data were provided as log ratio values.
In this study, rows (genes) with greater than 15 and were removed from analysis, reducing the dataset to 5643 spot values per cell line. Remaining missing values were imputed using a K nearest neighbour method, with 16 neighbours and a Euclidean distance metric (Troyanskaya et al., 2001). The dataset NCI60$Ross contains the subsets of 1375 reported by Scherf et al., 2000.
The Affy data were derived using high density Hu6800 Affymetrix microarrays containing 7129 probe sets (Staunton et al., 2001). The dataset was downloaded from the Whitehead Institute Cancer Genomics supplemental data to the paper from Staunton et al., http://www-genome.wi.mit.edu/mpr/NCI60/, where the data were provided as average difference (perfect match-mismatch) values. As described by Staunton et al., an expression value of 100 units was assigned to all average difference values less than 100. Genes whose expression was invariant across all 60 cell lines were not considered, reducing the dataset to 4515 probe sets. This dataset NCI60$Affy of 1517 probe set, contains genes in which the minimum change in gene expression across all 60 cell lines was greater than 500 average difference units. Data were logged (base 2) and median centred.
These pre-processed datasets were available as a supplement to the paper:
Culhane AC, Perriere G, Higgins DG. Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics. 2003 Nov 21;4(1):59. http://www.biomedcentral.com/1471-2105/4/59
Culhane AC, Perriere G, Higgins DG. Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics. 2003 Nov 21;4(1):59.
Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO: Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 2000, 24:227-235
Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, Eisen MB, Sausville EA, Pommier Y, Botstein D, Brown PO, Weinstein JN: A gene expression database for the molecular pharmacology of cancer.Nat Genet 2000, 24:236-244.
Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, Mesirov JP, Lander ES, Golub TR: Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci U S A 2001, 98:10787-10792.
Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB: Missing value estimation methods for DNA microarrays. Bioinformatics 2001, 17:520-525.
data(NCI60) summary(NCI60)