Microarray gene expression dataset from Khan et al., 2001

Description

Khan contains gene expression profiles of four types of small round blue cell tumours of childhood (SRBCT) published by Khan et al. (2001). It also contains further gene annotation retrieved from SOURCE at http://source.stanford.edu/.

Usage

data(khan)

Format

Khan is dataset containing the following:

$train:
data.frame of 2308 rows and 64 columns. The training dataset of 64 arrays and 2308 gene expression values
$test:
data.frame, of 2308 rows and 25 columns. The test dataset of 25 arrays and 2308 genes expression values
$gene.labels.imagesID:
vector of 2308 Image clone identifiers corresponding to the rownames of $train and $test.
$train.classes:
factor with 4 levels "EWS", "BL-NHL", "NB" and "RMS", which correspond to the four groups in the $train dataset
$test.classes:
factor with 5 levels "EWS", "BL-NHL", "NB", "RMS" and "Norm" which correspond to the five groups in the $test dataset
$annotation:
data.frame of 2308 rows and 8 columns. This table contains further gene annotation retrieved from SOURCE http://SOURCE.stanford.edu in May 2004. For each of the 2308 genes, it contains:
$CloneID
Image Clone ID
$UGCluster
The Unigene cluster to which the gene is assigned
$Symbol
The HUGO gene symbol
$LLID
The locus ID
$UGRepAcc
Nucleotide sequence accession number
$LLRepProtAcc
Protein sequence accession number
$Chromosome
chromosome location
$Cytoband
cytoband location

Details

Khan et al., 2001 used cDNA microarrays containing 6567 clones of which 3789 were known genes and 2778 were ESTs to study the expression of genes in of four types of small round blue cell tumours of childhood (SRBCT). These were neuroblastoma (NB), rhabdomyosarcoma (RMS), Burkitt lymphoma, a subset of non-Hodgkin lymphoma (BL), and the Ewing family of tumours (EWS). Gene expression profiles from both tumour biopsy and cell line samples were obtained and are contained in this dataset. This dataset contains the filtered dataset of 2308 gene expression profiles as described by Khan et al., 2001.

Source

khan contains a filtered data of 2308 gene expression profiles as published and provided by Khan et al. (2001) on the supplementary web site to their publication http://research.nhgri.nih.gov/microarray/Supplement/.

References

Culhane AC, et al., 2002 Between-group analysis of microarray data. Bioinformatics. 18(12):1600-8.

Khan,J., Wei,J.S., Ringner,M., Saal,L.H., Ladanyi,M., Westermann,F., Berthold,F., Schwab,M., Antonescu,C.R., Peterson,C. et al. (2001) Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat. Med., 7, 673-679.

Examples

data(khan)
summary(khan)