khan {dendextend} | R Documentation |
Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.
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
khan
Format
Khan is dataset containing the following:
- train:
data.frame
of 306 rows and 64 columns. The training dataset of 64 arrays and 306 gene expression values- test:
data.frame
, of 306 rows and 25 columns. The test dataset of 25 arrays and 306 genes expression values- gene.labels.imagesID:
vector
of 306 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 306 rows and 8 columns. This table contains further gene annotation retrieved from SOURCE http://SOURCE.stanford.edu in May 2004. For each of the 306 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. The dataset downloaded from the website contained the filtered dataset of 2308 gene expression profiles as described by Khan et al., 2001. This dataset was available from the url bioinf.ucd.ie/people/aedin/R/ (but the URL has been broken for a while since 2025)
In order to reduce the size of the MADE4 package, and produce small example datasets, the top 50 genes from the
ends of 3 axes following bga
were selected. This produced a reduced datasets of 306 genes.
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
OLD (site no longer found): https://research.nhgri.nih.gov/microarray/
The data was copied from the made4 package (https://www.bioconductor.org/packages/release/bioc/html/made4.html)
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)