cd09-1-lungData: Lung Cancer Gene Expression Dataset
In oompaData: Data to Illustrate OOMPA Algorithms
lungData-data R Documentation
Lung Cancer Gene Expression Dataset
Description
This data set contains clinical annotations and the log expression of
150 genes for a set of 444 lung cancer patients. The 150 genes were
selected randomly from a larger Affymetrix U133A dataset.
Usage
data(lungData)
Format
A data matrix (lung.dataset) containing the log
expression of 150 genes (rows) in 444 lung tumor samples (columns),
along with a data frame (lung.clinical) containing clinical
annotations of the patients.
Source
Supporting data for the Nature Medicine paper by Shedden et al. was
downloaded from the (now defunct) caArray web site. The original data
are still available by FTP from
ftp://caftpd.nci.nih.gov/pub/caARRAY/experiments/caArray_beer-00153/
and in the Gene Expression Omnibus at
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68571.
The data were log transformed by mapping the expression value x to
log2(1+x). A subset of genes and of clinical annotation columns were
selected to form this data set.
References
Abrams ZB, Zucker M, Wang M, Asiaee Taheri A, Abruzzo LV, Coombes KR.
Thirty biologically interpretable clusters of transcription
factors distinguish cancer type.
BMC Genomics. 2018 Oct 11;19(1):738. doi: 10.1186/s12864-018-5093-z.
Asiaee A, Abrams ZB, Nakayiza S, Sampath D, Coombes KR.
Explaining Gene Expression Using Twenty-One MicroRNAs.
J Comput Biol. 2020 Jul;27(7):1157-1170. doi: 10.1089/cmb.2019.0321.
oompaData documentation built on Dec. 29, 2022, 4:07 p.m.
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| lungData-data | R Documentation |
Lung Cancer Gene Expression Dataset
Description
This data set contains clinical annotations and the log expression of 150 genes for a set of 444 lung cancer patients. The 150 genes were selected randomly from a larger Affymetrix U133A dataset.
Usage
data(lungData)
Format
A data matrix (lung.dataset) containing the log
expression of 150 genes (rows) in 444 lung tumor samples (columns),
along with a data frame (lung.clinical) containing clinical
annotations of the patients.
Source
Supporting data for the Nature Medicine paper by Shedden et al. was downloaded from the (now defunct) caArray web site. The original data are still available by FTP from ftp://caftpd.nci.nih.gov/pub/caARRAY/experiments/caArray_beer-00153/ and in the Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68571. The data were log transformed by mapping the expression value x to log2(1+x). A subset of genes and of clinical annotation columns were selected to form this data set.
References
Abrams ZB, Zucker M, Wang M, Asiaee Taheri A, Abruzzo LV, Coombes KR.
Thirty biologically interpretable clusters of transcription
factors distinguish cancer type.
BMC Genomics. 2018 Oct 11;19(1):738. doi: 10.1186/s12864-018-5093-z.
Asiaee A, Abrams ZB, Nakayiza S, Sampath D, Coombes KR.
Explaining Gene Expression Using Twenty-One MicroRNAs.
J Comput Biol. 2020 Jul;27(7):1157-1170. doi: 10.1089/cmb.2019.0321.
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