To cite the curatedOvarianData package in publications use:
Benjamin Frederick Ganzfried, Markus Riester, Benjamin Haibe-Kains, Thomas Risch, Svitlana Tyekucheva, Ina Jazic, Xin Victoria Wang, Mahnaz Ahmadifar, Michael Birrer, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron. curatedOvarianData: Clinically Annotated Data for the Ovarian Cancer Transcriptome, Database 2013: bat013<doi:10.1093/database/bat013> published online April 2, 2013.
Corresponding BibTeX entry:
@Article{,
title = {curatedOvarianData: Clinically Annotated Data for the
Ovarian Cancer Transcriptome},
author = {Benjamin Frederick Ganzfried and Markus Riester and
Benjamin Haibe-Kains and Thomas Risch and Svitlana Tyekucheva and
Ina Jazic and Xin Victoria Wang and Mahnaz Ahmadifar and Michael
Birrer and Giovanni Parmigiani and Curtis Huttenhower and Levi
Waldron},
volume = {2013},
year = {2013},
doi = {10.1093/database/bat013},
abstract = {This article introduces a manually curated data
collection for gene expression meta-analysis of patients with
ovarian cancer and software for reproducible preparation of
similar databases. This resource provides uniformly prepared
microarray data for 2970 patients from 23 studies with curated
and documented clinical metadata. It allows users to efficiently
identify studies and patient subgroups of interest for analysis
and to perform meta-analysis immediately without the challenges
posed by harmonizing heterogeneous microarray technologies, study
designs, expression data processing methods and clinical data
formats. We confirm that the recently proposed biomarker CXCL12
is associated with patient survival, independently of stage and
optimal surgical debulking, which was possible only through
meta-analysis owing to insufficient sample sizes of the
individual studies. The database is implemented as the
curatedOvarianData Bioconductor package for the R statistical
computing language, providing a comprehensive and flexible
resource for clinically oriented investigation of the ovarian
cancer transcriptome. The package and pipeline for producing it
are available from
http://bcb.dfci.harvard.edu/ovariancancer.Database URL:
http://bcb.dfci.harvard.edu/ovariancancer},
url =
{http://database.oxfordjournals.org/content/2013/bat013.abstract},
eprint =
{http://database.oxfordjournals.org/content/2013/bat013.full.pdf+html},
journal = {Database},
}