title: curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome.
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.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
authors.forename: Benjamin Frederick
authors.initials: BF
authors.lastname: Ganzfried
authors.forename: Markus
authors.initials: M
authors.lastname: Riester
authors.forename: Benjamin
authors.initials: B
authors.lastname: Haibe-Kains
authors.forename: Thomas
authors.initials: T
authors.lastname: Risch
authors.forename: Svitlana
authors.initials: S
authors.lastname: Tyekucheva
authors.forename: Ina
authors.initials: I
authors.lastname: Jazic
authors.forename: Xin Victoria
authors.initials: XV
authors.lastname: Wang
authors.forename: Mahnaz
authors.initials: M
authors.lastname: Ahmadifar
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Birrer
authors.forename: Giovanni
authors.initials: G
authors.lastname: Parmigiani
authors.forename: Curtis
authors.initials: C
authors.lastname: Huttenhower
authors.forename: Levi
authors.initials: L
authors.lastname: Waldron
mesh_terms: D054377:Chemokine CXCL12 / Q000235:genetics; D002874:Chromosome Mapping; D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D058977:Molecular Sequence Annotation; D010051:Ovarian Neoplasms / Q000235:genetics*; D012985:Software Design; D016019:Survival Analysis; D059467:Transcriptome / Q000235:genetics*
chemical_list: C515255:CXCL12 protein, human; D054377:Chemokine CXCL12
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