Database Commons a catalog of biological databases

Database Commons - curatedOvarianData

curatedOvarianData

Citations: 30

z-index 3.72

Short name curatedOvarianData
Full name
Description curatedOvarianData contains clinically annotated data for the ovarian cancer transcriptome.
URL http://bcb.dfci.harvard.edu/ovariancancer/
Year founded 2013
Last update & version NA    v1.0
Availability Free to all users
University/Institution hosted Dana-Farber Cancer Institute
Address Boston,MA,02115,USA
City Boston
Province/State Maryland
Country/Region United States
Contact name Levi Waldron
Contact email levi@jimmy.harvard.edu
Data type(s)
Major organism(s)
Keyword(s)
  • gene expression
  • ovarian cancer
Publication(s)
  • curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. [PMID: 23550061]

    Benjamin Frederick Ganzfried, Markus Riester, Benjamin Haibe-Kains, Thomas Risch, Svitlana Tyekucheva, Ina Jazic, Xin Victoria Wang, Mahnaz Ahmadifar, Michael J Birrer, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron
    Database : the journal of biological databases and curation 2013:2013
    30 Citations (Google Scholar as of 2016-01-30)

    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.

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Accessibility

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200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
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200 OK2016-01-20
200 OK2016-01-18
200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
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200 OK2016-01-04

Tags

Expression
Homo sapiens
gene expression ovarian cancer

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Mengwei Li [2015-12-07]
    • Mengwei Li [2015-06-27]
Stats