OvMark: a user-friendly system for the identification of prognostic biomarkers in publically available ovarian cancer gene expression datasets

Article

Madden, S., Clarke, C., Stordal, B., Carey, M., Broaddus, R., Gallagher, W., Crown, J., Mills, G. and Hennessy, B. 2014. OvMark: a user-friendly system for the identification of prognostic biomarkers in publically available ovarian cancer gene expression datasets. Molecular Cancer. 13 (1), pp. 1-11. https://doi.org/10.1186/1476-4598-13-241
TypeArticle
TitleOvMark: a user-friendly system for the identification of prognostic biomarkers in publically available ovarian cancer gene expression datasets
AuthorsMadden, S., Clarke, C., Stordal, B., Carey, M., Broaddus, R., Gallagher, W., Crown, J., Mills, G. and Hennessy, B.
Abstract

Background: Ovarian cancer has the lowest survival rate of all gynaecologic cancers and is characterised by a lack of early symptoms and frequent late stage diagnosis. There is a paucity of robust molecular markers that are independent of and complementary to clinical parameters such as disease stage and tumour grade.
METHODS: We have developed a user-friendly, web-based system to evaluate the association of genes/miRNAs with outcome in ovarian cancer. The OvMark algorithm combines data from multiple microarray platforms (including probesets targeting miRNAs) and correlates them with clinical parameters (e.g. tumour grade, stage) and outcomes (disease free survival (DFS), overall survival). In total, OvMark combines 14 datasets from 7 different array platforms measuring the expression of ~17,000 genes and 341 miRNAs across 2,129 ovarian cancer samples.
RESULTS: To demonstrate the utility of the system we confirmed the prognostic ability of 14 genes and 2 miRNAs known to play a role in ovarian cancer. Of these genes, CXCL12 was the most significant predictor of DFS (HR = 1.42, p-value = 2.42x10-6). Surprisingly, those genes found to have the greatest correlation with outcome have not been heavily studied in ovarian cancer, or in some cases in any cancer. For instance, the three genes with the greatest association with survival are SNAI3, VWA3A and DNAH12.
CONCLUSIONS/IMPACT:
OvMark is a powerful tool for examining putative gene/miRNA prognostic biomarkers in ovarian cancer (available at http://glados.ucd.ie/OvMark/index.html). The impact of this tool will be in the preliminary assessment of putative biomarkers in ovarian cancer, particularly for research groups with limited bioinformatics facilities.

Research GroupBiomarkers for Cancer group
PublisherBioMed Central
JournalMolecular Cancer
ISSN1476-4598
Publication dates
Print24 Oct 2014
Publication process dates
Deposited28 Apr 2015
Submitted11 Apr 2014
Accepted26 Sep 2014
Output statusPublished
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Copyright Statement

© 2014 Madden et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated

Digital Object Identifier (DOI)https://doi.org/10.1186/1476-4598-13-241
PubMed ID25344116
PubMed Central ID4219121
Web of Science identifierWOS:000347112900001
LanguageEnglish
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