%0 Journal Article %A Deena Mohamad Ameen Gendoo %A Natchar Ratanasirigulchai %A Gregory M Chen %A Levi Waldron %A Benjamin Haibe-Kains %T MetaGxData: Breast and Ovarian Clinically Annotated Transcriptomics Datasets %D 2016 %R 10.1101/052910 %J bioRxiv %P 052910 %X A wealth of transcriptomic and clinical data on breast and ovarian cancers are underutilized due to unharmonized data storage and format. We have developed the MetaGxData package compendium, which includes manually-curated and standardized clinical, pathological, survival, and treatment metadata across both breast and ovarian cancer microarray data. MetaGxData is the largest compendium of breast and ovarian microarray data to date, spanning 65 datasets and encompassing 13,756 samples. Standardization of metadata across the two cancer types promotes the use of their expression datasets in a variety of cross-tumour analyses, including identification of common biomarkers, establishing common patterns of co-expression networks, assessing the validity of prognostic signatures, and the identification of new consensus signatures that reflects upon common biological mechanisms. Here, we present our flexible framework, unified nomenclature, as well as applications that demonstrate the analytical power that is harnessed by combining breast and ovarian cancer datasets. %U https://www.biorxiv.org/content/biorxiv/early/2016/05/12/052910.full.pdf