Overview
What Data Types Are Stored
ArrayExpress/BioStudies holds a wide range of functional genomics experiment types.
Relevance to Gynecologic Cancer
ArrayExpress is deeply embedded in gyne cancer research, primarily as a data deposition and retrieval resource rather than a disease-specific portal. Several specific ways it is relevant:
1. Historical microarray datasets for ovarian and endometrial cancer A literature review and repository search identified endometrial cancer microarray expression studies accessed from ArrayExpress and GEO, used to perform meta-analyses identifying gene expression profiles associated with aggressive disease and patient outcome — including a 9-gene signature associated with endometrioid endometrial cancer prognosis.
2. Cross-cancer comparative transcriptomics ArrayExpress datasets have been used in comparative gene expression analyses across ovarian, cervical, and endometrial cancers, identifying shared differentially expressed genes and showing that cell cycle and p53 signaling pathways are conserved across these three gynecologic cancer types.
3. miRNA profiling in gyne cancers ArrayExpress has hosted MSK-derived datasets profiling miRNA expression in endometrioid endometrial tumors (n=96) and serous ovarian tumors (n=96), collected 2000–2012, designed to address both biological questions and methodological questions about microarray study design in gynecologic cancer research.
4. Single-cell and spatial data deposition As scRNA-seq and spatial transcriptomics studies of gynecologic tumors proliferate — including work similar to Regner et al. and Kader et al. — ArrayExpress/BioStudies is one of the principal repositories where raw and processed data are deposited alongside publication, making it a key discovery layer for researchers seeking gyne cancer single-cell datasets.
Notes
Many datasets mirror GEO. Search both GEO and ArrayExpress for exhaustive coverage.