Table 1.

Examples of the most commonly used endocrine-related breast cancer public omic datasets.

Database	URL	Data spaces
CPTAC	https://proteomics.cancer.gov/data-portal	Proteome
EGA	https://ega-archive.org/datasets	Genome, Transcriptome
EMBL-EBI	https://www.ebi.ac.uk/services/all	Genome, Transcriptome, Proteome, Metabolome
GNPS/Massive	https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp	Metabolome
ICGC	https://dcc.icgc.org/	Genome, Transcriptome
MassIVE	https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp	Proteome
Metabolomics	https://www.metabolomicsworkbench.org/	Metabolome
Workbench
NCBI-GEO	https://www.ncbi.nlm.nih.gov/gds	Genome, Transcriptome
ONCOMINE	https://www.oncomine.org/resource/login.html	Genome, Transcriptome
ProteomeXchange (PX) Consortium	http://www.proteomexchange.org/	Proteome
ProteomicsDB	https://www.proteomicsdb.org/	Proteome
TCGA	https://portal.gdc.cancer.gov/	Genome, Transcriptome

Primary data and metadata quality vary across and within these sites. For example, clinical metadata for human subjects are often limited. The platform used for data collection in each omics space also can vary across and within these sites. While most provide access to the raw (unprocessed) data, ONCOMINE primarily exposes only processed data; the method of data processing can vary across individual studies.