UCSD Insel Lab

University of California, San Diego

MDS (Multidimensional Scaling) plots generated via EdgeR (Robinson et al, 2010) showing how TCGA and GTEX samples cluster

Files are plotted in Excel with X and Y coordinates for each point/sample on the MDS plots. These plots provide information about how closely or diffusely groups of samples cluster together, viz. gene expression. A useful primer on the principle of multidimensional scaling can be found here.

Information about samples (tumor subtype, whether primary tumor or matched normal etc.) are also provided as needed.

The tumor types below include tumor subtypes as described in Table 1, e.g. the file with Breast Cancer IDC includes Her2+, Hormone Receptor+, Triple + and Triple - subtypes of BRCA IDC.

Adrenocortical Cancer and Adrenal Gland

Bladder Cancer and Bladder

Breast Cancer Infiltrating Ductal Carcinoma and Breast

Breast Cancer Infiltrating Lobular Carcinoma and Breast

Cervical Cancer and Cervix Uteri

Colon Cancer and Colon

Esophageal Cancer and Esophagus

Kidney Chromophobe and Kidney

Kidney Clear Cell Carcinoma and Kidney

Kidney Papillary Cell Carcinoma and Kidney

Liver Hepatocellular Carcinoma and Liver

Lung Adenocarcinoma and Lung

Lung Squamous Cell Carcinoma and Lung

Skin Cutaneous Melanoma and Sun-exposed skin

Ovarian Cancer and Ovary

Pancreatic Cancer and Pancreas

Prostate Cancer and Prostate

Stomach Cancer and Stomach

Testicular Cancer and Testicle

Thyroid Cancer and Thyroid

Uterine Carcinosarcoma and Uterus