Each point is a transposable element (TE) subfamily. TEs that sit close together are co-expressed across tumors. Choose a cancer type and which principal components to plot, color by TE class or family, hover for names, and type TE names to highlight them.
Methods: TE expression (subfamily level) in TCGA primary tumors, one tumor per patient. TEs expressed in fewer than 10% of tumors were removed, and only TEs with roughly continuous expression (not zero-inflated) are shown. Each TE was centered and scaled within cancer type, and PCA was run with tumors as observations. A TE's coordinate on a component is its correlation with that component; the percentage on each axis is the variance explained. Single-cancer views include cancer types with more than 100 tumors. Component signs are arbitrary.