Gene Expression in Metastases Projects

These projects includes 22 Brain met pairs, 11 Bone met pairs, 14 Ovarian met pairs, and 7 GI met pairs. The ovarian mets had a good mix for the ILC and IDC subtypes while the brain had a good mix of ERpos vs ERneg mets, thus additional plots for these comparisons are shown below.

Transcript counts from all samples were quantified with Salmon v.0.8.2 and converted to gene-level counts using tximport. The gene-level counts from all studies were then normalized together using TMM with edgeR. Log2 transformed TMM-normalized counts per million [log2 (TMM-CPM+1)] are shown in the plots. NB: p-values are not corrected for multiple comparisons.

log2 (TMM-CPM+1) expression values, sample annotations, and code for shiny app available on the lab github

Publication references for samples: PMID:28878133 PMID:29961873 PMID:31263748