Transcriptomic signatures

Two transcriptomic signatures that I derived for Chapter 2 of my thesis using RNA-seq data from a xenograft model of breast cancer progression. This work is associated with a published manuscript (DOI: 10.1126/sciadv.abf4408) and the data is publicly available via GEO (GSE193369).

The first signature describes metastatic organotropism to lung and liver tumour microenvironments and in our paper we found that transcriptomic changes in the lung were reversible, microenvironment-induced, and represent potentially targetable plastic mechanisms. The second signature captures metastatic potential in an aggressive LeGO-barcoded clone (subclone 13) compared with a less dominant clone (subclone 2). These subclone differences are mentioned in the manuscript and explored further in my thesis, where I demonstrate that they are subclone-intrinsic and associated with prognosis.

The excel file contains the differential expression output and the gmt file contains the signatures as a GeneSetCollection object. The signatures can be loaded into R using GSEABase::getGmt() for further analyses.