Profiling the Expression of Transportome Genes in cancer: A systematic approach

Abstract

The transportome, the -omic layer encompassing all Ion Channels and Transporters (ICTs), is crucial for cell physiology. It is therefore reasonable to hypothesize a role of the transportome in disease, and in particular in cancer. Here, we present the Membrane Transport Protein DataBase (MTP-DB), a database collecting information on ICTs, and a pipeline that takes expression data and the MTP-DB as input to produce a broad overview of transportome dysregulation in cancer. The MTP-DB may prove useful for the study of the transportome in general, and the pipeline may be used to study the transportome in other diseases. Both tools are open source and can be found on GitHub at TCP-Lab/mtp-db and TCP-Lab/transportome_profiler, under permissive licenses. We detect that the transportome is dysregulated in cancer, and that dysregulation patterns are shared among different cancer types. It is still unclear how these patterns are linked to cancer patho-physiology.