Tumors are mixtures of different compartments. While global gene expression analysis profiles the average expression of all compartments in a sample, identifying the specific contribution of each compartment remains a challenge. With the increasing recognition of the importance of non-neoplastic components, the ability to breakdown the gene expression contribution of each is critical. DECODER, an integrated framework which performs de novo deconvolution and single-sample compartment weight estimation. Application of DECODER across cancer types advances the capability of identifying cellular compartments in an unknown sample and may have implications for identifying the tumor of origin for cancers of unknown primary.
- De novo compartment deconvolution 3 and weight estimation of tumor samples (DECODER) Nature Communications volume 10, Article number: 4729 (2019)