ProAct: quantifying the differential activity of biological processes in tissues, cells, and user-defined contexts

Abstract

The distinct functions and phenotypes of human tissues and cells derive from the activity of biological processes that varies in a context-dependent manner. Here, we present the Process Activity (ProAct) webserver that estimates the preferential activity of biological processes in tissues, cells, and other contexts. Users can upload a differential gene expression matrix measured across contexts or cells, or use a built-in matrix of differential gene expression in 34 human tissues. Per context, ProAct associates gene ontology (GO) biological processes with estimated preferential activity scores, which are inferred from the input matrix. ProAct visualizes these scores across processes, contexts, and process-associated genes. ProAct also offers potential cell-type annotations for cell subsets, by inferring them from the preferential activity of 2001 cell-type-specific processes. Thus, ProAct output can highlight the distinct functions of tissues and cell types in various contexts, and can enhance cell-type annotation efforts. The ProAct webserver is available at https://netbio.bgu.ac.il/ProAct/.

Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue

“…While a number of gene test testing approaches have been explored that account for tissue or cell type-specificity [ 24 – 27 ], the primary goal of these techniques was the identification of tissue-specific biological processes. None of these prior methods specifically focuses on cancer or uses the association between normal tissue-specificity and gene activity within dysplastic tissue.…”