TY - JOUR
T1 - ProAct
T2 - quantifying the differential activity of biological processes in tissues, cells, and user-defined contexts
AU - Sharon, Moran
AU - Gruber, Gil
AU - Argov, Chanan M.
AU - Volozhinsky, Miri
AU - Yeger-Lotem, Esti
N1 - Publisher Copyright: © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2023/5/19
Y1 - 2023/5/19
N2 - 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/.
AB - 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/.
UR - http://www.scopus.com/inward/record.url?scp=85164240932&partnerID=8YFLogxK
U2 - https://doi.org/10.1093/nar/gkad421
DO - https://doi.org/10.1093/nar/gkad421
M3 - Article
C2 - 37207335
SN - 0305-1048
VL - 51
SP - W478-W483
JO - Nucleic acids research
JF - Nucleic acids research
IS - W1
ER -