RRC ID 35654
Author Wagner A, Zarecki R, Reshef L, Gochev C, Sorek R, Gophna U, Ruppin E.
Title Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious.
Journal Proc. Natl. Acad. Sci. U.S.A.
Abstract Gene suppression and overexpression are both fundamental tools in linking genotype to phenotype in model organisms. Computational methods have proven invaluable in studying and predicting the deleterious effects of gene deletions, and yet parallel computational methods for overexpression are still lacking. Here, we present Expression-Dependent Gene Effects (EDGE), an in silico method that can predict the deleterious effects resulting from overexpression of either native or foreign metabolic genes. We first test and validate EDGE's predictive power in bacteria through a combination of small-scale growth experiments that we performed and analysis of extant large-scale datasets. Second, a broad cross-species analysis, ranging from microorganisms to multiple plant and human tissues, shows that genes that EDGE predicts to be deleterious when overexpressed are indeed typically down-regulated. This reflects a universal selection force keeping the expression of potentially deleterious genes in check. Third, EDGE-based analysis shows that cancer genetic reprogramming specifically suppresses genes whose overexpression impedes proliferation. The magnitude of this suppression is large enough to enable an almost perfect distinction between normal and cancerous tissues based solely on EDGE results. We expect EDGE to advance our understanding of human pathologies associated with up-regulation of particular transcripts and to facilitate the utilization of gene overexpression in metabolic engineering.
Volume 110(47)
Pages 19166-71
Published 2013-11-19
DOI 10.1073/pnas.1312361110
PII 1312361110
PMID 24198337
PMC PMC3839766
MeSH Algorithms* Computational Biology / methods* Gene Expression / genetics* Gene Expression Profiling / methods Gene Expression Regulation, Neoplastic / genetics Humans Metabolic Networks and Pathways / genetics* Models, Genetic*
IF 9.504
Times Cited 12
Prokaryotes E. coli ME5305(AG1) ASKA library