Difference between revisions of "PMID:21185072"
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==Main Points of the Paper == | ==Main Points of the Paper == | ||
| − | + | *Phenomic Profiling- quantitative description of the response of all single-gene deletions to physiologically relevant stresses and drug challenges | |
| + | **profiled ~4,000 genes in >300 perturbations | ||
| + | **identified thousands of phenotypes | ||
| + | **identified a diverse set of conditionally essential genes | ||
| + | **facilitates high-confidence association of genes of unknown function to those of known function | ||
| + | **generates numerous leads concerning drug function | ||
== Materials and Methods Used == | == Materials and Methods Used == | ||
Revision as of 13:47, 13 January 2011
| Citation |
Nichols, RJ, Sen, S, Choo, YJ, Beltrao, P, Zietek, M, Chaba, R, Lee, S, Kazmierczak, KM, Lee, KJ, Wong, A, Shales, M, Lovett, S, Winkler, ME, Krogan, NJ, Typas, A and Gross, CA (2011) Phenotypic landscape of a bacterial cell.Cell 144:143-56 |
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| Abstract |
The explosion of sequence information in bacteria makes developing high-throughput, cost-effective approaches to matching genes with phenotypes imperative. Using E. coli as proof of principle, we show that combining large-scale chemical genomics with quantitative fitness measurements provides a high-quality data set rich in discovery. Probing growth profiles of a mutant library in hundreds of conditions in parallel yielded > 10,000 phenotypes that allowed us to study gene essentiality, discover leads for gene function and drug action, and understand higher-order organization of the bacterial chromosome. We highlight new information derived from the study, including insights into a gene involved in multiple antibiotic resistance and the synergy between a broadly used combinatory antibiotic therapy, trimethoprim and sulfonamides. This data set, publicly available at http://ecoliwiki.net/tools/chemgen/, is a valuable resource for both the microbiological and bioinformatic communities, as it provides high-confidence associations between hundreds of annotated and uncharacterized genes as well as inferences about the mode of action of several poorly understood drugs. |
| Links |
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| Keywords |
phenotype; phenomic profiling; high-throughput; chemical genomics; antibiotic resistance; synergy |
| edit table |
Main Points of the Paper
- Phenomic Profiling- quantitative description of the response of all single-gene deletions to physiologically relevant stresses and drug challenges
- profiled ~4,000 genes in >300 perturbations
- identified thousands of phenotypes
- identified a diverse set of conditionally essential genes
- facilitates high-confidence association of genes of unknown function to those of known function
- generates numerous leads concerning drug function
Materials and Methods Used
Please list the materials and methods used in this paper (strains, plasmids, antibodies, etc).
Phenotype Annotations
See Help:AnnotationTable for details on how to edit this table.
<protect>
| Species | Taxon ID | Strain | Gene (if known) | OMP | Phenotype | Details | Evidence | Notes |
|---|---|---|---|---|---|---|---|---|
| edit table |
</protect>
Notes
References
See Help:References for how to manage references in omp dev.
