Literature DB >> 18420932

The chemical genomic portrait of yeast: uncovering a phenotype for all genes.

Maureen E Hillenmeyer1, Eula Fung, Jan Wildenhain, Sarah E Pierce, Shawn Hoon, William Lee, Michael Proctor, Robert P St Onge, Mike Tyers, Daphne Koller, Russ B Altman, Ronald W Davis, Corey Nislow, Guri Giaever.   

Abstract

Genetics aims to understand the relation between genotype and phenotype. However, because complete deletion of most yeast genes ( approximately 80%) has no obvious phenotypic consequence in rich medium, it is difficult to study their functions. To uncover phenotypes for this nonessential fraction of the genome, we performed 1144 chemical genomic assays on the yeast whole-genome heterozygous and homozygous deletion collections and quantified the growth fitness of each deletion strain in the presence of chemical or environmental stress conditions. We found that 97% of gene deletions exhibited a measurable growth phenotype, suggesting that nearly all genes are essential for optimal growth in at least one condition.

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Year:  2008        PMID: 18420932      PMCID: PMC2794835          DOI: 10.1126/science.1150021

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  28 in total

1.  Separate roles for the Golgi apparatus and lysosomes in the sequestration of drugs in the multidrug-resistant human leukemic cell line HL-60.

Authors:  Yuping Gong; Muralikrishna Duvvuri; Jeffrey P Krise
Journal:  J Biol Chem       Date:  2003-09-30       Impact factor: 5.157

2.  Chemogenomic profiling: identifying the functional interactions of small molecules in yeast.

Authors:  Guri Giaever; Patrick Flaherty; Jochen Kumm; Michael Proctor; Corey Nislow; Daniel F Jaramillo; Angela M Chu; Michael I Jordan; Adam P Arkin; Ronald W Davis
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-12       Impact factor: 11.205

Review 3.  Analysis of the tangled relationships between P-glycoprotein-mediated multidrug resistance and the lipid phase of the cell membrane.

Authors:  J Ferté
Journal:  Eur J Biochem       Date:  2000-01

4.  Multiple knockout analysis of genetic robustness in the yeast metabolic network.

Authors:  David Deutscher; Isaac Meilijson; Martin Kupiec; Eytan Ruppin
Journal:  Nat Genet       Date:  2006-09       Impact factor: 38.330

5.  A proteomic analysis of lysosomal integral membrane proteins reveals the diverse composition of the organelle.

Authors:  Richard D Bagshaw; Don J Mahuran; John W Callahan
Journal:  Mol Cell Proteomics       Date:  2004-12-02       Impact factor: 5.911

6.  Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast.

Authors:  Ainslie B Parsons; Andres Lopez; Inmar E Givoni; David E Williams; Christopher A Gray; Justin Porter; Gordon Chua; Richelle Sopko; Renee L Brost; Cheuk-Hei Ho; Jiyi Wang; Troy Ketela; Charles Brenner; Julie A Brill; G Esteban Fernandez; Todd C Lorenz; Gregory S Payne; Satoru Ishihara; Yoshikazu Ohya; Brenda Andrews; Timothy R Hughes; Brendan J Frey; Todd R Graham; Raymond J Andersen; Charles Boone
Journal:  Cell       Date:  2006-08-11       Impact factor: 41.582

7.  Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast.

Authors:  Adam M Deutschbauer; Daniel F Jaramillo; Michael Proctor; Jochen Kumm; Maureen E Hillenmeyer; Ronald W Davis; Corey Nislow; Guri Giaever
Journal:  Genetics       Date:  2005-02-16       Impact factor: 4.562

8.  The yeast multidrug transporter Pdr5 of the plasma membrane is ubiquitinated prior to endocytosis and degradation in the vacuole.

Authors:  R Egner; K Kuchler
Journal:  FEBS Lett       Date:  1996-01-08       Impact factor: 4.124

9.  Endocytic recycling compartments altered in cisplatin-resistant cancer cells.

Authors:  Xing-Jie Liang; Sushmita Mukherjee; Ding-Wu Shen; Frederick R Maxfield; Michael M Gottesman
Journal:  Cancer Res       Date:  2006-02-15       Impact factor: 12.701

10.  Subcellular localization and activity of multidrug resistance proteins.

Authors:  Asha Rajagopal; Sanford M Simon
Journal:  Mol Biol Cell       Date:  2003-04-17       Impact factor: 4.138

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  494 in total

1.  Recruitment of genes and enzymes conferring resistance to the nonnatural toxin bromoacetate.

Authors:  Kevin K Desai; Brian G Miller
Journal:  Proc Natl Acad Sci U S A       Date:  2010-10-04       Impact factor: 11.205

Review 2.  Bugs, drugs and chemical genomics.

Authors:  Terry Roemer; Julian Davies; Guri Giaever; Corey Nislow
Journal:  Nat Chem Biol       Date:  2011-12-15       Impact factor: 15.040

3.  Temporal variation in selection accelerates mutational decay by Muller's ratchet.

Authors:  Alison M Wardlaw; Aneil F Agrawal
Journal:  Genetics       Date:  2012-04-27       Impact factor: 4.562

4.  Diving through the "-omics": the case for deep phenotyping and systems epidemiology.

Authors:  Robin Haring; Henri Wallaschofski
Journal:  OMICS       Date:  2012-02-09

5.  Differential and integral views of genetics in computational systems biology.

Authors:  Denis Noble
Journal:  Interface Focus       Date:  2010-11-17       Impact factor: 3.906

6.  Systematic discovery of nonobvious human disease models through orthologous phenotypes.

Authors:  Kriston L McGary; Tae Joo Park; John O Woods; Hye Ji Cha; John B Wallingford; Edward M Marcotte
Journal:  Proc Natl Acad Sci U S A       Date:  2010-03-22       Impact factor: 11.205

7.  Yet1p and Yet3p, the yeast homologs of BAP29 and BAP31, interact with the endoplasmic reticulum translocation apparatus and are required for inositol prototrophy.

Authors:  Joshua D Wilson; Charles Barlowe
Journal:  J Biol Chem       Date:  2010-04-08       Impact factor: 5.157

8.  A complex-based reconstruction of the Saccharomyces cerevisiae interactome.

Authors:  Haidong Wang; Boyko Kakaradov; Sean R Collins; Lena Karotki; Dorothea Fiedler; Michael Shales; Kevan M Shokat; Tobias C Walther; Nevan J Krogan; Daphne Koller
Journal:  Mol Cell Proteomics       Date:  2009-01-27       Impact factor: 5.911

9.  H3K4 methyltransferase Set1 is involved in maintenance of ergosterol homeostasis and resistance to Brefeldin A.

Authors:  Paul F South; Kayla M Harmeyer; Nina D Serratore; Scott D Briggs
Journal:  Proc Natl Acad Sci U S A       Date:  2013-02-04       Impact factor: 11.205

Review 10.  Chemical genomics for studying parasite gene function and interaction.

Authors:  Jian Li; Jing Yuan; Ken Chih-Chien Cheng; James Inglese; Xin-zhuan Su
Journal:  Trends Parasitol       Date:  2013-11-09
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