Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile

Maya Schuldiner, Sean Collins, Natalie J. Thompson, Vladimir Denic, Arunashree Bhamidipati, Thanuja Punna, Jan Ihmels, Brenda Andrews, Charles Boone, Jack F. Greenblatt, Jonathan S. Weissman, Nevan J. Krogan

Research output: Contribution to journalArticle

612 Citations (Scopus)

Abstract

We present a strategy for generating and analyzing comprehensive genetic-interaction maps, termed E-MAPs (epistatic miniarray profiles), comprising quantitative measures of aggravating or alleviating interactions between gene pairs. Crucial to the interpretation of E-MAPs is their high-density nature made possible by focusing on logically connected gene subsets and including essential genes. Described here is the analysis of an E-MAP of genes acting in the yeast early secretory pathway. Hierarchical clustering, together with novel analytical strategies and experimental verification, revealed or clarified the role of many proteins involved in extensively studied processes such as sphingolipid metabolism and retention of HDEL proteins. At a broader level, analysis of the E-MAP delineated pathway organization and components of physical complexes and illustrated the interconnection between the various secretory processes. Extension of this strategy to other logically connected gene subsets in yeast and higher eukaryotes should provide critical insights into the functional/organizational principles of biological systems.

Original languageEnglish (US)
Pages (from-to)507-519
Number of pages13
JournalCell
Volume123
Issue number3
DOIs
StatePublished - Nov 4 2005
Externally publishedYes

Fingerprint

Secretory Pathway
Yeast
Genes
Yeasts
Sphingolipids
Essential Genes
Eukaryota
Cluster Analysis
Biological systems
Proteins
Metabolism

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. / Schuldiner, Maya; Collins, Sean; Thompson, Natalie J.; Denic, Vladimir; Bhamidipati, Arunashree; Punna, Thanuja; Ihmels, Jan; Andrews, Brenda; Boone, Charles; Greenblatt, Jack F.; Weissman, Jonathan S.; Krogan, Nevan J.

In: Cell, Vol. 123, No. 3, 04.11.2005, p. 507-519.

Research output: Contribution to journalArticle

Schuldiner, M, Collins, S, Thompson, NJ, Denic, V, Bhamidipati, A, Punna, T, Ihmels, J, Andrews, B, Boone, C, Greenblatt, JF, Weissman, JS & Krogan, NJ 2005, 'Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile', Cell, vol. 123, no. 3, pp. 507-519. https://doi.org/10.1016/j.cell.2005.08.031
Schuldiner, Maya ; Collins, Sean ; Thompson, Natalie J. ; Denic, Vladimir ; Bhamidipati, Arunashree ; Punna, Thanuja ; Ihmels, Jan ; Andrews, Brenda ; Boone, Charles ; Greenblatt, Jack F. ; Weissman, Jonathan S. ; Krogan, Nevan J. / Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. In: Cell. 2005 ; Vol. 123, No. 3. pp. 507-519.
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