title: Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile.
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.
authors.affiliation: Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94143, USA.
authors.forename: Maya
authors.initials: M
authors.lastname: Schuldiner
authors.forename: Sean R
authors.initials: SR
authors.lastname: Collins
authors.forename: Natalie J
authors.initials: NJ
authors.lastname: Thompson
authors.forename: Vladimir
authors.initials: V
authors.lastname: Denic
authors.forename: Arunashree
authors.initials: A
authors.lastname: Bhamidipati
authors.forename: Thanuja
authors.initials: T
authors.lastname: Punna
authors.forename: Jan
authors.initials: J
authors.lastname: Ihmels
authors.forename: Brenda
authors.initials: B
authors.lastname: Andrews
authors.forename: Charles
authors.initials: C
authors.lastname: Boone
authors.forename: Jack F
authors.initials: JF
authors.lastname: Greenblatt
authors.forename: Jonathan S
authors.initials: JS
authors.lastname: Weissman
authors.forename: Nevan J
authors.initials: NJ
authors.lastname: Krogan
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology; D004721:Endoplasmic Reticulum / Q000235:genetics / Q000378:metabolism; D004843:Epistasis, Genetic; D020869:Gene Expression Profiling; D006031:Glycosylation; D008565:Membrane Proteins / Q000235:genetics; D009154:Mutation; D025941:Protein Interaction Mapping; D021381:Protein Transport / Q000235:genetics; D018000:Receptors, Peptide / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*
chemical_list: C064922:ERD2 protein, S cerevisiae; D008565:Membrane Proteins; D018000:Receptors, Peptide; D029701:Saccharomyces cerevisiae Proteins