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Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniarray Profile
Open accessAbstract
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.
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“positive interactions were also enriched between genes involved in mRNA decay and essential gene DAmP alleles (13)”
From A global genetic interaction network maps a wiring diagram of cellular function (2016) · cites this paper as [13]
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Self-citationFunctional modules predict genetic interactions, revealing evolutionary conservation and rewiringPreprint
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BackgroundInfluentialGenetic and Chemical Genetic Analysis of the Cell Cycle
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Self-citationGenetic interactions and network reliability
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Yeast Cells as a Discovery Platform for Parkinson's Disease and other Protein Misfolding Diseases
Allendoerfer, K. L., Su, L. J., & Lindquist, S. L. (2008) · Elsevier eBooks · doi:10.1016/b978-0-12-374028-1.00038-5
Mapping genetic interactions across many phenotypes in metazoan cells
Laufer, C., Billmann, M., & Boutros, M. (2015) · Cambridge University Press eBooks · doi:10.1017/cbo9781139012751.003
Transcriptional Dynamics of the Eukaryotic Cell
Batenchuk, C. (2011) · Library and Archives Canada (Government of Canada) · doi:10.20381/ruor-4391
“…it is possible infer regulatory hierarchies, identify functional complexes, and infer genes functioning within common or parallel pathways (Avery and Wasserman, 1992; Onge et al., 2007; Segrè et al., 2005; Aylor and Zeng, 2008; Schuldiner et al., 2005; Collins et al., 2007; Fiedler et al., 2009).”
InfluentialIdentification of Proteins Involved in the Maintenance of Genome Stability
Cheng, Y., & Hang, E. (2015) · TSpace (University of Toronto)
The Exocyst Subunit Sec6 Interacts with Assembled Exocytic Snare Complexes: A Dissertation
Dubuke, M. L. (2015) · eScholarship@UMassChan · doi:10.13028/m2b01m
“The COG4 subunit has also been shown to physically interact with the SM protein Sly1 (Laufman et al., 2009), and several COG subunits genetically interact with the GEF for Ypt6, Ric1 (Costanzo et al., 2011; Hoppins et al., 2011; Schuldiner et al., 2005; Tong, 2004).”
BackgroundGlobal Analysis of Kinase Interactions in Budding Yeast using Synthetic Dosage Lethality
Sharifpoor, S. (2012) · TSpace (University of Toronto)
Chen, B.-R. (2011) · OhioLink ETD Center (Ohio Library and Information Network)
Metadata
- Authors
- Schuldiner, M., Collins, S. R., Thompson, N. J., Denic, V., Bhamidipati, A., Punna, T., Ihmels, J., Andrews, B., Boone, C., Greenblatt, J. F., Weissman, J. S., & Krogan, N. J.
- Affiliations
- Howard Hughes Medical Institute (US)
- University of Toronto (CA)
- Corresponding author
- Weissman, Jonathan S.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2005-11
- Volume
- 123
- Issue
- 3
- Pages
- 507-519
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2042688172
- Cited by
- 870
- References
- 45
- Citations by year
- 2026: 12 · 2025: 12 · 2024: 15 · 2023: 19 · 2022: 23 · 2021: 30 · 2020: 34 · 2019: 30 · 2018: 36 · 2017: 41 · 2016: 25 · 2015: 47 · 2014: 54 · 2013: 57 · 2012: 61
- FWCI
- 20.53
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
- Keywords
- genetic interaction mapping, sphingolipid metabolism, protein complex formation, essential genes, hierarchical clustering, Saccharomyces cerevisiae
- MeSH terms
- Endoplasmic Reticulum, Epistasis, Genetic, Glycosylation, Membrane Proteins, Mutation, Saccharomyces cerevisiae, Cluster Analysis, Receptors, Peptide, Computational Biology, Gene Expression Profiling, Protein Transport, Protein Interaction Mapping, Saccharomyces cerevisiae Proteins
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