The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Cluster analysis and display of genome-wide expression patterns
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 16,184
Functional organization of the yeast proteome by systematic analysis of protein complexes
Gavin, A., Böesche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A., Cruciat, C., et al. (2002) · Nature · doi:10.1038/415141a · Cited by 4,729
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706
Functional profiling of the Saccharomyces cerevisiae genome
Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316
Global analysis of protein localization in budding yeast
Huh, W.-K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., & O'Shea, E. K. (2003) · Nature · doi:10.1038/nature02026 · Cited by 4,248 · cited 8×
“…proteins revealed that most of the GET complex shifted in its localization from the ER to punctate structures (which in part but not entirely colocalize with the Golgi marker ANP1; Huh et al., 2003; data not shown) when cells were shifted from growth in rich to minimal medium (Figure 5B).”
BackgroundMethodInfluentialSelf-citationGlobal analysis of protein expression in yeast
Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., & Weissman, J. S. (2003) · Nature · doi:10.1038/nature02046 · Cited by 3,750
Self-citationSystematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Ho, Y., Gruhler, A., Heilbut, A. M., Bader, G. D., Moore, L., Adams, S., Millar, A., Taylor, P. P., Bennett, K. L., Boutilier, K., et al. (2002) · Nature · doi:10.1038/415180a · Cited by 3,573
A comprehensive two-hybrid analysis to explore the yeast protein interactome
Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566
Functional Discovery via a Compendium of Expression Profiles
Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R. B., Armour, C. D., Bennett, H. A., Coffey, E. M., Dai, H. A., He, Y. D., et al. (2000) · Cell · doi:10.1016/s0092-8674(00)00015-5 · Cited by 2,534
Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants
Tong, A. H. Y., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D., Pagé, N., Robinson, M., Raghibizadeh, S., Hogue, C. W. V., Bussey, H., et al. (2001) · Science · doi:10.1126/science.1065810 · Cited by 2,138
Self-citationGlobal Mapping of the Yeast Genetic Interaction Network
Tong, A. H. Y., Lesage, G., Bader, G. D., Ding, H., Xu, H., Xin, X., Young, J., Berriz, G. F., Brost, R. L., Chang, M., et al. (2004) · Science · doi:10.1126/science.1091317 · Cited by 2,089
Self-citationOxidative protein folding in eukaryotes
Tu, B. P., & Weissman, J. S. (2004) · The Journal of Cell Biology · doi:10.1083/jcb.200311055 · Cited by 1,041
Self-citationPatil, C., & Walter, P. (2001) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(00)00219-2 · Cited by 779
Subcellular localization of the yeast proteomePreprint
Kumar, A., Agarwal, S., Heyman, J. A., Matson, S., Heidtman, M. I., Piccirillo, S., Umansky, L., Drawid, A., Jansen, R., Liu, Y., et al. (2002) · Genes & Development · doi:10.1101/gad.970902 · Cited by 737
Cell Wall Architecture in Yeast: New Structure and New Challenges
Lipke, P. N., & Ovalle, R. (1998) · Journal of Bacteriology · doi:10.1128/jb.180.15.3735-3740.1998 · Cited by 701
Parsons, A. B., Brost, R. L., Ding, H., Li, Z., Zhang, C., Sheikh, B., Brown, G. W., Kane, P. M., Hughes, T. R., & Boone, C. M. (2003) · Nature Biotechnology · doi:10.1038/nbt919 · Cited by 651
Self-citationExploration of Essential Gene Functions via Titratable Promoter Alleles
Mnaimneh, S., Davierwala, A. P., Haynes, J., Moffat, J., Peng, W.-T., Zhang, W., Yang, X., Pootoolal, J., Chua, G., Lopez, A., et al. (2004) · Cell · doi:10.1016/j.cell.2004.06.013 · Cited by 604 · cited 1×
“DAmP utilizes simple, PCR-based homologous recombination to disrupt the natural 3#UTR by insertion of an antibiotic-resistance marker, thus greatly destabilizing the corresponding messages (Muhlrad and Parker, 1999).”
MethodSelf-citationModular epistasis in yeast metabolism
Segrè, D., DeLuna, A., Church, G. M., & Kishony, R. (2005) · Nature Genetics · doi:10.1038/ng1489 · Cited by 575
Epistasis and the Evolutionary Process
Hurst, L. D. (2000) · Heredity · doi:10.1111/j.1365-2540.2000.0846b.pp.x · Cited by 571
Semenza, J. C., Hardwick, K., Dean, N., & Pelham, H. R. B. (1990) · Cell · doi:10.1016/0092-8674(90)90698-e · Cited by 539
Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast
Giaever, G. N., Flaherty, P., Kumm, J., Proctor, M. J., Nislow, C., Jaramillo, D. F., Chu, A. M., Jordan, M. I., Arkin, A. P., & Davis, R. W. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307490100 · Cited by 506
RNA Polymerase II Elongation Factors of Saccharomyces cerevisiae: a Targeted Proteomics Approach
Krogan, N. J., Kim, M., Ahn, S., Zhong, G., Kobor, M. S., Cagney, G., Emili, A., Shilatifard, A., Buratowski, S., & Greenblatt, J. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.20.6979-6992.2002 · Cited by 497
Self-citationVesicle tethering complexes in membrane traffic
Whyte, J. R. C., & Munro, S. (2002) · Journal of Cell Science · doi:10.1242/jcs.115.13.2627 · Cited by 457
Genetic Basis of Mitochondrial Function and Morphology in Saccharomyces cerevisiae
Dimmer, K. S., Fritz, S., Fuchs, F., Messerschmitt, M., Weinbach, N., Neupert, W., & Westermann, B. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.01-12-0588 · Cited by 443
Systematic interpretation of genetic interactions using protein networks
Kelley, R., & Ideker, T. (2005) · Nature Biotechnology · doi:10.1038/nbt1096 · Cited by 437
Epistasis and the Evolutionary Process
Wolf, J. B., Brodie, E. D., & Wade, M. J. (2000) · Cited by 434
Test of synergistic interactions among deleterious mutations in bacteria
Elena, S. F., & Lenski, R. E. (1997) · Nature · doi:10.1038/37108 · Cited by 416
A sphingosine-1-phosphate receptor regulates cell migration during vertebrate heart development
Kupperman, E., An, S. M., Osborne, N., Waldron, S., & Stainier, D. Y. R. (2000) · Nature · doi:10.1038/35018092 · Cited by 394
A Robust Toolkit for Functional Profiling of the Yeast Genome
Pan, X., Yuan, D., Xiang, D., Wang, X., Sookhai-Mahadeo, S., Bader, J. S., Hieter, P., Spencer, F. A., & Boeke, J. D. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.09.035 · Cited by 314
Large-Scale Functional Genomic Analysis of Sporulation and Meiosis in Saccharomyces cerevisiae
Enyenihi, A. H., & Saunders, W. S. (2003) · Genetics · doi:10.1093/genetics/163.1.47 · Cited by 252
Sütterlin, C., Hsu, P., Mallabiabarrena, A., & Malhotra, V. (2002) · Cell · doi:10.1016/s0092-8674(02)00720-1 · Cited by 252
Aberrant mRNAs with extended 3′ UTRs are substrates for rapid degradation by mRNA surveillance
Muhlrad, D., & Parker, R. (1999) · RNA · doi:10.1017/s1355838299990829 · Cited by 242
Bhamidipati, A., Denic, V., Toyama, E. Q., & Weissman, J. S. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.07.027 · Cited by 234
Self-citationGenetic Selection of Peptide Inhibitors of Biological Pathways
Norman, T., Smith, D. L., Sorger, P. K., Drees, B., O’Rourke, S. M., Hughes, T. R., Roberts, C. J., Friend, S. H., Fields, S., & Murray, A. W. (1999) · Science · doi:10.1126/science.285.5427.591 · Cited by 190
Ric1p and Rgp1p form a complex that catalyses nucleotide exchange on Ypt6p
Siniossoglou, S., Peak‐Chew, S. Y., & Pelham, H. R. B. (2000) · The EMBO Journal · doi:10.1093/emboj/19.18.4885 · Cited by 170
Sato, K., & Nakano, A. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.e02-01-0027 · Cited by 115
Vashist, S., Frank, C. G., Jakob, C. A., & Ng, D. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.02-06-0090 · Cited by 97
Simons, J. F., Ebersold, M., & Helenius, A. (1998) · The EMBO Journal · doi:10.1093/emboj/17.2.396 · Cited by 93
The Saccharomyces cerevisiae Arr4p is involved in metal and heat tolerance*
Shen, J., Hsu, C., Kang, B.-K., Rosen, B. P., & Bhattacharjee, H. (2003) · BioMetals · doi:10.1023/a:1022504311669 · Cited by 75
Balakrishnan, R. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki023 · Cited by 70
Yeast Genes Controlling Responses to Topogenic Signals in a Model Transmembrane Protein
Tipper, D. J., & Harley, C. A. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.01-10-0488 · Cited by 63
Shahinian, S., Dijkgraaf, G. J. P., Sdicu, A., Thomas, D. Y., Jakob, C. A., Aebi, M., & Bussey, H. (1998) · Genetics · doi:10.1093/genetics/149.2.843 · Cited by 62
Lester, R. L., & Dickson, R. C. (2001) · Analytical Biochemistry · doi:10.1006/abio.2001.5368 · Cited by 55
de Martin, P. E., Du, Y., Novick, P., & Ferro‐Novick, S. (2004) · Journal of Cell Science · doi:10.1242/jcs.01583 · Cited by 53
Li, D., Gonzalez, O., Bachinski, L. L., & Roberts, R. (2000) · Gene · doi:10.1016/s0378-1119(00)00347-4 · Cited by 39
Flagged first, then by citations
Cited by
Sorted by citations
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A., et al. (2006) · Nature · doi:10.1038/nature04670 · Cited by 2,964
Self-citationMolecular mechanisms and physiological functions of mitophagy
Onishi, M., Yamano, K., Sato, M., Matsuda, N., & Okamoto, K. (2021) · The EMBO Journal · doi:10.15252/embj.2020104705 · Cited by 1,469
“The Get1/2 complex is important for insertion of tail-anchored proteins into the ER membrane (Schuldiner et al , 2005; Schuldiner et al , 2008; Wang et al , 2014).”
An ER-Mitochondria Tethering Complex Revealed by a Synthetic Biology Screen
Kornmann, B., Currie, E., Collins, S. R., Schuldiner, M., Nunnari, J., Weissman, J. S., & Walter, P. (2009) · Science · doi:10.1126/science.1175088 · Cited by 1,275
Self-citationA global genetic interaction network maps a wiring diagram of cellular function
Costanzo, M., VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., et al. (2016) · Science · doi:10.1126/science.aaf1420 · Cited by 1,240
“In a similar regulatory relationship, positive interactions were also enriched between genes involved in mRNA decay and essential gene DAmP alleles (13), which often affect mRNA stability via disruption of their 3′ untranslated region (fig.”
BackgroundSelf-citationGlobal analysis of the yeast lipidome by quantitative shotgun mass spectrometry
Ejsing, C. S., Sampaio, J. L., Surendranath, V., Duchoslav, E., Ekroos, K., Klemm, R. W., Simons, K., & Shevchenko, A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0811700106 · Cited by 1,053
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
