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The interaction map of yeast: terra incognita?

Mellor J, DeLisi C - J. Biol. (2006)

Bottom Line: A systematic curation of the literature on Saccharomyces cerevisiae has yielded a comprehensive collection of experimentally observed interactions.This new resource augments current views of the topological structure of yeast's physical and genetic networks, but also reveals that existing studies cover only a fraction of the cell.

View Article: PubMed Central - HTML - PubMed

Affiliation: Program in Bioinformatics, 24 Cummington Street, Boston University, Boston, MA 02215, USA. mellor@bu.edu

ABSTRACT
A systematic curation of the literature on Saccharomyces cerevisiae has yielded a comprehensive collection of experimentally observed interactions. This new resource augments current views of the topological structure of yeast's physical and genetic networks, but also reveals that existing studies cover only a fraction of the cell.

Show MeSH
Topological view of the curated protein-protein network of yeast interactions. Adapted from data in Reguly and Breitkreutz et al. [1]. Links are curated from thousands of literature articles referencing proteins in the Saccharoymyces cerevisiae genome. Links shown in black are interactions also recovered by any of five commonly used datasets derived from high-throughput yeast two-hybrid or mass spectrometric screening techniques. Visualization was performed with the VisANT analysis tool [19].
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Figure 1: Topological view of the curated protein-protein network of yeast interactions. Adapted from data in Reguly and Breitkreutz et al. [1]. Links are curated from thousands of literature articles referencing proteins in the Saccharoymyces cerevisiae genome. Links shown in black are interactions also recovered by any of five commonly used datasets derived from high-throughput yeast two-hybrid or mass spectrometric screening techniques. Visualization was performed with the VisANT analysis tool [19].

Mentions: An important new paper by Reguly and Breitkreutz et al. [1] in Journal of Biology makes it clear that the landscape of even the best-studied eukaryote, the budding yeast Saccharomyces cerevisiae, remains significantly unexplored. The authors used the extensive literature based on decades of research to curate a reference network of known interactions in yeast. This literature-curated collection corresponds to a network of some 33,000 high-confidence interactions between proteins or genes in yeast. Surprisingly, it shows little overlap with the published physical [2-6] and genetic [7] interaction networks reported in recent years by large-scale assays. Even with apparent similarities in topology or connectivity, only a fraction of the information in the curated network has been recovered by various high-throughput screening techniques such as systematic yeast two-hybrid analysis or synthetic genetic arrays (see Figure 1). Different views may exist on why this should be, for example in regard to levels and sources of false positives and false negatives in high-throughput datasets [8], but even the most optimistic assessment suggests that tens of thousands of interactions remain to be discovered in yeast. This in turn conveys the enormous scale of the problem of finding similar networks in higher organisms such as worm, mouse or human.


The interaction map of yeast: terra incognita?

Mellor J, DeLisi C - J. Biol. (2006)

Topological view of the curated protein-protein network of yeast interactions. Adapted from data in Reguly and Breitkreutz et al. [1]. Links are curated from thousands of literature articles referencing proteins in the Saccharoymyces cerevisiae genome. Links shown in black are interactions also recovered by any of five commonly used datasets derived from high-throughput yeast two-hybrid or mass spectrometric screening techniques. Visualization was performed with the VisANT analysis tool [19].
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1561582&req=5

Figure 1: Topological view of the curated protein-protein network of yeast interactions. Adapted from data in Reguly and Breitkreutz et al. [1]. Links are curated from thousands of literature articles referencing proteins in the Saccharoymyces cerevisiae genome. Links shown in black are interactions also recovered by any of five commonly used datasets derived from high-throughput yeast two-hybrid or mass spectrometric screening techniques. Visualization was performed with the VisANT analysis tool [19].
Mentions: An important new paper by Reguly and Breitkreutz et al. [1] in Journal of Biology makes it clear that the landscape of even the best-studied eukaryote, the budding yeast Saccharomyces cerevisiae, remains significantly unexplored. The authors used the extensive literature based on decades of research to curate a reference network of known interactions in yeast. This literature-curated collection corresponds to a network of some 33,000 high-confidence interactions between proteins or genes in yeast. Surprisingly, it shows little overlap with the published physical [2-6] and genetic [7] interaction networks reported in recent years by large-scale assays. Even with apparent similarities in topology or connectivity, only a fraction of the information in the curated network has been recovered by various high-throughput screening techniques such as systematic yeast two-hybrid analysis or synthetic genetic arrays (see Figure 1). Different views may exist on why this should be, for example in regard to levels and sources of false positives and false negatives in high-throughput datasets [8], but even the most optimistic assessment suggests that tens of thousands of interactions remain to be discovered in yeast. This in turn conveys the enormous scale of the problem of finding similar networks in higher organisms such as worm, mouse or human.

Bottom Line: A systematic curation of the literature on Saccharomyces cerevisiae has yielded a comprehensive collection of experimentally observed interactions.This new resource augments current views of the topological structure of yeast's physical and genetic networks, but also reveals that existing studies cover only a fraction of the cell.

View Article: PubMed Central - HTML - PubMed

Affiliation: Program in Bioinformatics, 24 Cummington Street, Boston University, Boston, MA 02215, USA. mellor@bu.edu

ABSTRACT
A systematic curation of the literature on Saccharomyces cerevisiae has yielded a comprehensive collection of experimentally observed interactions. This new resource augments current views of the topological structure of yeast's physical and genetic networks, but also reveals that existing studies cover only a fraction of the cell.

Show MeSH