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PMID: 16762047 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.

Journal of biology ·Vol. 5 ·No. 4 ·2006-00-00 ·Pages 11

Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M

Abstract

The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference. We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID (http://www.thebiogrid.org) and SGD (http://www.yeastgenome.org/) databases. Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks.

MeSH Terms
Computational Biology Protein Interaction Mapping Saccharomyces cerevisiae/genetics,metabolism Saccharomyces cerevisiae Proteins/genetics,metabolism
Chemicals
Saccharomyces cerevisiae Proteins
Authors & Affiliations
20 authors, click to expand affiliations / ORCID
Reguly Teresa
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada.
Breitkreutz Ashton
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada.
Boucher Lorrie
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada. | Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada.
Breitkreutz Bobby-Joe
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada.
Hon Gary C
Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA.
Myers Chad L
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA. | Department of Computer Science, Princeton University, NJ 08544, USA.
Parsons Ainslie
Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada. | Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada.
Friesen Helena
Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada.
Oughtred Rose
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA.
Tong Amy
Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada. | Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada.
Stark Chris
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada.
Ho Yuen
Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada.
Botstein David
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA.
Andrews Brenda
Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada. | Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada.
Boone Charles
Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada. | Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada.
Troyanskya Olga G
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA. | Department of Computer Science, Princeton University, NJ 08544, USA.
Ideker Trey
Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA.
Dolinski Kara
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA.
Batada Nizar N
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada.
Tyers Mike
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada. | Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada.
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Article Info
Journal
Journal of biology
Abbr.
J Biol
ISSN
1475-4924
DOI
10.1186/jbiol36
Published
2006-00-00
Epub
2006-00-08
Pages
11
Language
English
Region
England
NLM ID
101147570
PMCID
PMC1561585
Subset
IM
Corrections
CommentIn
PMID: 16762048
External Links
PubMed source DOI: 10.1186/jbiol36 PMC Full Text
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