Harvesting the Genome's Bounty: Integrative Genomics

Jorgensen, Paul; Breitkreutz, Bobby-Joe; Breitkreutz, K.; Stark, Chris; Liu, G.; Cook, Michael A.; Sharom, Jeffrey R.; Nishikawa, Joy L.; Ketela, Troy; Bellows, David S.; Breitkreutz, Ashton; Rupeš, Ivan; Boucher, Lorrie; Dewar, Danielle; Vo, Mai-Tram; Angeli, Marc; Reguly, Teresa; Tong, Amy; Andrews, Brenda; Boone, Charles; Tyers, Mike

doi:10.1101/sqb.2003.68.431

Cited by 9 publications

(8 citation statements)

References 94 publications

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“…HTP approaches to identify novel protein and gene networks have begun to augment hypothesis-driven biochemical and genetic approaches ( 14 ). These hypothesis-generating HTP techniques include the two-hybrid (2-H) method for detecting pair-wise protein interactions ( 15 – 17 ), mass spectrometric (MS) analysis of purified protein complexes ( 12 , 18 ), and the synthetic genetic array (SGA) and molecular barcode (dSLAM) methods for systematic detection of synthetic lethal genetic interactions ( 19 , 20 ).…”

Section: High Throughput Interactionsmentioning

confidence: 99%

BioGRID: a general repository for interaction datasets

Stark

Breitkreutz²,

Reguly³

et al. 2006

Nucleic Acids Research

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3,494

2,994

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Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at . BioGRID release version 2.0 includes >116 000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. Over 30 000 interactions have recently been added from 5778 sources through exhaustive curation of the Saccharomyces cerevisiae primary literature. An internally hyper-linked web interface allows for rapid search and retrieval of interaction data. Full or user-defined datasets are freely downloadable as tab-delimited text files and PSI-MI XML. Pre-computed graphical layouts of interactions are available in a variety of file formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID.

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Section: High Throughput Interactionsmentioning

confidence: 99%

BioGRID: a general repository for interaction datasets

Stark

Breitkreutz²,

Reguly³

et al. 2006

Nucleic Acids Research

Self Cite

3,494

2,994

View full text Add to dashboard Cite

show abstract

“…Completion of the S. cerevisiae genome sequence nearly a decade ago spawned a host of functional genomic tools for interrogation of gene and protein function, including DNA microarrays for global gene-expression profiling and location of DNA-binding factors, and a comprehensive set of gene deletion strains for phenotypic analysis [ 1 , 2 ]. In the post-genome sequence era, high-throughput (HTP) screening techniques aimed at identifying novel protein complexes and gene networks have begun to complement conventional biochemical and genetic approaches [ 3 , 4 ]. Systematic elucidation of protein interactions in S. cerevisiae has been carried out by the two-hybrid method, which detects pair-wise interactions [ 5 - 7 ], and by mass spectrometric (MS) analysis of purified protein complexes [ 8 , 9 ].…”

Section: Introductionmentioning

confidence: 99%

Untitled

Reguly

Breitkreutz

Boucher

et al. 2006

J Biol

279

167

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Background: 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.

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“…It is used to study a large range of conserved cellular processes, including the cell cycle, metabolism, and stress responses. Yeast was the first organism whose genome was sequenced completely (1), and many other systems-wide biology screens were first carried out in the yeast model (2–6). Large scale proteomics has also been pioneered in yeast, identifying first hundreds and then thousands of proteins (7–13).…”

mentioning

confidence: 99%

System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

Nagaraj

Kulak

Cox

et al. 2012

Molecular & Cellular Proteomics

363

374

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Yeast remains an important model for systems biology and for evaluating proteomics strategies. In-depth shotgun proteomics studies have reached nearly comprehensive coverage, and rapid, targeted approaches have been developed for this organism. Recently, we demonstrated that single LC-MS/MS analysis using long columns and gradients coupled to a linear ion trap Orbitrap instrument had an unexpectedly large dynamic range of protein identification (Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Frohlich, F., Cox, J., and Mann, M.

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Harvesting the Genome's Bounty: Integrative Genomics

Cited by 9 publications

References 94 publications

BioGRID: a general repository for interaction datasets

BioGRID: a general repository for interaction datasets

Untitled

System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

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