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Kemmeren P van Berkum NL Vilo J Bijma T Donders R Brazma A Holstege FC 《Molecular cell》2002,9(5):1133-1143
Assays capable of determining the properties of thousands of genes in parallel present challenges with regard to accurate data processing and functional annotation. Collections of microarray expression data are applied here to assess the quality of different high-throughput protein interaction data sets. Significant differences are found. Confidence in 973 out of 5342 putative two-hybrid interactions from S. cerevisiae is increased. Besides verification, integration of expression and interaction data is employed to provide functional annotation for over 300 previously uncharacterized genes. The robustness of these approaches is demonstrated by experiments that test the in silico predictions made. This study shows how integration improves the utility of different types of functional genomic data and how well this contributes to functional annotation. 相似文献
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Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae 总被引:1,自引:0,他引:1
Collins SR Kemmeren P Zhao XC Greenblatt JF Spencer F Holstege FC Weissman JS Krogan NJ 《Molecular & cellular proteomics : MCP》2007,6(3):439-450
Defining protein complexes is critical to virtually all aspects of cell biology. Two recent affinity purification/mass spectrometry studies in Saccharomyces cerevisiae have vastly increased the available protein interaction data. The practical utility of such high throughput interaction sets, however, is substantially decreased by the presence of false positives. Here we created a novel probabilistic metric that takes advantage of the high density of these data, including both the presence and absence of individual associations, to provide a measure of the relative confidence of each potential protein-protein interaction. This analysis largely overcomes the noise inherent in high throughput immunoprecipitation experiments. For example, of the 12,122 binary interactions in the general repository of interaction data (BioGRID) derived from these two studies, we marked 7504 as being of substantially lower confidence. Additionally, applying our metric and a stringent cutoff we identified a set of 9074 interactions (including 4456 that were not among the 12,122 interactions) with accuracy comparable to that of conventional small scale methodologies. Finally we organized proteins into coherent multisubunit complexes using hierarchical clustering. This work thus provides a highly accurate physical interaction map of yeast in a format that is readily accessible to the biological community. 相似文献
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ArrayExpress: a public database of gene expression data at EBI 总被引:3,自引:0,他引:3
Rocca-Serra P Brazma A Parkinson H Sarkans U Shojatalab M Contrino S Vilo J Abeygunawardena N Mukherjee G Holloway E Kapushesky M Kemmeren P Lara GG Oezcimen A Sansone SA 《Comptes rendus biologies》2003,326(10-11):1075-1078
ArrayExpress is a public repository for microarray-based gene expression data, resulting from the implementation of the MAGE object model to ensure accurate data structuring and the MIAME standard, which defines the annotation requirements. ArrayExpress accepts data as MAGE-ML files for direct submissions or data from MIAMExpress, the MIAME compliant web-based annotation and submission tool of EBI. A team of curators supports the submission process, providing assistance in data annotation. Data retrieval is performed through a dedicated web interface. Relevant results may be exported to ExpressionProfiler, the EBI based expression analysis tool available online (http://www.ebi.ac.uk/arrayexpress). 相似文献
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Philip Lijnzaad Dik van Leenen Marian JA Groot Koerkamp Patrick Kemmeren Frank CP Holstege 《The EMBO journal》2017,36(3):274-290
An important distinction is frequently made between constitutively expressed housekeeping genes versus regulated genes. Although generally characterized by different DNA elements, chromatin architecture and cofactors, it is not known to what degree promoter classes strictly follow regulatability rules and which molecular mechanisms dictate such differences. We show that SAGA‐dominated/TATA‐box promoters are more responsive to changes in the amount of activator, even compared to TFIID/TATA‐like promoters that depend on the same activator Hsf1. Regulatability is therefore an inherent property of promoter class. Further analyses show that SAGA/TATA‐box promoters are more dynamic because TATA‐binding protein recruitment through SAGA is susceptible to removal by Mot1. In addition, the nucleosome configuration upon activator depletion shifts on SAGA/TATA‐box promoters and seems less amenable to preinitiation complex formation. The results explain the fundamental difference between housekeeping and regulatable genes, revealing an additional facet of combinatorial control: an activator can elicit a different response dependent on core promoter class. 相似文献
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Sameith Katrin Amini Saman Groot Koerkamp Marian J. A. van Leenen Dik Brok Mariel Brabers Nathalie Lijnzaad Philip van Hooff Sander R. Benschop Joris J. Lenstra Tineke L. Apweiler Eva van Wageningen Sake Snel Berend Holstege Frank C. P. Kemmeren Patrick 《BMC biology》2015,13(1):1-7
Karrikins are a family of compounds produced by wildfires that can stimulate the germination of dormant seeds of plants from numerous families. Seed plants could have ‘discovered’ karrikins during fire-prone times in the Cretaceous period when flowering plants were evolving rapidly. Recent research suggests that karrikins mimic an unidentified endogenous compound that has roles in seed germination and early plant development. The endogenous signalling compound is presumably not only similar to karrikins, but also to the related strigolactone hormones. 相似文献