ArticleMolecular systems biology2005
Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium.
Article in Molecular systems biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
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- Molecular mechanisms of system responses to novel stimuli are predictable from public data.Nucleic acids research · 2014Article
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- Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium.BMC systems biology · 2010Article
- Revealing system-level correlations between aging and calorie restriction using a mouse transcriptome.Age (Dordrecht, Netherlands) · 2010Article
- Predicting meiotic pathways in human fetal oogenesis.Biology of reproduction · 2010Article
- Expander: from expression microarrays to networks and functions.Nature protocols · 2010Article
- Integrative approaches to the prediction of protein functions based on the feature selection.BMC bioinformatics · 2009Article
- Probabilistic retrieval and visualization of biologically relevant microarray experiments.Bioinformatics (Oxford, England) · 2009Article
- Biological Resource Centers and Systems Biology.Bioscience · 2009Article
- MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data.Genome biology · 2008Article
- A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.Genome biology · 2008Article
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- EDISA: extracting biclusters from multiple time-series of gene expression profiles.BMC bioinformatics · 2007Article
- Network-based prediction of protein function.Molecular systems biology · 2007Review
- Quantification of protein half-lives in the budding yeast proteome.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks.BMC bioinformatics · 2006Article
- Mining published lists of cancer related microarray experiments: identification of a gene expression signature having a critical role in cell-cycle control.BMC bioinformatics · 2005Article
- Functional Annotation: extracting functional and regulatory order from microarrays.Molecular systems biology · 2005Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Biological systems are orchestrated by heterogeneous regulatory programs that control complex processes and adapt to a dynamic environment. Recent advances in high-throughput experimental methods provide genome-wide perspectives on such regulatory programs. A considerable amount of data on the behavior of model systems in a variety of conditions is rapidly accumulating. Still, the dominant paradigm is to analyze new genome-wide experiments separately from any other extant data, for example, by clustering the new data alone. Here we introduce a new methodology for analyzing the results of a new functional genomic study vis-à-vis a large compendium of previously published results from heterogeneous experimental techniques. We demonstrate our methodology on Saccharomyces cerevisiae, using a compendium of some 2000 experiments from 60 different publications. Most importantly, we show how the integrated analysis reveals unexpected connections among biological processes, and differentiates between novel and known effects in the analyzed experiments. Such characterization is impossible when new data sets are studied in isolation. Our results exemplify the power of the integrative approach in the analysis of genomic scale data sets and call for a paradigm shift in their study.
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