ArticleGenome research2006
Disentangling information flow in the Ras-cAMP signaling network.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- Establishing chromosomal design-build-test-learn through a synthetic chromosome and its combinatorial reconfiguration.Cell genomics · 2023Article
- A novel connection between the Cell Wall Integrity and the PKA pathways regulates cell wall stress response in yeast.Scientific reports · 2017Article
- Differential regulation of antagonistic pleiotropy in synthetic and natural populations suggests its role in adaptation.G3 (Bethesda, Md.) · 2015Article
- Predicting the effects of copy-number variation in double and triple mutant combinations.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2012Article
- Use of pleiotropy to model genetic interactions in a population.PLoS genetics · 2012Article
- Multiple signals converge on a differentiation MAPK pathway.PLoS genetics · 2010Article
- Information flow during gene activation by signaling molecules: ethylene transduction in Arabidopsis cells as a study system.BMC systems biology · 2009Article
- Semi-supervised gene shaving method for predicting low variation biological pathways from genome-wide data.BMC bioinformatics · 2009Article
- Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis.BMC bioinformatics · 2008Article
- Integrating physical and genetic maps: from genomes to interaction networks.Nature reviews. Genetics · 2007Review
- Prediction of phenotype and gene expression for combinations of mutations.Molecular systems biology · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The perturbation of signal-transduction molecules elicits genomic-expression effects that are typically neither restricted to a small set of genes nor uniform. Instead there are broad, varied, and complex changes in expression across the genome. These observations suggest that signal transduction is not mediated by isolated pathways of information flow to distinct groups of genes in the genome. Rather, multiple entangled paths of information flow influence overlapping sets of genes. Using the Ras-cAMP pathway in Saccharomyces cerevisiae as a model system, we perturbed key pathway elements and collected genomic-expression data. Singular value decomposition was applied to separate the genome-wide transcriptional response into weighted expression components exhibited by overlapping groups of genes. Molecular interaction data were integrated to connect gene groups to perturbed signaling elements. The resulting series of linked subnetworks maps multiple putative pathways of information flow through a dense signaling network, and provides a set of testable hypotheses for complex gene-expression effects across the genome.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.