ArticleGenome biology2009
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
33 citing papers in PubMed, 54 citations in OpenAlex.
- Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data.NPJ systems biology and applications · 2023Review
- Using genome-wide expression compendia to study microorganisms.Computational and structural biotechnology journal · 2022Review
- Network Modeling in Biology: Statistical Methods for Gene and Brain Networks.Statistical science : a review journal of the Institute of Mathematical Statistics · 2021Article
- Computational biology approaches for mapping transcriptional regulatory networks.Computational and structural biotechnology journal · 2021Review
- Associating expression and genomic data using co-occurrence measures.Biology direct · 2019Article
- Markov chain Monte Carlo simulation of a Bayesian mixture model for gene network inference.Genes & genomics · 2019Article
- Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources.BMC bioinformatics · 2017Article
- Article
- A graph theoretical approach to data fusion.Statistical applications in genetics and molecular biology · 2016Article
- An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network.Molecular systems biology · 2015Article
- cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.Nucleic acids research · 2015Article
- An integrated approach to reconstructing genome-scale transcriptional regulatory networks.PLoS computational biology · 2015Article
- Inference of gene interaction networks using conserved subsequential patterns from multiple time course gene expression datasets.BMC genomics · 2015Article
- Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists.Bioinformatics and biology insights · 2015Review
- A comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries.Journal of experimental botany · 2014Article
- A system-level model for the microbial regulatory genome.Molecular systems biology · 2014Article
- Prediction of kinase inhibitor response using activity profiling, in vitro screening, and elastic net regression.BMC systems biology · 2014Article
- Network portal: a database for storage, analysis and visualization of biological networks.Nucleic acids research · 2014Article
- Article
- COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia.Nucleic acids research · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present DISTILLER, a data integration framework for the inference of transcriptional module networks. Experimental validation of predicted targets for the well-studied fumarate nitrate reductase regulator showed the effectiveness of our approach in Escherichia coli. In addition, the condition dependency and modularity of the inferred transcriptional network was studied. Surprisingly, the level of regulatory complexity seemed lower than that which would be expected from RegulonDB, indicating that complex regulatory programs tend to decrease the degree of modularity.
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.