ArticleNucleic acids research2005
Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed.
- Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast.BMC bioinformatics · 2019Article
- Properly defining the targets of a transcription factor significantly improves the computational identification of cooperative transcription factor pairs in yeast.BMC genomics · 2015Article
- A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae.BMC systems biology · 2014Article
- Identifying cooperative transcription factors in yeast using multiple data sources.BMC systems biology · 2014Article
- Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data.BMC systems biology · 2013Article
- Identifying a Transcription Factor's Regulatory Targets from its Binding Targets.Gene regulation and systems biology · 2010Article
- Signaling to transcription networks in the neuronal retrograde injury response.Science signaling · 2010Article
- A Bayesian approach to joint modeling of protein-DNA binding, gene expression and sequence data.Statistics in medicine · 2010Article
- Functional characterization of variations on regulatory motifs.PLoS genetics · 2008Article
- High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae.Genome biology · 2008Article
- Global and local architecture of the mammalian microRNA-transcription factor regulatory network.PLoS computational biology · 2007Article
- Delineation of the Salmonella enterica serovar Typhimurium HilA regulon through genome-wide location and transcript analysis.Journal of bacteriology · 2007Article
- Validating module network learning algorithms using simulated data.BMC bioinformatics · 2007Article
- Prediction of synergistic transcription factors by function conservation.Genome biology · 2007Article
- Coding limits on the number of transcription factors.BMC genomics · 2006Article
- Integrated assessment and prediction of transcription factor binding.PLoS computational biology · 2006Article
- Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Communication between levels of transcriptional control improves robustness and adaptivity.Molecular systems biology · 2006Article
- A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites.Nucleic acids research · 2006Article
- Discovering functional transcription-factor combinations in the human cell cycle.Genome research · 2005Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Deciphering gene regulatory network architecture amounts to the identification of the regulators, conditions in which they act, genes they regulate, cis-acting motifs they bind, expression profiles they dictate and more complex relationships between alternative regulatory partnerships and alternative regulatory motifs that give rise to sub-modalities of expression profiles. The 'location data' in yeast is a comprehensive resource that provides transcription factor-DNA interaction information in vivo. Here, we provide two contributions: first, we developed means to assess the extent of noise in the location data, and consequently for extracting signals from it. Second, we couple signal extraction with better characterization of the genetic network architecture. We apply two methods for the detection of combinatorial associations between transcription factors (TFs), the integration of which provides a global map of combinatorial regulatory interactions. We discover the capacity of regulatory motifs and TF partnerships to dictate fine-tuned expression patterns of subsets of genes, which are clearly distinct from those displayed by most genes assigned to the same TF. Our findings provide carefully prioritized, high-quality assignments between regulators and regulated genes and as such should prove useful for experimental and computational biologists alike.
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.