ArticleNucleic acids research1997
A computational genomics approach to the identification of gene networks.
Article in Nucleic acids research, 1997. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 38 citations in OpenAlex.
- The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding.Genome biology · 2011Article
- Statistical detection of cooperative transcription factors with similarity adjustment.Bioinformatics (Oxford, England) · 2009Article
- A Fast Implementation of a Scan Statistic for Identifying Chromosomal Patterns of Genome Wide Association Studies.Computational statistics & data analysis · 2009Article
- Searching for bidirectional promoters in Arabidopsis thaliana.BMC bioinformatics · 2009Article
- Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses.Genome biology · 2009Article
- Conservation and implications of eukaryote transcriptional regulatory regions across multiple species.BMC genomics · 2008Article
- Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining.BMC bioinformatics · 2007Article
- Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules.Algorithms for molecular biology : AMB · 2007Article
- Rapid detection of positive selection in genes and genomes through variation clusters.Genetics · 2007Article
- Statistical significance of cis-regulatory modules.BMC bioinformatics · 2007Article
- Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test.BMC bioinformatics · 2005Article
- Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription.Nucleic acids research · 2003Article
- Homotypic regulatory clusters in Drosophila.Genome research · 2003Article
- Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae.Genome research · 2002Article
- rVista for comparative sequence-based discovery of functional transcription factor binding sites.Genome research · 2002Article
- Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes.BMC bioinformatics · 2002Article
- cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships.Genome research · 2001Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To delineate the astronomical number of possible interactions of all genes in a genome is a task for which conventional experimental techniques are ill-suited. Sorely needed are rapid and inexpensive methods that identify candidates for interacting genes, candidates that can be further investigated by experiment. Such a method is introduced here for an important class of gene interactions, i.e., transcriptional regulation via transcription factors (TFs) that bind to specific enhancer or silencer sites. The method addresses the question: which of the genes in a genome are likely to be regulated by one or more TFs with known DNA binding specificity? It takes advantage of the fact that many TFs show cooperativity in transcriptional activation which manifests itself in closely spaced TF binding sites. Such 'clusters' of binding sites are very unlikely to occur by chance alone, as opposed to individual sites, which are often abundant in the genome. Here, statistical information about binding site clusters in the genome, is complemented by information about (i) known biochemical functions of the TF, (ii) the structure of its binding site, and (iii) function of the genes near the cluster, to identify genes likely to be regulated by a given transcription factor. Several applications are illustrated with the genome of Saccharomyces cerevisiae , and four different DNA binding activities, SBF, MBF, a sub-class of bHLH proteins and NBF. The technique may aid in the discovery of interactions between genes of known function, and the assignment of biological functions to putative open reading frames.
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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.