ArticleGenome research2001
cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships.
Article in Genome research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Structural and functional analysis of somatic coding and UTR indels in breast and lung cancer genomes.Scientific reports · 2021Article
- Inferring Transcriptional Interactions by the Optimal Integration of ChIP-chip and Knock-out Data.Bioinformatics and biology insights · 2009Article
- Classifying transcription factor targets and discovering relevant biological features.Biology direct · 2008Article
- Topological comparison of methods for predicting transcriptional cooperativity in yeast.BMC genomics · 2008Article
- Computational methods to dissect cis-regulatory transcriptional networks.Journal of biosciences · 2007Review
- Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.BMC structural biology · 2007Article
- Machine learning for regulatory analysis and transcription factor target prediction in yeast.Systems and synthetic biology · 2007Article
- Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle.BMC bioinformatics · 2006Article
- Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data.BMC bioinformatics · 2006Article
- A survey of motif discovery methods in an integrated framework.Biology direct · 2006Article
- Computational identification of transcriptional regulatory elements in DNA sequence.Nucleic acids research · 2006Review
- Ab initio identification of putative human transcription factor binding sites by comparative genomics.BMC bioinformatics · 2005Article
- Genes Induced by Reovirus Infection Have a Distinct Modular Cis-Regulatory Architecture.Current genomics · 2005Article
- Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination.Nucleic acids research · 2005Article
- Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification.Nucleic acids research · 2004Article
- Transcription factor binding element detection using functional clustering of mutant expression data.Nucleic acids research · 2004Article
- Reconciling gene expression data with known genome-scale regulatory network structures.Genome research · 2003Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We report a simple new algorithm, cis/TF, that uses genomewide expression data and the full genomic sequence to match transcription factors to their binding sites. Most previous computational methods discovered binding sites by clustering genes having similar expression patterns and then identifying over-represented subsequences in the promoter regions of those genes. By contrast, cis/TF asserts that B is a likely binding site of a transcription factor T if the expression pattern of T is correlated to the composite expression patterns of all genes containing B, even when those genes are not mutually correlated. Thus, our method focuses on binding sites rather than genes. The algorithm has successfully identified experimentally-supported transcription factor binding relationships in tests on several data sets from Saccharomyces cerevisiae.
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