ArticleBMC bioinformatics2005
Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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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.
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Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- Characterization of Schistosome Sox Genes and Identification of a Flatworm Class of Sox Regulators.Pathogens (Basel, Switzerland) · 2023Article
- Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator.eLife · 2017Article
- Developmentally regulated internal transcription initiation during meiosis in budding yeast.PloS one · 2017Article
- Functional Profiling of Human MeCP2 by Automated Data Comparison Analysis and Computerized Expression Pathway Modeling.Healthcare informatics research · 2016Article
- Identification and characterization of a Mef2 transcriptional activator in schistosome parasites.PLoS neglected tropical diseases · 2012Article
- Cdc7-Dbf4 is a gene-specific regulator of meiotic transcription in yeast.Molecular and cellular biology · 2012Article
- An orthologue of the Myelin-gene Regulatory Transcription Factor regulates Dictyostelium prestalk differentiation.The International journal of developmental biology · 2012Article
- The functional consequences of relative substrate specificity in complex biochemical systems.Frontiers in genetics · 2011Article
- Mitotic expression of Spo13 alters M-phase progression and nucleolar localization of Cdc14 in budding yeast.Genetics · 2010Article
- Identification of functional TFAP2A and SP1 binding sites in new TFAP2A-modulated genes.BMC genomics · 2010Article
- An in silico strategy identified the target gene candidates regulated by dehydration responsive element binding proteins (DREBs) in Arabidopsis genome.Plant molecular biology · 2009Article
- Computational methods to dissect cis-regulatory transcriptional networks.Journal of biosciences · 2007Review
- Gene expression from random libraries of yeast promoters.Genetics · 2006Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundA major challenge in computational genomics is the development of methodologies that allow accurate genome-wide prediction of the regulatory targets of a transcription factor. We present a method for target identification that combines experimental characterization of binding requirements with computational genomic analysis.
resultsOur method identified potential target genes of the transcription factor Ndt80, a key transcriptional regulator involved in yeast sporulation, using the combined information of binding affinity, positional distribution, and conservation of the binding sites across multiple species. We have also developed a mathematical approach to compute the false positive rate and the total number of targets in the genome based on the multiple selection criteria.
conclusionWe have shown that combining biochemical characterization and computational genomic analysis leads to accurate identification of the genome-wide targets of a transcription factor. The method can be extended to other transcription factors and can complement other genomic approaches to transcriptional regulation.
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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.