ArticleProceedings of the National Academy of Sciences of the United States of America2005
Reliable prediction of transcription factor binding sites by phylogenetic verification.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Ribosomal proteins: the missing piece in the inflammation puzzle?Molecular and cellular biochemistry · 2025Review
- The homeostatic regulation of ribosome biogenesis.Seminars in cell & developmental biology · 2023Review
- Regulation of ribosomal protein genes: An ordered anarchy.Wiley interdisciplinary reviews. RNA · 2021Review
- Shared distal regulatory regions may contribute to the coordinated expression of human ribosomal protein genes.Genomics · 2020Article
- A sequence-specific core promoter-binding transcription factor recruits TRF2 to coordinately transcribe ribosomal protein genes.Nucleic acids research · 2017Article
- Integrative analyses shed new light on human ribosomal protein gene regulation.Scientific reports · 2016Article
- Identification and de novo sequencing of housekeeping genes appropriate for gene expression analyses in farmed maraena whitefish (Coregonus maraena) during crowding stress.Fish physiology and biochemistry · 2015Article
- Ribosome biogenesis in african trypanosomes requires conserved and trypanosome-specific factors.Eukaryotic cell · 2014Article
- SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data.Nucleic acids research · 2014Article
- Article
- Systematic prediction of cis-regulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics.Plant physiology · 2012Article
- Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins.Plant molecular biology · 2012Article
- Evolutionary tinkering with conserved components of a transcriptional regulatory network.PLoS biology · 2010Article
- Using genome-wide measurements for computational prediction of SH2-peptide interactions.Nucleic acids research · 2009Article
- Evolution of transcription factor binding sites in mammalian gene regulatory regions: handling counterintuitive results.Journal of molecular evolution · 2009Article
- Article
- Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter.Genomics, proteomics & bioinformatics · 2008Article
- Strategies for reliable exploitation of evolutionary concepts in high throughput biology.Evolutionary bioinformatics online · 2008Article
- Transcription factor substitution during the evolution of fungal ribosome regulation.Molecular cell · 2008Article
- Genomic structure and expression of uncoupling protein 2 genes in rainbow trout (Oncorhynchus mykiss).BMC genomics · 2006Article
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3 authors.
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Abstract
We present a statistical methodology that largely improves the accuracy in computational predictions of transcription factor (TF) binding sites in eukaryote genomes. This method models the cross-species conservation of binding sites without relying on accurate sequence alignment. It can be coupled with any motif-finding algorithm that searches for overrepresented sequence motifs in individual species and can increase the accuracy of the coupled motif-finding algorithm. Because this method is capable of accurately detecting TF binding sites, it also enhances our ability to predict the cis-regulatory modules. We applied this method on the published chromatin immunoprecipitation (ChIP)-chip data in Saccharomyces cerevisiae and found that its sensitivity and specificity are 9% and 14% higher than those of two recent methods. We also recovered almost all of the previously verified TF binding sites and made predictions on the cis-regulatory elements that govern the tight regulation of ribosomal protein genes in 13 eukaryote species (2 plants, 4 yeasts, 2 worms, 2 insects, and 3 mammals). These results give insights to the transcriptional regulation in eukaryotic organisms.
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