Reliable prediction of transcription factor binding sites by phylogenetic verification.
Explore this paper's citation graph
Summary
A statistical methodology that largely improves the accuracy in computational predictions of transcription factor (TF) binding sites in eukaryote genomes and is 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.
- Type
- article
- Published
- 2005-11-22
- Cited by
- 46
- References
- 42
- OpenAlex
- https://openalex.org/W16286651
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:8622672
Keywords
Nitromethane, Ab initio, Materials science, Computational chemistry, Chemistry
References
- Active conservation of noncoding sequences revealed by three-way species comparisons.
- Whole-genome discovery of transcription factor binding sites by network-level conservation.
- The CAGTCACA box in the fission yeast Schizosaccharomyces pombe functions like a TATA element and binds a novel factor.
- Small families mean better health for mothers and kids.
- The Value of Prior Knowledge in Discovering Motifs with MEME
- FootPrinter: a program designed for phylogenetic footprinting
- Identifying protein-binding sites from unaligned DNA fragments.
- TRANSFAC: a database on transcription factors and their DNA binding sites
- Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.
- A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryo.
- Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons.
- Eukaryotic regulatory element conservation analysis and identification using comparative genomics.
- Extensive and divergent circadian gene expression in liver and heart
- In synergy with various cis‐acting elements, plant insterstitial telomere motifs regulate gene expression in Arabidopsis root meristems
- Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting
- Transcriptional regulatory code of a eukaryotic genome
- EZ-Retrieve: a web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites.
- Sampling motifs on phylogenetic trees.
- Equipotent mouse ribosomal protein promoters have a similar architecture that includes internal sequence elements.
- Effects of dependence in high-dimensional multiple testing problems
Cited by
- Bioinformatics tools for modeling transcription factor target genes and epigenetic changes.
- Practical computational methods for regulatory genomics: a cisGRN-Lexicon and cisGRN-browser for gene regulatory networks.
- Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology
- Genomic structure and expression of uncoupling protein 2 genes in rainbow trout (Oncorhynchus mykiss)
- Identification and de novo sequencing of housekeeping genes appropriate for gene expression analyses in farmed maraena whitefish (Coregonus maraena) during crowding stress
- The JNK-Like MAPK KGB-1 of Caenorhabditis Elegans Promotes Reproduction, Lifespan, and Gene Expressions for Protein Biosynthesis and Germline Homeostasis but Interferes with Hyperosmotic Stress Tolerance
- Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Handling Counterintuitive Results
- Profiling of the yak skeletal muscle tissue gene expression and comparison with the domestic cattle by genome array.
- Primary Respiratory Chain Disease Causes Tissue-Specific Dysregulation of the Global Transcriptome and Nutrient-Sensing Signaling Network
- Genetic containment of forest plantations
- Nuclear receptor-mediated transcriptional regulation in Phase I, II, and III xenobiotic metabolizing systems.
- Transcription factor substitution during the evolution of fungal ribosome regulation.
- Evolutionary Tinkering with Conserved Components of a Transcriptional Regulatory Network
- Ribosome Biogenesis in African Trypanosomes Requires Conserved and Trypanosome-Specific Factors
- Bioinformatical and experimental approaches to investigation of transcription factor binding sites in vertebrate genes
- Casein kinase 2 inhibits HomolD‐directed transcription by Rrn7 in Schizosaccharomyces pombe
- Delineating Slowly and Rapidly Evolving Fractions of the Drosophila Genome
- Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins
- Human BSAP and BLIMP1 conform an autoregulatory feedback loop.
- PromoterSweep: a tool for identification of transcription factor binding sites
Related papers
- Ab initio investigations of β-Ba(OH)2 and its high pressure phase β-II-Ba(OH)2
- Ab initio intermolecular potential of solid C-60 in the low-temperature phase.
- Solvent effects on vibrational spectra of hydrogen-bonded complexes of formaldehyde and water: an ab initio study
- Vibrational Spectra of Aniline in Gas Phase: An Ab-Initio Study
- Ab initio calculations on the benzyl radical
- Quantum effects on vibrational and electronic spectra of hydrazine studied by "on-the-fly" ab initio ring polymer molecular dynamics.
- Ab initio study of Pressure-induced structural Transformation of Solid Bromine II
- Ab initio study of vibrational spectra of alanine in gas phase