Whole-genome discovery of transcription factor binding sites by network-level conservation.

PubWeight™: 2.54‹?› | Rank: Top 2%

🔗 View Article (PMC 314286)

Published in Genome Res on December 12, 2003

Authors

Moshe Pritsker1, Yir-Chung Liu, Michael A Beer, Saeed Tavazoie

Author Affiliations

1: Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.

Articles citing this

Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21

Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci U S A (2005) 3.58

Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci U S A (2005) 2.84

Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol (2005) 2.82

Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol (2004) 2.81

Practical strategies for discovering regulatory DNA sequence motifs. PLoS Comput Biol (2006) 2.53

Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput Biol (2005) 2.04

Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res (2006) 1.88

Identifying the conserved network of cis-regulatory sites of a eukaryotic genome. Proc Natl Acad Sci U S A (2005) 1.72

Deciphering principles of transcription regulation in eukaryotic genomes. Mol Syst Biol (2006) 1.61

Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae. Eukaryot Cell (2006) 1.55

Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Res (2005) 1.54

Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence. Genome Res (2005) 1.44

The orientation of transcription factor binding site motifs in gene promoter regions: does it matter? BMC Genomics (2016) 1.41

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics (2008) 1.34

Dynamical remodeling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: differential response and role of Msn2 and/or Msn4 and other factors in galactose and glucose media. Mol Cell Biol (2005) 1.28

Systems approaches to identifying gene regulatory networks in plants. Annu Rev Cell Dev Biol (2008) 1.21

Caste development and reproduction: a genome-wide analysis of hallmarks of insect eusociality. Insect Mol Biol (2006) 1.21

Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics. Genome Biol (2006) 1.08

Reliable prediction of transcription factor binding sites by phylogenetic verification. Proc Natl Acad Sci U S A (2005) 1.02

ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? Genome Biol (2008) 0.99

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. BMC Bioinformatics (2007) 0.99

Microarray profiling of phage-display selections for rapid mapping of transcription factor-DNA interactions. PLoS Genet (2009) 0.98

Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. Nucleic Acids Res (2009) 0.98

Genome-wide analysis identifies MYND-domain protein Mub1 as an essential factor for Rpn4 ubiquitylation. Mol Cell Biol (2007) 0.95

Fine-tuning enhancer models to predict transcriptional targets across multiple genomes. PLoS One (2007) 0.95

Identification of the GATA factor TRPS1 as a repressor of the osteocalcin promoter. J Biol Chem (2009) 0.94

Systematic identification of regulatory elements in conserved 3' UTRs of human transcripts. Cell Rep (2014) 0.90

Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis. BMC Bioinformatics (2005) 0.89

A novel non-overlapping bi-clustering algorithm for network generation using living cell array data. Bioinformatics (2007) 0.88

Microarray data analysis and mining tools. Bioinformation (2011) 0.88

Machine learning for regulatory analysis and transcription factor target prediction in yeast. Syst Synth Biol (2007) 0.86

Global identification of conserved post-transcriptional regulatory programs in trypanosomatids. Nucleic Acids Res (2013) 0.85

Identifying pattern-defined regulatory islands in mammalian genomes. Proc Natl Acad Sci U S A (2007) 0.84

Prediction and experimental validation of novel STAT3 target genes in human cancer cells. PLoS One (2009) 0.83

Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen Phytophthora infestans. PLoS One (2012) 0.81

High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis. BMC Genomics (2010) 0.81

NPEST: a nonparametric method and a database for transcription start site prediction. Quant Biol (2013) 0.81

A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks. BMC Genomics (2013) 0.80

Identifying promoter features of co-regulated genes with similar network motifs. BMC Bioinformatics (2009) 0.79

The identification of functional motifs in temporal gene expression analysis. Evol Bioinform Online (2007) 0.79

Classifying transcription factor targets and discovering relevant biological features. Biol Direct (2008) 0.78

Gene promoter scan methodology for identifying and classifying coregulated promoters. Methods Enzymol (2007) 0.76

Universal attenuators and their interactions with feedback loops in gene regulatory networks. Nucleic Acids Res (2017) 0.75

Articles cited by this

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47

Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97

Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell (1998) 62.20

Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science (1993) 36.84

Sequence logos: a new way to display consensus sequences. Nucleic Acids Res (1990) 36.74

Functional discovery via a compendium of expression profiles. Cell (2000) 31.39

Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16

Systematic determination of genetic network architecture. Nat Genet (1999) 25.45

A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell (1998) 19.67

Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science (2003) 16.49

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol (2000) 14.30

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol (1998) 13.99

MIPS: a database for genomes and protein sequences. Nucleic Acids Res (2002) 11.98

Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell (2001) 9.63

Regulatory element detection using correlation with expression. Nat Genet (2001) 8.92

Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci (1995) 5.96

Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies. Genome Res (2002) 5.67

Protein database searches for multiple alignments. Proc Natl Acad Sci U S A (1990) 5.52

Specificity, free energy and information content in protein-DNA interactions. Trends Biochem Sci (1998) 5.00

Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J Mol Biol (1988) 4.75

Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res (2000) 4.34

Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res (2001) 4.29

Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res (2002) 4.25

Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res (2001) 4.22

Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol Cell Biol (2000) 4.15

Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies. FEBS Lett (2000) 3.71

Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes. Mol Cell Biol (1992) 3.57

RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: a negative feedback circuit. Proc Natl Acad Sci U S A (2001) 2.85

Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc Natl Acad Sci U S A (1995) 2.65

The phosphatase system in Saccharomyces cerevisiae. Genes Genet Syst (1997) 2.29

The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons. Genome Res (2002) 2.22

Identification of the binding sites of regulatory proteins in bacterial genomes. Proc Natl Acad Sci U S A (2002) 2.07

Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res (2002) 2.04

Fugu and human sequence comparison identifies novel human genes and conserved non-coding sequences. Gene (2002) 1.34

Articles by these authors

Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Mol Cell (2007) 14.58

Predicting gene expression from sequence. Cell (2004) 8.12

Mapping global histone acetylation patterns to gene expression. Cell (2004) 5.57

A universal framework for regulatory element discovery across all genomes and data types. Mol Cell (2007) 4.50

Predictive behavior within microbial genetic networks. Science (2008) 4.48

Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation. Proc Natl Acad Sci U S A (2009) 3.76

Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol (2007) 3.53

A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies. Nat Genet (2009) 3.36

Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat Genet (2002) 3.18

Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol (2005) 2.82

Revealing global regulatory perturbations across human cancers. Mol Cell (2009) 2.62

A comprehensive genetic characterization of bacterial motility. PLoS Genet (2007) 2.33

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Res (2007) 2.27

Protein occupancy landscape of a bacterial genome. Mol Cell (2009) 2.24

Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput Biol (2005) 2.04

Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res (2011) 2.02

Bacterial adaptation through loss of function. PLoS Genet (2013) 1.99

A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model. Cell Rep (2013) 1.92

Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature (2012) 1.80

Ras and Gpa2 mediate one branch of a redundant glucose signaling pathway in yeast. PLoS Biol (2004) 1.76

let-7 Overexpression leads to an increased fraction of cells in G2/M, direct down-regulation of Cdc34, and stabilization of Wee1 kinase in primary fibroblasts. J Biol Chem (2009) 1.65

Genetic architecture of intrinsic antibiotic susceptibility. PLoS One (2009) 1.61

Fitness landscape transformation through a single amino acid change in the rho terminator. PLoS Genet (2012) 1.59

Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks. Mol Syst Biol (2006) 1.49

Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli. Mol Syst Biol (2010) 1.47

Analysis of gene networks in white adipose tissue development reveals a role for ETS2 in adipogenesis. Development (2011) 1.36

Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res (2012) 1.35

Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition. Development (2009) 1.34

Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics (2009) 1.28

A cross-genomic approach for systematic mapping of phenotypic traits to genes. Genome Res (2004) 1.23

Global discovery of adaptive mutations. Nat Methods (2009) 1.23

kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets. Nucleic Acids Res (2013) 1.20

Newly identified genetic variations in common Escherichia coli MG1655 stock cultures. J Bacteriol (2011) 1.13

Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PLoS One (2010) 1.11

Large mutational target size for rapid emergence of bacterial persistence. Proc Natl Acad Sci U S A (2012) 1.03

Genetic dissection of an exogenously induced biofilm in laboratory and clinical isolates of E. coli. PLoS Pathog (2009) 1.02

Microarray profiling of phage-display selections for rapid mapping of transcription factor-DNA interactions. PLoS Genet (2009) 0.98

Role of transcription factor Kar4 in regulating downstream events in the Saccharomyces cerevisiae pheromone response pathway. Mol Cell Biol (2006) 0.97

Robust k-mer frequency estimation using gapped k-mers. J Math Biol (2013) 0.92

Recombination and migration of Cryphonectria hypovirus 1 as inferred from gene genealogies and the coalescent. Genetics (2004) 0.92

Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms. PLoS Pathog (2011) 0.90

Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region. Mol Cell Biol (2005) 0.89

Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome. J Proteomics Bioinform (2011) 0.87

Accurate proteome-wide protein quantification from high-resolution 15N mass spectra. Genome Biol (2011) 0.87

The dawn of virtual cell biology. Cell (2012) 0.86

Antibiotics and the post-genome revolution. Curr Opin Microbiol (2011) 0.84

Fastcompare: a nonalignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation. Methods Mol Biol (2007) 0.81

Beyond homeostasis: a predictive-dynamic framework for understanding cellular behavior. Annu Rev Cell Dev Biol (2012) 0.81

Revealing the genetic basis of natural bacterial phenotypic divergence. J Bacteriol (2013) 0.77

Microarray-based genetic footprinting strategy to identify strain improvement genes after competitive selection of transposon libraries. Methods Mol Biol (2011) 0.77

Group normalization for genomic data. PLoS One (2012) 0.75

TARBP2 binding structured RNA elements drives metastasis. Cell Cycle (2014) 0.75