Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.

PubWeight™: 21.55‹?› | Rank: Top 0.1% | All-Time Top 10000

🔗 View Article (PMID 11206552)

Published in Nature on January 25, 2001

Authors

V R Iyer1, C E Horak, C S Scafe, D Botstein, M Snyder, P O Brown

Author Affiliations

1: Department of Biochemistry, Stanford University Medical Center, California 94305, USA.

Articles citing this

(truncated to the top 100)

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63

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

An extended transcriptional network for pluripotency of embryonic stem cells. Cell (2008) 14.64

Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A (2006) 13.68

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28

E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev (2002) 10.06

Genomic targets of the human c-Myc protein. Genes Dev (2003) 9.67

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res (2008) 8.89

Osmotic stress signaling and osmoadaptation in yeasts. Microbiol Mol Biol Rev (2002) 8.02

Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93

Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A (2002) 7.67

A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc Natl Acad Sci U S A (2003) 7.30

Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc (2006) 7.29

Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A (2007) 7.07

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res (2008) 6.83

Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev (2002) 6.74

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods (2008) 6.51

Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell (2001) 6.39

BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol (2002) 6.35

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol (2008) 6.30

Genomic views of distant-acting enhancers. Nature (2009) 6.27

Pioneer transcription factors: establishing competence for gene expression. Genes Dev (2011) 6.01

Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci U S A (2003) 5.64

Global nucleosome occupancy in yeast. Genome Biol (2004) 5.49

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26

High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res (2009) 5.11

Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2002) 4.97

Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell (2005) 4.41

Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res (2006) 4.32

Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol (2002) 4.24

Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol (2003) 4.24

Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell (2007) 4.13

Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae. PLoS Biol (2004) 4.03

Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol (2006) 4.01

Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. Genes Dev (2002) 3.93

Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89

Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide. Mol Cell Biol (2005) 3.83

Differential network biology. Mol Syst Biol (2012) 3.74

Global position and recruitment of HATs and HDACs in the yeast genome. Mol Cell (2004) 3.74

Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proc Natl Acad Sci U S A (2005) 3.72

Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle. Proc Natl Acad Sci U S A (2002) 3.70

Direct isolation and identification of promoters in the human genome. Genome Res (2005) 3.68

Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res (2006) 3.67

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61

Genome-wide analysis of the biology of stress responses through heat shock transcription factor. Mol Cell Biol (2004) 3.61

Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci U S A (2004) 3.60

The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev (2006) 3.58

A systems approach to mapping DNA damage response pathways. Science (2006) 3.55

Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51

Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci U S A (2004) 3.49

Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2006) 3.49

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc (2009) 3.48

Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48

ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol (2008) 3.46

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics (2010) 3.42

Chromosomal distribution of PcG proteins during Drosophila development. PLoS Biol (2006) 3.41

GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A (2002) 3.41

Computational prediction of transcription-factor binding site locations. Genome Biol (2003) 3.39

Positive feedback of G1 cyclins ensures coherent cell cycle entry. Nature (2008) 3.32

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics (2004) 3.31

Interlocking transcriptional feedback loops control white-opaque switching in Candida albicans. PLoS Biol (2007) 3.27

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27

A gateway-compatible yeast one-hybrid system. Genome Res (2004) 3.23

Gcn4p, a master regulator of gene expression, is controlled at multiple levels by diverse signals of starvation and stress. Eukaryot Cell (2002) 3.21

PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res (2004) 3.20

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr Opin Plant Biol (2009) 3.18

Cell wall assembly in Saccharomyces cerevisiae. Microbiol Mol Biol Rev (2006) 3.08

Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters. PLoS Genet (2006) 3.08

Defining the sequence-recognition profile of DNA-binding molecules. Proc Natl Acad Sci U S A (2006) 2.97

Linking cell cycle to histone modifications: SBF and H2B monoubiquitination machinery and cell-cycle regulation of H3K79 dimethylation. Mol Cell (2009) 2.91

Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A (2009) 2.83

Infrequently transcribed long genes depend on the Set2/Rpd3S pathway for accurate transcription. Genes Dev (2007) 2.82

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

Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet (2007) 2.77

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol (2011) 2.68

Structure and function of a transcriptional network activated by the MAPK Hog1. Nat Genet (2008) 2.67

Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet (2011) 2.65

Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J Bacteriol (2003) 2.65

Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae. Mol Cell (2009) 2.65

Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res (2006) 2.63

The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships. Proc Natl Acad Sci U S A (2003) 2.61

Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes. Genome Res (2002) 2.60

PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Mol Syst Biol (2007) 2.56

Publishing perishing? Towards tomorrow's information architecture. BMC Bioinformatics (2007) 2.55

The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD). BMC Bioinformatics (2003) 2.54

Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle. Genes Dev (2002) 2.52

Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol (2005) 2.50

Genomic location analysis by ChIP-Seq. J Cell Biochem (2009) 2.44

TOS9 regulates white-opaque switching in Candida albicans. Eukaryot Cell (2006) 2.42

Identifying transcription factor functions and targets by phenotypic activation. Proc Natl Acad Sci U S A (2006) 2.39

Target hub proteins serve as master regulators of development in yeast. Genes Dev (2006) 2.39

Annotating non-coding regions of the genome. Nat Rev Genet (2010) 2.38

Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin. Proc Natl Acad Sci U S A (2003) 2.33

The transcription factor Rim101p governs ion tolerance and cell differentiation by direct repression of the regulatory genes NRG1 and SMP1 in Saccharomyces cerevisiae. Mol Cell Biol (2003) 2.29

Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics (2003) 2.23

DNA microarray technologies for measuring protein-DNA interactions. Curr Opin Biotechnol (2006) 2.22

Genome-wide location of yeast RNA polymerase III transcription machinery. EMBO J (2003) 2.15

Articles by these authors

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52

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

Molecular portraits of human breast tumours. Nature (2000) 94.14

Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (1995) 88.48

Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics (1989) 79.44

Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet (1980) 75.25

Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A (2001) 71.82

Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature (2000) 64.32

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

Exploring the metabolic and genetic control of gene expression on a genomic scale. Science (1997) 60.15

The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37

The transcriptional program of sporulation in budding yeast. Science (1998) 37.23

Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science (1999) 36.25

Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09

Two differentially regulated mRNAs with different 5' ends encode secreted with intracellular forms of yeast invertase. Cell (1982) 25.10

Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet (2000) 24.22

Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci U S A (1996) 24.18

A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res (1996) 23.16

Genetic and physical maps of Saccharomyces cerevisiae. Nature (1997) 21.48

Missing value estimation methods for DNA microarrays. Bioinformatics (2001) 20.84

Genetic engineering in vivo using translocatable drug-resistance elements. New methods in bacterial genetics. J Mol Biol (1977) 20.29

SGD: Saccharomyces Genome Database. Nucleic Acids Res (1998) 20.26

A Saccharomyces cerevisiae genomic plasmid bank based on a centromere-containing shuttle vector. Gene (1987) 19.68

Sterile host yeasts (SHY): a eukaryotic system of biological containment for recombinant DNA experiments. Gene (1979) 19.39

The transcriptional program in the response of human fibroblasts to serum. Science (1999) 19.19

Exploring the new world of the genome with DNA microarrays. Nat Genet (1999) 19.05

Integrating functional genomic information into the Saccharomyces genome database. Nucleic Acids Res (2000) 18.52

Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A (2000) 18.42

Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci U S A (2001) 17.36

A common language for physical mapping of the human genome. Science (1989) 17.36

Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet (1996) 15.73

Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet (1999) 14.96

Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci U S A (1999) 14.16

Global analysis of protein activities using proteome chips. Science (2001) 13.74

Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. Nucleic Acids Res (1999) 13.65

A gene expression database for the molecular pharmacology of cancer. Nat Genet (2000) 13.31

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet (2001) 13.05

DNA arrays for analysis of gene expression. Methods Enzymol (1999) 12.50

Homozygosity mapping: a way to map human recessive traits with the DNA of inbred children. Science (1987) 12.20

Mutagenesis by insertion of a drug-resistance element carrying an inverted repetition. J Mol Biol (1975) 11.14

Correct integration of retroviral DNA in vitro. Cell (1987) 10.73

Structure and function of the yeast URA3 gene: expression in Escherichia coli. Gene (1984) 10.07

Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature (1999) 9.87

Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med (1998) 9.72

Strategies for studying heterogeneous genetic traits in humans by using a linkage map of restriction fragment length polymorphisms. Proc Natl Acad Sci U S A (1986) 9.51

A nucleoprotein complex mediates the integration of retroviral DNA. Genes Dev (1989) 8.80

Mitotic stability of yeast chromosomes: a colony color assay that measures nondisjunction and chromosome loss. Cell (1985) 8.78

Phenotypic analysis of temperature-sensitive yeast actin mutants. Cell (1985) 8.53

Mapping complex genetic traits in humans: new methods using a complete RFLP linkage map. Cold Spring Harb Symp Quant Biol (1986) 8.22

Gaussian models for genetic linkage analysis using complete high-resolution maps of identity by descent. Am J Hum Genet (1993) 8.05

The Stanford Microarray Database. Nucleic Acids Res (2001) 7.77

Integration of murine leukemia virus DNA depends on mitosis. EMBO J (1993) 7.62

The yeast GTP-binding YPT1 protein and a mammalian counterpart are associated with the secretion machinery. Cell (1988) 7.39

Plasmid construction by homologous recombination in yeast. Gene (1987) 7.26

Diverse effects of beta-tubulin mutations on microtubule formation and function. J Cell Biol (1988) 6.88

Lethal disruption of the yeast actin gene by integrative DNA transformation. Science (1982) 6.88

Evidence for transcriptional regulation of orotidine-5'-phosphate decarboxylase in yeast by hybridization of mRNA to the yeast structural gene cloned in Escherichia coli. Proc Natl Acad Sci U S A (1979) 6.81

Properties of the translocatable tetracycline-resistance element Tn10 in Escherichia coli and bacteriophage lambda. Genetics (1978) 6.73

Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell (2001) 6.39

Energy coupling in DNA gyrase and the mechanism of action of novobiocin. Proc Natl Acad Sci U S A (1978) 6.33

Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Genetics (2001) 6.29

Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science (1998) 6.28

Isolation of the beta-tubulin gene from yeast and demonstration of its essential function in vivo. Cell (1983) 6.22

Specialized transduction of tetracycline resistance by phage P22 in Salmonella typhimurium. II. Properties of a high-frequency-transducing lysate. Virology (1972) 6.21

Mutants of yeast defective in sucrose utilization. Genetics (1981) 6.20

Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes Dev (1994) 6.12

DNA topoisomerase II is required at the time of mitosis in yeast. Cell (1985) 6.08

Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc Natl Acad Sci U S A (2001) 6.07

Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci U S A (1997) 5.59

Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2000) 5.57

Yeast actin-binding proteins: evidence for a role in morphogenesis. J Cell Biol (1988) 5.46

Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci U S A (1999) 5.45

'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Genome Biol (2000) 5.29

A rapid, efficient method for isolating DNA from yeast. Gene (1986) 5.20

Ultrastructure of the yeast actin cytoskeleton and its association with the plasma membrane. J Cell Biol (1994) 5.14

Secretion of beta-lactamase requires the carboxy end of the protein. Cell (1980) 5.03

Systematic mutational analysis of the yeast ACT1 gene. Genetics (1992) 5.02

Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus. Science (1992) 4.97

Simple Mendelian inheritance of the reiterated ribosomal DNA of yeast. Proc Natl Acad Sci U S A (1977) 4.86

Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia. J Exp Med (2001) 4.83

Yeast genes fused to beta-galactosidase in Escherichia coli can be expressed normally in yeast. Proc Natl Acad Sci U S A (1981) 4.79