Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function

[1]  K. Nakai,et al.  Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. , 2005, Gene.

[2]  Maria Stepanova,et al.  A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas , 2005, Bioinform..

[3]  Ramana V. Davuluri,et al.  OMGProm: a database of orthologous mammalian gene promoters , 2005, Bioinform..

[4]  Michael Q. Zhang,et al.  Similarity of position frequency matrices for transcription factor binding sites , 2005, Bioinform..

[5]  H. Herzel,et al.  Inferring combinatorial regulation of transcription in silico , 2005, Nucleic acids research.

[6]  William Stafford Noble,et al.  Assessing computational tools for the discovery of transcription factor binding sites , 2005, Nature Biotechnology.

[7]  Matthew W. Hahn,et al.  Positive Selection on MMP3 Regulation Has Shaped Heart Disease Risk , 2004, Current Biology.

[8]  Nicola J. Rinaldi,et al.  Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.

[9]  Kevin Gardner,et al.  Kinetic profiles of p300 occupancy in vivo predict common features of promoter structure and coactivator recruitment. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Serafim Batzoglou,et al.  A suite of web-based programs to search for transcriptional regulatory motifs , 2004, Nucleic Acids Res..

[11]  S. Kasif,et al.  Identification of Transcription Factor Binding Sites Upstream of Human Genes Regulated by the Phosphatidylinositol 3-Kinase and MEK/ERK Signaling Pathways* , 2004, Journal of Biological Chemistry.

[12]  Kimberly Van Auken,et al.  WormBase: a multi-species resource for nematode biology and genomics , 2004, Nucleic Acids Res..

[13]  Dixie L Mager,et al.  Complex controls: the role of alternative promoters in mammalian genomes. , 2003, Trends in genetics : TIG.

[14]  D. Mercola,et al.  Egr1 Signaling in Prostate Cancer , 2003, Cancer biology & therapy.

[15]  Alan M. Moses,et al.  Position specific variation in the rate of evolution in transcription factor binding sites , 2003, BMC Evolutionary Biology.

[16]  R. Tjian,et al.  Transcription regulation and animal diversity , 2003, Nature.

[17]  R. Tjian,et al.  Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression. , 2003, Genes & development.

[18]  K. Elenitoba-Johnson,et al.  Comparative Microarray Analysis of Gene Expression During Activation of Human Peripheral Blood T Cells and Leukemic Jurkat T Cells , 2003, Laboratory Investigation.

[19]  Michael Karin,et al.  NF-κB in cancer: a marked target , 2003 .

[20]  Michael Ashburner,et al.  Ontologies for biologists: a community model for the annotation of genomic data. , 2003 .

[21]  Michael Karin,et al.  NF-kappaB in cancer: a marked target. , 2003, Seminars in cancer biology.

[22]  Alexander E. Kel,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[23]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[24]  May D. Wang,et al.  GoMiner: a resource for biological interpretation of genomic and proteomic data , 2003, Genome Biology.

[25]  Y. Zhuang,et al.  Regulation of early lymphocyte development by E2A family proteins. , 2002, Seminars in immunology.

[26]  J. T. Kadonaga,et al.  The RNA polymerase II core promoter: a key component in the regulation of gene expression. , 2002, Genes & development.

[27]  Ash A. Alizadeh,et al.  Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[28]  M. Gorospe,et al.  Global analysis of stress-regulated mRNA turnover by using cDNA arrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Jun S. Liu,et al.  An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments , 2002, Nature Biotechnology.

[30]  A. Michelson.  Deciphering genetic regulatory codes: A challenge for functional genomics , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Kenta Nakai,et al.  DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs , 2002, Nucleic Acids Res..

[32]  Roberto Marcondes Cesar Junior,et al.  Inference from Clustering with Application to Gene-Expression Microarrays , 2002, J. Comput. Biol..

[33]  J. T. Kadonaga,et al.  Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. , 2001, Genes & development.

[34]  P. Pandolfi,et al.  Mzf1 controls cell proliferation and tumorigenesis. , 2001, Genes & development.

[35]  M. Bar‐eli.  Gene regulation in melanoma progression by the AP-2 transcription factor. , 2001, Pigment cell research.

[36]  R. Buettner,et al.  Regulatory roles of AP-2 transcription factors in vertebrate development, apoptosis and cell-cycle control. , 2000, Gene.

[37]  D. Botstein,et al.  Singular value decomposition for genome-wide expression data processing and modeling. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[38]  A. Weiss,et al.  Signal transduction by the TCR for antigen. , 2000, Current opinion in immunology.

[39]  T. Misteli,et al.  High mobility of proteins in the mammalian cell nucleus , 2000, Nature.

[40]  R. Schwartz,et al.  The -180 site of the IL-2 promoter is the target of CREB/CREM binding in T cell anergy. , 1999, Journal of immunology.

[41]  D. Dean,et al.  Independent Repressor Domains in ZEB Regulate Muscle and T-Cell Differentiation , 1999, Molecular and Cellular Biology.

[42]  D. Wechsler,et al.  Expression of MXI1, a Myc Antagonist, Is Regulated by Sp1 and AP2* , 1999, The Journal of Biological Chemistry.

[43]  G. Church,et al.  Systematic determination of genetic network architecture , 1999, Nature Genetics.

[44]  W. Butscher,et al.  Coordinate Transactivation of the Interleukin-2 CD28 Response Element by c-Rel and ATF-1/CREB2* , 1998, The Journal of Biological Chemistry.

[45]  A. Weiss,et al.  CD28 mediates transcriptional upregulation of the interleukin-2 (IL-2) promoter through a composite element containing the CD28RE and NF-IL-2B AP-1 sites , 1997, Molecular and cellular biology.

[46]  M. Klemsz,et al.  Hematopoietic transcriptional regulation by the myeloid zinc finger gene, MZF-1. , 1996, Current topics in microbiology and immunology.

[47]  J. W. Rooney,et al.  Novel NFAT sites that mediate activation of the interleukin-2 promoter in response to T-cell receptor stimulation , 1995, Molecular and cellular biology.

[48]  M. Neumann,et al.  The architecture of the interleukin-2 promoter: a reflection of T lymphocyte activation. , 1995, Biochimica et biophysica acta.

[49]  G. Edelman,et al.  Structural and functional similarities between the promoters for mouse tenascin and chicken cytotactin. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[50]  T. Werner,et al.  MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. , 1995, Nucleic acids research.

[51]  T. Kadesch,et al.  Displacement of an E-box-binding repressor by basic helix-loop-helix proteins: implications for B-cell specificity of the immunoglobulin heavy-chain enhancer , 1994, Molecular and cellular biology.

[52]  J. McQuillan,et al.  Vascular cell adhesion molecule 1: contrasting transcriptional control mechanisms in muscle and endothelium. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[53]  M. Frommer,et al.  CpG islands in vertebrate genomes. , 1987, Journal of molecular biology.

[54]  Donald W. Bouldin,et al.  A Cluster Separation Measure , 1979, IEEE Transactions on Pattern Analysis and Machine Intelligence.