Tissue-specific Regulatory Elements in Mammalian Promoters: Supplementary Information 1 Transcripts and Promoters under Tissue-specific Regulation

[1]  Jun Kawai,et al.  Evolutionary turnover of mammalian transcription start sites. , 2006, Genome research.

[2]  Michael Q. Zhang,et al.  A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome , 2006, Nucleic acids research.

[3]  Martin S. Taylor,et al.  Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.

[4]  Michael Q. Zhang,et al.  DNA motifs in human and mouse proximal promoters predict tissue-specific expression. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Kenta Nakai,et al.  DBTSS: DataBase of Human Transcription Start Sites, progress report 2006 , 2005, Nucleic Acids Res..

[6]  Obi L. Griffith,et al.  cisRED: a database system for genome-scale computational discovery of regulatory elements , 2005, Nucleic Acids Res..

[7]  R. Myers,et al.  Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. , 2005, Genome research.

[8]  A. Sidow,et al.  De novo discovery of a tissue-specific gene regulatory module in a chordate. , 2005, Genome research.

[9]  Leah Barrera,et al.  A high-resolution map of active promoters in the human genome , 2005, Nature.

[10]  Michael Q. Zhang,et al.  Genome-wide promoter extraction and analysis in human, mouse, and rat , 2005, Genome Biology.

[11]  J. Shendure,et al.  Discovering functional transcription-factor combinations in the human cell cycle. , 2005, Genome research.

[12]  R. Evans,et al.  The Nuclear Receptor Superfamily: a Rosetta Stone for Physiology , 1985 .

[13]  Jun S. Liu,et al.  De novo cis-regulatory module elicitation for eukaryotic genomes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[14]  K. Lindblad-Toh,et al.  Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals , 2005, Nature.

[15]  Michael Q. Zhang,et al.  Identifying tissue-selective transcription factor binding sites in vertebrate promoters. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

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

[17]  Michael Q. Zhang,et al.  Mining ChIP-chip data for transcription factor and cofactor binding sites , 2005, ISMB.

[18]  O. Nerman,et al.  Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals , 2005, BMC Genomics.

[19]  B. Frey,et al.  The functional landscape of mouse gene expression , 2004, Journal of biology.

[20]  Jun S. Liu,et al.  Decoding human regulatory circuits. , 2004, Genome research.

[21]  W. Wong,et al.  CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[22]  P. Sassone-Corsi,et al.  Testis-specific transcription mechanisms promoting male germ-cell differentiation. , 2004, Reproduction.

[23]  H. Schrem,et al.  Liver-Enriched Transcription Factors in Liver Function and Development. Part II: the C/EBPs and D Site-Binding Protein in Cell Cycle Control, Carcinogenesis, Circadian Gene Regulation, Liver Regeneration, Apoptosis, and Liver-Specific Gene Regulation , 2004, Pharmacological Reviews.

[24]  S. Batalov,et al.  A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Michael Levine,et al.  Coordinate enhancers share common organizational features in the Drosophila genome. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Nicola J. Rinaldi,et al.  Control of Pancreas and Liver Gene Expression by HNF Transcription Factors , 2004, Science.

[27]  Jan Jensen,et al.  Gene regulatory factors in pancreatic development , 2004, Developmental dynamics : an official publication of the American Association of Anatomists.

[28]  Qiang Wu,et al.  Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation. , 2003, Genome research.

[29]  Bing Ren,et al.  Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. , 2004, Methods in enzymology.

[30]  Wyeth W. Wasserman,et al.  JASPAR: an open-access database for eukaryotic transcription factor binding profiles , 2004, Nucleic Acids Res..

[31]  J. Castle,et al.  Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays , 2003, Science.

[32]  Doron Lancet,et al.  GeneNote: whole genome expression profiles in normal human tissues. , 2003, Comptes rendus biologies.

[33]  John D. Storey,et al.  Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

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

[35]  V. Harley,et al.  Sex with two SOX on: SRY and SOX9 in testis development , 2002, Trends in Endocrinology & Metabolism.

[36]  Daiya Takai,et al.  Comprehensive analysis of CpG islands in human chromosomes 21 and 22 , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[37]  H. Schrem,et al.  Liver-Enriched Transcription Factors in Liver Function and Development. Part I: The Hepatocyte Nuclear Factor Network and Liver-Specific Gene Expression , 2002, Pharmacological Reviews.

[38]  Yoshio Miki,et al.  Human Regulatory Factor X 4 (RFX4) Is a Testis-specific Dimeric DNA-binding Protein That Cooperates with Other Human RFX Members* , 2002, The Journal of Biological Chemistry.

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

[40]  W. Wasserman,et al.  A predictive model for regulatory sequences directing liver-specific transcription. , 2001, Genome research.

[41]  M. Connor,et al.  Contractile Activity-induced Transcriptional Activation of Cytochrome c Involves Sp1 and Is Proportional to Mitochondrial ATP Synthesis in C2C12 Muscle Cells* , 2001, The Journal of Biological Chemistry.

[42]  Ian Korf,et al.  MaskerAid : a performance enhancement to RepeatMasker , 2000, Bioinform..

[43]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[44]  Gary D. Stormo,et al.  DNA binding sites: representation and discovery , 2000, Bioinform..

[45]  Philipp Bucher,et al.  The Eukaryotic Promoter Database (EPD) , 2000, Nucleic Acids Res..

[46]  R. Hauptmann,et al.  Unusual 5' transcript complexity of plectin isoforms: novel tissue-specific exons modulate actin binding activity. , 1999, Human molecular genetics.

[47]  V. Luu‐The,et al.  Assignment1 of steroid 5β-reductase (SRD5B1) and its pseudogene (SRD5BP1) to human chromosome bands 7q32→q33 and 1q23→q25, respectively, byin situ hybridization , 1999, Cytogenetic and Genome Research.

[48]  V. Luu‐The,et al.  Assignment of steroid 5beta-reductase (SRD5B1) and its pseudogene (SRD5BP1) to human chromosome bands 7q32-->q33 and 1q23-->q25, respectively, by in situ hybridization. , 1999, Cytogenetics and cell genetics.

[49]  G. Rousseau,et al.  Isoforms of Hepatocyte Nuclear Factor-6 Differ in DNA-binding Properties, Contain a Bifunctional Homeodomain, and Define the New ONECUT Class of Homeodomain Proteins* , 1998, The Journal of Biological Chemistry.

[50]  J. Fickett,et al.  Identification of regulatory regions which confer muscle-specific gene expression. , 1998, Journal of molecular biology.

[51]  Huaiyu Zhu On Information and Sufficiency , 1997 .

[52]  R. Costa,et al.  The transcriptional activator hepatocyte nuclear factor 6 regulates liver gene expression , 1996, Molecular and cellular biology.

[53]  P. Duprey,et al.  Control of skeletal muscle-specific transcription: involvement of paired homeodomain and MADS domain transcription factors. , 1994, The International journal of developmental biology.

[54]  T. Lee,et al.  Transforming growth factor-beta response elements of the skeletal alpha-actin gene. Combinatorial action of serum response factor, YY1, and the SV40 enhancer-binding protein, TEF-1. , 1994, The Journal of biological chemistry.

[55]  J. Manfredi,et al.  Spacing and orientation of bipartite DNA-binding motifs as potential functional determinants for POU domain factors. , 1993, Genes & development.

[56]  M. Boguski,et al.  dbEST — database for “expressed sequence tags” , 1993, Nature Genetics.

[57]  A. Agresti [A Survey of Exact Inference for Contingency Tables]: Rejoinder , 1992 .

[58]  W. Liao,et al.  Two adjacent C/EBP-binding sequences that participate in the cell-specific expression of the mouse serum amyloid A3 gene , 1990, Molecular and cellular biology.

[59]  Douglas G. Altman,et al.  Practical statistics for medical research , 1990 .

[60]  G. Ciliberto,et al.  Binding of a liver-specific factor to the human albumin gene promoter and enhancer , 1990, Molecular and cellular biology.

[61]  L. Kedes,et al.  Identification and characterization of a factor that binds to two human sarcomeric actin promoters. , 1989, The Journal of biological chemistry.

[62]  T. Tamaoki,et al.  Interaction of a hepatoma-specific nuclear factor with transcription-regulatory sequences of the human alpha-fetoprotein and albumin genes , 1988, Molecular and cellular biology.

[63]  L. Kedes,et al.  A common factor regulates skeletal and cardiac alpha-actin gene transcription in muscle , 1988, Molecular and cellular biology.

[64]  R. Cortese,et al.  Purification of a NF1‐like DNA‐binding protein from rat liver and cloning of the corresponding cDNA. , 1988, The EMBO journal.

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

[66]  K. Watanabe,et al.  The human albumin gene. Characterization of the 5' and 3' flanking regions and the polymorphic gene transcripts. , 1986, The Journal of biological chemistry.