Genome-wide analysis of mammalian promoter architecture and evolution based upon human and mouse CAGE data, Supplementary Data

Piero Carninci 2* Albin Sandelin , Boris Lenhard †, Shintaro Katayama, Kazuro Shimokawa, Jasmina Ponjavic◆, Colin A. M. Semple , Martin S. Taylor , Pär G. Engström, Martin C. Frith , Alistair R. R. Forrest, Wynand B. Alkema, Sin Lam Tan, Charles Plessy, Rimantas Kodzius, Timothy Ravasi 6, , Takeya Kasukawa , Shiro Fukuda, Mutsumi Kanamori-Katayama, Yayoi Kitazume, Hideya Kawaji , Chikatoshi Kai, Mari Nakamura, Hideaki Konno, Kenji Nakano , Salim Mottagui-Tabar, Peter Arner, Alessandra Chesi, Stefano Gustincich, Francesca Persichetti, Harukazu Suzuki, Sean M. Grimmond, Christine A. Wells, Valerio Orlando, Claes Wahlestedt, Edison T. Liu, Matthias Harbers, Jun Kawai, Vladimir B. Bajic , David A. Hume , Yoshihide Hayashizaki 2, 17, 18***

[1]  C. Kai,et al.  CAGE: cap analysis of gene expression , 2006, Nature Methods.

[2]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

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

[4]  Boris Lenhard,et al.  Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes , 2004, BMC Genomics.

[5]  A. Kornblihtt,et al.  Multiple links between transcription and splicing. , 2004, RNA.

[6]  S Miyano,et al.  Open source clustering software. , 2004, Bioinformatics.

[7]  A. Sandelin,et al.  Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. , 2004, Journal of molecular biology.

[8]  Lisa M. D'Souza,et al.  Genome sequence of the Brown Norway rat yields insights into mammalian evolution , 2004, Nature.

[9]  D. Haussler,et al.  Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.

[10]  A. Sandelin,et al.  Applied bioinformatics for the identification of regulatory elements , 2004, Nature Reviews Genetics.

[11]  Kazuro Shimokawa,et al.  Absolute expression values for mouse transcripts: re‐annotation of the READ expression database by the use of CAGE and EST sequence tags , 2004, FEBS letters.

[12]  S. Akira,et al.  TIR domain-containing adaptors define the specificity of TLR signaling. , 2004, Molecular immunology.

[13]  J. Kawai,et al.  Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[14]  David Haussler,et al.  Combining phylogenetic and hidden Markov models in biosequence analysis , 2003, RECOMB '03.

[15]  E. Wingender,et al.  MATCH: A tool for searching transcription factor binding sites in DNA sequences. , 2003, Nucleic acids research.

[16]  Sumio Sugano,et al.  Construction of a full-length enriched and a 5'-end enriched cDNA library using the oligo-capping method. , 2003, Methods in molecular biology.

[17]  Vladimir B. Bajic,et al.  Content analysis of the core promoter region of human genes , 2003, Silico Biol..

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

[19]  Terrence S. Furey,et al.  The UCSC Genome Browser Database , 2003, Nucleic Acids Res..

[20]  Wyeth W. Wasserman,et al.  TFBS: Computational framework for transcription factor binding site analysis , 2002, Bioinform..

[21]  G. Schultz,et al.  Identification of an initiator-like element essential for the expression of the tissue inhibitor of metalloproteinases-4 (Timp-4) gene. , 2002, The Biochemical journal.

[22]  X. Moore,et al.  Expression of the 11beta-hydroxysteroid dehydrogenase 2 gene in the mouse. , 2000, Kidney international.

[23]  F. Talamantes,et al.  Structure and expression of the mouse growth hormone receptor/growth hormone binding protein gene. , 1999, Journal of molecular endocrinology.

[24]  Michael C. Ostrowski,et al.  TFEC is a macrophage-restricted member of the microphthalmia-TFE subfamily of basic helix-loop-helix leucine zipper transcription factors. , 1999, Journal of immunology.

[25]  N. Copeland,et al.  Structure and mapping of the G protein gamma3 subunit gene and a divergently transcribed novel gene, gng3lg. , 1998, Genomics.

[26]  M. Oishi,et al.  Genomic Structure of MUNC18-1 Protein, Which Is Involved in Docking and Fusion of Synaptic Vesicles in Brain* , 1998, The Journal of Biological Chemistry.

[27]  Michael C. Ostrowski,et al.  Interaction between PU.1 and Another Ets Family Transcription Factor Promotes Macrophage-specific Basal Transcription Initiation* , 1998, The Journal of Biological Chemistry.

[28]  H. Xiao,et al.  Genomic organization, chromosomal localization, and expression of the murine thromboxane synthase gene. , 1997, Genomics.

[29]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[30]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[31]  J. Horst,et al.  The genomic organization of the murine Pax 8 gene and characterization of its basal promoter. , 1997, Genomics.

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

[33]  S. Baylin,et al.  New 5′ Regions of the Murine and Human Genes for DNA (Cytosine-5)-methyltransferase* , 1996, The Journal of Biological Chemistry.

[34]  R. Kramer,et al.  Identification and Characterization of the Cell Type-specific and Developmentally Regulated α7 Integrin Gene Promoter* , 1996, The Journal of Biological Chemistry.

[35]  E. Romanik,et al.  Structural analysis of transcripts for the protein L-isoaspartyl methyltransferase reveals multiple transcription initiation sites and a distinct pattern of expression in mouse testis: identification of a 5'-flanking sequence with promoter activity. , 1994, Archives of biochemistry and biophysics.

[36]  D. Hume,et al.  Edinburgh Research Explorer Expression of mRNA encoding the macrophage colony-stimulating factor receptor (c-fms) is controlled by a constitutive promoter and tissue-specific transcription elongation , 2022 .

[37]  K. Csiszȧr,et al.  Structure of the mouse lysyl oxidase gene. , 1993, Genomics.

[38]  M. Meisler,et al.  Isolation of the murine ribonuclease gene Rib-1: structure and tissue specific expression in pancreas and parotid gland. , 1991, Nucleic acids research.

[39]  S Karlin,et al.  Assessment of inhomogeneities in an E. coli physical map. , 1991, Nucleic acids research.

[40]  B. Kwon,et al.  Structure of the mouse pore-forming protein (perforin) gene: analysis of transcription initiation site, 5' flanking sequence, and alternative splicing of 5' untranslated regions , 1991, The Journal of experimental medicine.

[41]  R. Nusse,et al.  The Wnt-1 (int-1) oncogene promoter and its mechanism of activation by insertion of proviral DNA of the mouse mammary tumor virus , 1990, Molecular and cellular biology.

[42]  P. Bucher Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. , 1990, Journal of molecular biology.

[43]  Y. Yamada,et al.  Characterization of the promoter for the alpha 1 (IV) collagen gene. DNA sequences within the first intron enhance transcription. , 1988, The Journal of biological chemistry.

[44]  D. Kwiatkowski,et al.  Muscle is the major source of plasma gelsolin. , 1988, The Journal of biological chemistry.

[45]  P. Burbelo,et al.  The laminin B2 chain promoter contains unique repeat sequences and is active in transient transfection. , 1988, The Journal of biological chemistry.

[46]  P. Farnham,et al.  Heterogeneity at the 5' termini of mouse dihydrofolate reductase mRNAs. Evidence for multiple promoter regions. , 1985, Journal of Biological Chemistry.