Using CorePromoter to Find Human Core Promoters

Michael Q. Zhang1

1 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 2.9
DOI:  10.1002/0471250953.bi0209s10
Online Posting Date:  July, 2005
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Abstract

The CorePromoter program is very useful for identification of transcriptional start sites (TSS) and core promoter regions when 5′‐upstream genomic DNA sequences of human genes are available. It is very simple to use and can be accessed either through the Web or after downloading to a local computer. The protocols in this unit introduce its basic methodology and discuss how to apply it to a sample problem in conjunction with other gene‐finding programs.

Keywords: Core promoter; QDA; TSS; Transcriptional Initiation Site; PIC; Pre‐Initiation Complex

     
 
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Table of Contents

  • Basic Protocol 1: Using the Web Interface of CorePromoter to Locate Core Promoter Regions
  • Alternate Protocol 1: Using the Command‐Line Version of CorePromoter to Locate Core Promoter Regions
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

   Bucher, P. and Trifonov, E.N. 1986. Compilation and analysis of eukaryotic POL II promoter sequences. Nucl. Acids Res. 14:10009‐10026.
   Davuluri, R., Grosse, I., and Zhang, M.Q. 2001. Computational identification of promoters and first exons in the human genome. Nature Genet. 29:412‐417.
   Ioshikhes, I. and Zhang, M.Q. 2000. Large‐scale human promoter mapping using CpG islands. Nature Genet. 26:61‐63.
   Tanner, M.A. and Wong, W.H. 1987. The calculation of posterior distribution by data augmentation. J. Am. Stat. Ass. 82:528‐550.
   Zhang, M.Q. 1997. Identification of protein coding regions in the human genome based on quadratic discriminant analysis. Proc. Natl. Acad. Sci. U.S.A. 94:565‐568.
   Zhang, M.Q. 1998a. Identification of human gene core‐promoters in silico. Genome Res. 8:319‐326.
   Zhang, M.Q. 1998b. A discrimination study of human core‐promoters. In Proceedings of Pacific Symposium on Biocomputing 1998 (R.B. Altman, A.K. Dunker, L. Hunter, K. Lauderdale, and T.E. Klein, eds.) pp. 240‐251. World Scientific, Singapore.
   Zhang, M.Q. 1998c. Statistical features of human exons and their flanking regions. Hum. Mol. Genet. 7:919‐932.
   Zhang, M.Q. 2000. Discriminant analysis and its application in DNA sequence motif recognition. Briefings in Bioinformatics 1:331‐342.
   Zhang, M.Q. 2002. Computational prediction of eukaryotic protein coding genes. Nat. Rev. Genet. 3:698‐709.
Internet Resources
   http://rulai.cshl.org/tools/genefinder/CPROMOTER/
  CorePromoter Web server
   http://www.cshl.org/mzhanglab
  Papers and other related information
   ftp://cshl.org/pub/science/mzhanglab/promoter/
  CorePromoter FTP site
Key References
   Zhang, 1998a. See above.
  This is the original CorePromoter publication.
   Zhang, 1998b. See above.
  This is a statistical analysis of sequence features in human core promoters.
   Zhang, 2000. See above.
  This is a tutorial including more theory and examples on how to combine different gene‐structure analysis programs in real applications.
   Zhang, 2003. See above.
  Background on discrimination analysis and QDA
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