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Using CorePromoter to Find Human Core Promoters
Publication Name:
Current Protocols in Bioinformatics
Unit Number:
Unit 2.9
DOI:
10.1002/0471250953.bi0209s10
Online Posting Date:
July, 2005 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
Table of Contents
- Unit Introduction
- Basic Protocol: Using the Web Interface of CorePromoter to Locate Core Promoter Regions
- Alternate Protocol: Using the Command-Line Version of CorePromoter to Locate Core Promoter Regions
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
- Tables
Figures
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Figure 2.9.1The sequence of the upstream region of the human proto-oncogene c-Myc (extracted from EPD), used here as a sample data file (mycEPD2k.seq). -
Figure 2.9.2Screen shot of the Human CorePromoter data-input Web page, with the sequence from the sequence data file mycEPD2k.seq pasted into the text field. -
Figure 2.9.3Screen shot of the resuts from the example run with mycEPD2k.seq and default parameters on the Web. -
Figure 2.9.4Graphical depiction of the 13 overlapping windows within which the 13 feature variables were computed for the QDA studies.
Literature Cited
| 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. | |
| This is the original CorePromoter publication. | |
| Zhang, 1998b. | |
| This is a statistical analysis of sequence features in human core promoters. | |
| Zhang, 2000. | |
| 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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