Using CorePromoter to Find Human Core Promoters
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- Abstract
- Table of Contents
- Figures
- Literature Cited
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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PDF or HTML at Wiley Online LibraryTable 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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Figure 2.9.1 The sequence of the upstream region of the human proto‐oncogene c‐Myc (extracted from EPD), used here as a sample data file (mycEPD2k.seq). View Image -
Figure 2.9.2 Screen shot of the Human CorePromoter data‐input Web page, with the sequence from the sequence data file mycEPD2k.seq pasted into the text field. View Image -
Figure 2.9.3 Screen shot of the resuts from the example run with mycEPD2k.seq and default parameters on the Web. View Image -
Figure 2.9.4 Graphical depiction of the 13 overlapping windows within which the 13 feature variables were computed for the QDA studies. View Image
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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