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PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups

Wen-Chi Chang1, Tzong-Yi Lee2, Hsien-Da Huang23*, His-Yuan Huang2 and Rong-Long Pan14*

Author affiliations

1 Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsin-Chu 300, Taiwan

2 Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan

3 Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan

4 College of Life Sciences, National Tsing Hua University, Hsin-Chu 300, Taiwan

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Citation and License

BMC Genomics 2008, 9:561  doi:10.1186/1471-2164-9-561

Published: 26 November 2008

Abstract

Background

The elucidation of transcriptional regulation in plant genes is important area of research for plant scientists, following the mapping of various plant genomes, such as A. thaliana, O. sativa and Z. mays. A variety of bioinformatic servers or databases of plant promoters have been established, although most have been focused only on annotating transcription factor binding sites in a single gene and have neglected some important regulatory elements (tandem repeats and CpG/CpNpG islands) in promoter regions. Additionally, the combinatorial interaction of transcription factors (TFs) is important in regulating the gene group that is associated with the same expression pattern. Therefore, a tool for detecting the co-regulation of transcription factors in a group of gene promoters is required.

Results

This study develops a database-assisted system, PlantPAN (Plant Promoter Analysis Navigator), for recognizing combinatorial cis-regulatory elements with a distance constraint in sets of plant genes. The system collects the plant transcription factor binding profiles from PLACE, TRANSFAC (public release 7.0), AGRIS, and JASPER databases and allows users to input a group of gene IDs or promoter sequences, enabling the co-occurrence of combinatorial transcription factor binding sites (TFBSs) within a defined distance (20 bp to 200 bp) to be identified. Furthermore, the new resource enables other regulatory features in a plant promoter, such as CpG/CpNpG islands and tandem repeats, to be displayed. The regulatory elements in the conserved regions of the promoters across homologous genes are detected and presented.

Conclusion

In addition to providing a user-friendly input/output interface, PlantPAN has numerous advantages in the analysis of a plant promoter. Several case studies have established the effectiveness of PlantPAN. This novel analytical resource is now freely available at http://PlantPAN.mbc.nctu.edu.tw webcite.