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

热1 wffsdxy 添加于 2010-4-23 15:36 | 3697 次阅读 | 0 个评论

作者
Chang W-C, Lee T-Y, Huang H-D, Huang H-Y, Pan R-L
摘要
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.
详细资料
- 文献种类:期刊
- 期刊名称: BMC Genomics
- 期刊缩写: BMC Genomics
- 期卷页: 2008年第9卷第1期 561页
- ISBN: 1471-2164
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植物生物工程研究室
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PlantPAN
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PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups

wffsdxy 的文献笔记订阅

[原创]

植物基因的转录因子的阐明是研究植物很重要，随着很多植物（如拟南芥、水稻、玉米）物理图谱的建立，各种各样生物信息学服务器或植物启动子数据库的已建立，但是转录因子结合位点更值得关注。

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.

转录因子的收集来源于：PLACE, TRANSFAC (public release 7.0), AGRIS, and JASPER databases

启动子的输入形式：基因ID或fasta格式序列

预测原则：Enabling the co-occurrence of combinatorial transcription factor binding sites (TFBSs) within a defined distance (20 bp to 200 bp) to be identified.

另外：The regulatory elements in the conserved regions of the promoters across homologous genes are detected and presented.

网址：http://plantpan.mbc.nctu.edu.tw/

本文的特色是输入一promoter的fasta格式序列，能预测并以图解形式清楚显示与启动子相互作用的转录因子及其具体位置。

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