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. 2005;6(8):R72.
doi: 10.1186/gb-2005-6-8-r72. Epub 2005 Aug 1.

Genome-wide promoter extraction and analysis in human, mouse, and rat

Zhenyu Xuan  1 , Fang Zhao, Jinhua Wang, Gengxin Chen, Michael Q Zhang
Affiliations

Genome-wide promoter extraction and analysis in human, mouse, and rat

Zhenyu Xuan et al. Genome Biol. 2005.

Abstract

Large-scale and high-throughput genomics research needs reliable and comprehensive genome-wide promoter annotation resources. We have conducted a systematic investigation on how to improve mammalian promoter prediction by incorporating both transcript and conservation information. This enabled us to build a better multispecies promoter annotation pipeline and hence to create CSHLmpd (Cold Spring Harbor Laboratory Mammalian Promoter Database) for the biomedical research community, which can act as a starting reference system for more refined functional annotations.

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Figures

Figure 1
Figure 1
Distribution of conservation scores in promoter alignments. (a) Pairwise promoter alignments of human-rodent and mouse-rat non-orthologous genes (control set II) with different promoter GC content. (b) Pairwise promoter alignments of most conserved promoter pairs and randomly selected 1 kb sequence pairs (control set I). (c) Alignments of mouse-rat and human-rodent homologous promoter pairs. (d) Three-way promoter alignments of homologous promoter triplets and sequence triplets from control set II.
Figure 2
Figure 2
Flowchart of the pipeline to construct the promoter database. Ovals indicate data and rectangles the method. The ovals shaded gray represent the data stored in CSHLmpd.
Figure 3
Figure 3
Sensitivity and specificity of promoter prediction for CpG-island related and non-CpG-island related promoters in different gene sets. (a) 5,893 human genes with homologous rodent promoters. (b) All 8,949 human genes in the test set. The definition of different methods is described in the text and in Materials and methods.
Figure 4
Figure 4
Screen shots of the CSHLmpd user interface. (a) Gbrowse for genome-wide gene and promoter display. (b) Homologous promoter search and analysis.
See this image and copyright information in PMC

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