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. 2008 Jan;36(Database issue):D102-6.
doi: 10.1093/nar/gkm955. Epub 2007 Nov 15.

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

Jan Christian Bryne  1 , Eivind Valen, Man-Hung Eric Tang, Troels Marstrand, Ole Winther, Isabelle da Piedade, Anders Krogh, Boris Lenhard, Albin Sandelin
Affiliations

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

Jan Christian Bryne et al. Nucleic Acids Res. 2008 Jan.

Abstract

JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR database-the JASPAR CORE sub-database-has increased by 12% in size, and three new specialized sub-databases have been added. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. JASPAR is available at http://jaspar.genereg.net.

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Figures

Figure 1.
Figure 1.
New features in the JASPAR database web interface. (A) A listing of matrices in the JASPAR-CORE database resulting from selection of MADS and bHLH-type factors. These models are used in the clustering analysis in panel C. (B) A pop-up window showing detail information on the MA0001 model, with expected predictions/bp statistics. (C) Dynamic clustering of selected profiles. At the top, a dendrogram describing the similarities of the input profiles is shown. Clusters of similar modes are merged into familial binding profiles, shown below. In this case, two larger clusters are produced, corresponding to bHLH and MADS type matrices. Two smaller clusters correspond to outliers in both groups.
See this image and copyright information in PMC

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