Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2005 Jan 1;33(Database issue):D91-7.
doi: 10.1093/nar/gki103.

The MAPPER Database: A Multi-Genome Catalog of Putative Transcription Factor Binding Sites

Affiliations
Free PMC article

The MAPPER Database: A Multi-Genome Catalog of Putative Transcription Factor Binding Sites

Voichita D Marinescu et al. Nucleic Acids Res. .
Free PMC article

Abstract

We describe a comprehensive map of putative transcription factor binding sites (TFBSs) across multiple genomes created using a search method that relies on hidden Markov models built from experimentally determined TFBSs. Using the information in the TRANSFAC and JASPAR databases, we built 1134 models for TFBSs and used them to scan regions 10 kb upstream of the start of the transcript for all known genes in the human, mouse and Drosophila melanogaster genomes. The results, together with homology information on clusters of ortholog genes across the three genomes, were used to create a multi-organism catalog of annotated TFBSs. The catalog can be queried through a web interface accessible at http://bio.chip.org/mapper that allows the identification, visualization and selection of TFBSs occurring in the promoter of a gene of interest and also the common factors predicted to bind across the cluster of orthologs that includes that gene. Alternatively, the interface allows the user to retrieve binding sites for a single transcription factor of interest in a single gene or in all genes of the human, mouse or fruit fly genomes.

Figures

Figure 1
Figure 1
MAPPER output for the promoter of the mouse gtse1 gene. (A) The MAPPER query for putative TFBSs found within 500 bp upstream of the ATG in the mouse gtse1 gene identifies an experimentally characterized p53-responsive element composed of three half sites situated between positions −126 and −96 (28). The models retrieving these sites are boxed. For each hit, a pop-up window displays the alignment between the sequence and the model at the putative site (the match between the model M00761 and the plus strand of the sequence is shown). (B) The consensus sequence displayed in the page for model M00761 shows that the model can accommodate insertion or deletions (represented by a dot character) between the half-sites but not elsewhere. Additional information on the model and its hit statistics over the entire database are also provided.
Figure 2
Figure 2
Graphical export options for the hit set found in the promoter of the mouse gtse1 gene. The hit set presented as a list in Figure 1A is displayed graphically along the promoter of the gene (A) or exported in the GoldenPath browser (B).

Similar articles

See all similar articles

Cited by 62 articles

See all "Cited by" articles

References

    1. Davidson E.H., Rast,J.P., Oliveri,P., Ransick,A., Calestani,C., Yuh,C.H., Minokawa,T., Amore,G., Hinman,V., Arenas-Mena,C. et al. (2002) A genomic regulatory network for development. Science, 295, 1669–1678. - PubMed
    1. Levine M. and Tjian,R. (2003) Transcription regulation and animal diversity. Nature, 424, 147–151. - PubMed
    1. Bailey T.L. and Noble,W.S. (2003) Searching for statistically significant regulatory modules. Bioinformatics, 19 (Suppl. 2), II16–II25. - PubMed
    1. Sinha S., Van Nimwegen,E. and Siggia,E.D. (2003) A probabilistic method to detect regulatory modules. Bioinformatics, 19 (Suppl. 1), I292–I301. - PubMed
    1. Rajewsky N., Vergassola,M., Gaul,U. and Siggia,E.D. (2002) Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics, 3, 30. - PMC - PubMed

Substances

Feedback