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. 2007 Jan;35(Database issue):D137-40.
doi: 10.1093/nar/gkl1041.

TRED: a transcriptional regulatory element database, new entries and other development

C Jiang  1 , Z Xuan, F Zhao, M Q Zhang
Affiliations

TRED: a transcriptional regulatory element database, new entries and other development

C Jiang et al. Nucleic Acids Res. 2007 Jan.

Abstract

Transcriptional factors (TFs) and many of their target genes are involved in gene regulation at the level of transcription. To decipher gene regulatory networks (GRNs) we require a comprehensive and accurate knowledge of transcriptional regulatory elements. TRED (http://rulai.cshl.edu/TRED) was designed as a resource for gene regulation and function studies. It collects mammalian cis- and trans-regulatory elements together with experimental evidence. All the regulatory elements were mapped on to the assembled genomes. In this new release, we included a total of 36 TF families involved in cancer. Accordingly, the number of target promoters and genes for TF families has increased dramatically. There are 11,660 target genes (7479 in human, 2691 in mouse and 1490 in rat) and 14,908 target promoters (10,225 in human, 2985 in mouse and 1698 in rat). Additionally, we constructed GRNs for each TF family by connecting the TF-target gene pairs. Such interaction data between TFs and their target genes will assist detailed functional studies and help to obtain a panoramic view of the GRNs for cancer research.

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Figures

Figure 1
Figure 1
Sample pages showing access to the gene regulatory network of TF family GLI (glioma-associated oncogene homolog) in human. Ellipses, TFs; and squares, genes. Arrows indicate interactions between two genes. Red arrows imply that the binding quality level is known. Only official gene symbols are used in the network.
See this image and copyright information in PMC

References

    1. Safran M., Chalifa-Caspi V., Shmueli O., Olender T., Lapidot M., Rosen N., Shmoish M., Peter Y., Glusman G., Feldmesser E., et al. Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. Nucleic Acids Res. 2003;31:142–146. - PMC - PubMed
    1. Matys V., Kel-Margoulis O.V., Fricke E., Liebich I., Land S., Barre-Dirrie A., Reuter I., Chekmenev D., Krull M., Hornischer K., et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 2006;34:D108–D110. - PMC - PubMed
    1. Zhao F., Xuan Z., Liu L., Zhang M.Q. TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res. 2005;33:D103–D107. - PMC - PubMed
    1. Davuluri R.V., Grosse I., Zhang M.Q. Computational identification of promoters and first exons in the human genome. Nature Genet. 2001;29:412–417. - PubMed
    1. Schmid C.D., Perier R., Praz V., Bucher P. EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res. 2006;34:D82–D85. - PMC - PubMed

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