Transcriptional Regulatory Element Database

Database Statistics
Browse Database
Retrieve Promoters
Search TF Target Genes
Retrieve TF Motifs
Gene Regulatory Networks
Search Orthologs
Sequence Analysis Tools
Useful Links


In order to understand gene regulation, accurate and comprehensive knowledge of transcriptional regulatory elements is essential. Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present.

Genome-wide human, mouse and rat promoter annotation in TRED was realized by an automated pipeline to extract known promoters from databases such as Genbank, EPD and DBTSS, and employ promoter finding program FirstEF combined with mRNA/EST information and cross-species comparisons. We have also carried out hand curation to assess computational prediction and ensure data accuracy. A quality level is assigned to each promoter based on the reliability of the supporting evidence.

Curation has also been done for transcriptional regulation information, including transcription factor binding motifs and experimental evidence. Binding motifs are mapped on promoters of the corresponding genes and binding quality levels are assigned based on definitiveness of the binding evidence. Curation is currently focusing on target genes of 36 cancer-related TF families.

Distinguishing features of TRED include:
  • relatively complete genome wide promoter annotation for human, mouse and rat
  • availability of transcription factor binding and regulation information
  • data accuracy is ensured by curation, which continues to expand
  • easy and flexible data retrieval
  • availability of on-the-fly sequence analysis tools

  • TRED can provide good training datasets for further genome wide cis-regulatory element prediction, assist detailed functional studies, and facilitate to decipher the gene regulatory networks.

    Michael Zhang Lab, Cold Spring Harbor Laboratory, all rights reserved
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