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.
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.
Useful tool for transcription start site prediction for several organisms.
Last time of review with multiple attempts: 7/23/2020
Site has been experiencing bouts of significant instability resulting in inaccessibility on most days; intermittent webserver failures render tools unreliable as a resource.