TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies

Abstract

In order to understand gene regulation, accurate and comprehensive knowledge of transcriptional regulatory elements is essential. Here, we report our efforts in building a mammalian Transcriptional Regulatory Element Database (TRED) with associated data analysis functions. It collects cis- and trans-regulatory elements and is dedicated to easy data access and analysis for both single-gene-based and genome-scale studies. Distinguishing features of TRED include: (i) relatively complete genome-wide promoter annotation for human, mouse and rat; (ii) availability of gene transcriptional regulation information including transcription factor binding sites and experimental evidence; (iii) data accuracy is ensured by hand curation; (iv) efficient user interface for easy and flexible data retrieval; and (v) implementation of on-the-fly sequence analysis tools. TRED can provide good training datasets for further genome-wide cis-regulatory element prediction and annotation, assist detailed functional studies and facilitate the decipher of gene regulatory networks (http://rulai.cshl.edu/TRED).

Figure 1

Sample pages showing TRED user-interface for gene promoter search, promoter search results, gene information and promoter information.

Figure 2

Sample pages showing TRED user-interface for promoter retrieval for target genes of a transcription factor, on-the-fly sequence analysis results, transcription factor binding motif retrieval and biding site information.