WEB INTERFACE

Data access and retrieval
A CGI/Perl-based web interface was built to facilitate easy visualization and retrieval of both single-gene-based and batch data. It carries the following major functionalities. Search promoters for a gene or a list of genes by gene name, GenBank ID or chromosome location (Figure 1). The resulting page contains all annotated promoters for the gene, ranked from the highest quality to the lowest. Links for gene information and promoter information (including localization of transcription factor binding sites) are provided by the hotlinks in ‘Gene ID’ and ‘Promoter ID’ columns, respectively (see Figure 1). Sequence retrieval of desired promoters can be achieved by checking the box on the left of each entry. Sequence length for retrieval can be decided by users, with the default being 1 kb (700 bp upstream and 299 bp downstream of TSS). Promoter sequences of interest can also be conveniently sent to ‘on-the-fly analysis’ page for further analysis (see below).
Gene information page displays the annotation and promoter links for a particular gene, as well as transcription factors that regulate the gene, experimental evidence and literature references. A link is provided to locate the gene on UCSC Genome Browser and access additional annotations (Figure 1).
Promoter information page includes genomic localization of the promoter, annotation references and the sequence, with transcription factor binding sites marked and hot linked to detailed binding information and literature references. A link is provided to locate the promoter on UCSC Genome Browser and access its genomic context (Figure 1).
Retrieve promoter sequences for all target genes of a transcription factor, with the option of filtering sequences for desired promoters and binding qualities (Figure 2). This will conveniently produce good datasets for computational studies on transcriptional regulons and networks, as well as for the development and training of computational tools such as motif-finding programs.
Retrieve all binding motifs for a transcription factor (Figure 2). This can greatly facilitate the construction of transcription factor binding positional weight matrices (PWMs) for target gene identification and gene regulation studies.
Browse the genome for genes/promoters located in a particular chromosome.
Search for orthologous genes based on the annotation in Ensembl.

On-the-fly analysis tools
On-the-fly analysis tools were implemented for sequences retrieved from TRED or imported from other resources (Figure 2). They currently include simple sequence manipulation and analysis tools for users' convenience and motif-matching programs based on regular expression and PWM. A word counting-based motif searching tool DWE (15) and PromoterWise, a program specifically for pair-wise promoter local alignment (E. Birney, unpublished), are also implemented. Promoters on various TRED sub-pages can be directly sent to these analysis tools at a click of a button.
In addition to the on-the-fly tools, TRED also provides links to many other sequence analysis and motif-finding programs such as MEME (16) and Gibbs sampler (17).