Figure 3.

Web interface of the potential binding site search. (a) Web interface of potential binding site search. Gene IDs can be input in the form of either gene names (synonyms supported) or NCBI Entrez gene ID. There are currently three species to choose from (human, mouse, and rat) and it is optional to display whether the binding site sequence goes across genomes or to display all binding sites regardless of conservation across species. The user can specify a range of interest with three choices of regions (upstream from the transcription start site, upstream from the start codon, or downstream from the stop codon). Other than binding sites in the Transcription Factor Database (TFD), the user can input binding site sequences using standard IUB/IUPAC nucleic acid codes. For output option, the user can choose the visualization option for the promoter browser or a text file output. (b) Visualization of the CDC2 upstream region using GeneACT promoter browser. CDC2 upstream region (-500 to +100 base pairs) is shown, where +1 is the transcription start site. Only binding site sequences that go across all genomes are shown. Chromosomal locations of the binding site sequences and the full sequences are available in text file format via the 'download result' and 'download FASTA file' links. (c) Visualization of elongation factor-2 (E2F)-binding sites in the CDC2 upstream region. It is the same region as is shown in Figure 3b, with only the E2F sites highlighted. Other binding sites were suppressed by the toggle.