Overview of the GeneACT architecture and method.

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.

E2F1 and E2F4 occupancies in different promoter regions predicted by differential binding site search. A chromatin immunoprecipitation experiment was performed as described in the text. Mock experiments were done using no antibodies (No Ab), which served as a negative control for the experiment. Input lane represents polymerase chain reactions using 0.1% of total input chromatin. E2F, elongation factor-2.

Graphic display of transcription binding sites in the DHFR promoter region. (a) Visualization of DHFR upstream region. Same parameters were used as for MCM5 (see Figure 6). (b) Same region as shown in panel a, with only the E2F sites highlighted. E2F, elongation factor-2.

Web interface of the differential binding site search. Gene IDs from control gene set (unchanged in DNA microarray data) and regulated gene set (upregulated or downregulated from microarray data) are pasted into respective windows. The threshold of binding site ratio is defined by the user. 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). TF, transcription factor.

Search transcription factor binding site database. (a) Custom transcription factor database based on Transcription Factor Database (TFD). Database can be queried by sequence and name. New entries into the database can be added by the system administrator. (b) Display of the search result of a transcription factor binding site. The literature information of the binding site is shown.

Graphic display of transcription binding sites in the MCM5 promoter region. (a) Visualization of the MCM5 upstream region. MCM5 upstream region (-600 to +100 base pairs) is shown, where +1 is the transcription start site. Only binding site sequences that go across genomes are shown. (b) The same region as is shown in panel a, with only the E2F sites highlighted.