Figure 4

Example query: search by transcription factor. By clicking on the 'TFMART' department store at the left hand side of the mall, users can perform a TF-specific query. The 'TF View', color-coded in red, is very similar to the 'Gene View' (see Figure 3) with a summary table of all of the TFs obtained from the search at the top followed by details and binding sites for each of them individually. Here, the results show that the queried TF (HUMAN_NF1) has annotations in two different projects. The binding sites can be genomic sequences with defined coordinates or they can be artificial (for example, oligonucleotide representing a consensus sequence). All the sites are aligned and a TF binding profile is built dynamically using the MEME pattern discovery algorithm [31]. Users can construct a custom scoring matrix and binding profile based upon a subset of the sequences for that TF by clicking in the check boxes of those sequences meant to be included and clicking 'Generate PFM with selected sequences'. Alternatively, users can generate scoring matrices and binding profiles based upon just genomic or artificial sequences by clicking on 'Select genomic sequences' or 'Select artificial sequences', respectively.