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60 Gonye et al.exGeneList.txt) is available online at http://www.dbi.tju.edu/dbi/publications/MiMBchapter/.3.1.2. TRNA Using PAINTIn this step, the gene list from Subheading 3.1.1. will be used to retrieve promotersequences, analyze them using TRANSFAC Public, build a Feasnet, andanalyze the resultant Feasnet as compared with a reference Feasnet to derivehypotheses on overrepresented TREs.1. Use a web browser to open the web page http://www.dbi.tju/dbi/tools/paint/.2. Follow the link “Start New Analysis” on the main page.3. Select Mus Musculus (mouse) as the Organism Name, 2000 for the Desiredupstream length, Accession Number for Gene Identifier type, Gene IdentifiersList for Upload text file of type. Refer to the Notes 4.1 and 4.2 for issues involvedin the selection of the gene identifiers and the size of the gene list.4. Click the Browse button to locate and select the file exGeneList.txt on thecomputer.5. Ensure that the checkbox next to TFRetriever is selected.6. Select MATCH (TRANSFAC Public) for TRE finding program. Refer to Note 4.3on the issues involved in the choice of the TRE-finding programs.7. Enter the user name and password for logging into the website http://www.generegulation.com.8. Select Minimize False-Positives for the MATCH filter option.9. Select 1.00 for the Core similarity threshold. Check the box for Find TREs oncomplementary strand?10. Click the button Execute Feasnet Builder at the end of the form. A new page willbe loaded indicating the status of the analysis. Note down the job key at the top ofthe status page for later access, as the analysis might take considerable time dependingon the size of the gene list.11. Once the FeasnetBuilder analysis is complete, the highlighted status text at the topof the page will be replaced by a link to the ZIP file containing all the results includingthe status page.12. After completion of FeasnetBuilder, the status page indicates the number of promotersthat were retrieved (refer to Note 4.4 on how redundancy in the gene list ishandled), the promoter sequences in the FASTA format, and also a link to a list ofgenes for which the promoter sequences were not found in the database. Next, thepage indicates whether the gene list was split into multiple parts for processingusing MATCH. Links to the actual HTML output from MATCH are provided nextto each of the split sequence files. Last, the overall Feasnet corresponding to theinput gene list is given next to the text Feasnet file.13. After completion of the FeasnetBuilder step, the status page contains a link to thefollow-up overrepresentation analysis and visualization. Click on the link indicatedby the text Click here to continue with Feasnet Analysis and Visualization.