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Table 1Web URLs of Promoter, TF Databases, and TFBs Prediction ProgramsProgram name Description Organism Web URL ReferencesTRANSFAC Database of TFs, their genomic, Eukaryotes http://www.gene-regulation.com 12binding sites and DNAbindingprofilesJASPAR Database of TF–DNA binding Eukaryotes http://mordor.cgb.ki.se/cgi- 11preferences, modeled bin/jaspar2005/jaspar_db.plas matricesMPromDb Database of mammalian Mammals http://bioinformatics.med.ohio- 15gene promoters state.edu/MPromDbOMGProm Database of orthologous Human, mouse, http://bioinformatics.med.ohio- 61mammalian gene promoters and rat state.edu/OMGPromDBTSS Database of transcription Human, mouse, http://dbtss.hgc.jp 16start sites zebrafish, malaria,and schyzonEPD Database of eukaryotic Eukaryotes http://www.epd.isb-sib.ch 67gene promotersUCSC Genome browser at UCSC Genome sequences http://genome.ucsc.edu 68and annotationsincluding human–mouse–ratconserved blocksMatch Program to search for TFBSs Eukaryotes http://www.gene-regulation.com/ 19using TRANSFAC PWMs pub/programs.html#matchTESS Program to predict TFBSs Eukaryotes http://www.cbil.upenn. –edu/cgi-bin/tess/tessMatInspector Program to search for TFBSs Eukaryotes http://www.genomatix.de/products/ 50using TRANSFAC PWMs MatInspector/MatInspector1.html132