BMC Genomics 2006, 7:116 http://www.biomedcentral.com/1471-2164/7/116 FDiagtua-rmein1ing interface Data-mining interface. The "Filter database" data-mining interface allows users to select a gene set that meets specific expression, keyword, and sequence criteria. Input fields include a) differential expression quantified from stage- and tissue-spe- cific expression microarray analyses, b) keywords included in functional annotation gathered by Ano-Xcel [5] from the ENSEMBL, NCBI non-redundant, PFAM, GO, and SMART databases, and c) presence of transcription factor binding sites and other conserved DNA sequences contained within promoter, 3' UTR, or coding regions of the An. gambiae genome. Each filter is imposed on the current gene set being examined, beginning with the entire An. gambiae genome, thus selecting and reducing the gene set in a stepwise fashion as genes matching previous filter criteria are eliminated by subsequent filters. The parameters specified here are those that are used in the prophenoloxidase case study described in the text. The resulting output from the analysis contains three parts. First, a comparison matrix is displayed indicating the number of conserved motifs found in each pair-wise comparison among every gene in the gene set (Figure 4). FGiegnuerese2t with analysis menu Gene set with analysis menu. The six transcripts comprising the prophenoloxidase case study gene set, listed by ENSANGT identifiers, are shown in the background. The link to each transcript invokes a gene entry page, an example of which is represented in Figure 3. The analysis drop-down menu allows users to execute a search for conserved DNA sequence motifs in the promoter regions of the six genes in this gene set, build a keyword distribution from the functional annotation of these genes, display expression profiles of genes in the set, export promoter, 3' UTR, or cDNA sequences of the genes in FASTA format, or export the gene set. Page 3 of 11 (page number not for citation purposes)