BMC Genomics 2006, 7:116 http://www.biomedcentral.com/1471-2164/7/116 efforts to meet these expectations, we generated and organized large data sets using gene expression microar- rays to quantify genome-wide transcription in different developmental stages and tissues of this mosquito [3,4]. Arrangement of these data into a searchable format has streamlined the elucidation of genes expressed with stage- , tissue-, and sex-specificity. In addition, by juxtaposing these microarray findings with DNA comparative algo- rithms, the regulation of genes co-ordinately expressed in specific spatial and temporal patterns can be studied at a mechanistic level. We provide here a public database and web-based data-mining tool that combine stage and tissue expression microarray data, functional annotation, and regulatory DNA sequence comparison algorithms to pro- vide insight into gene expression and regulation in An. gambiae. Construction and content Data collection Stage-specific transcriptional signal values were imported from genome-wide microarray analyses of An. gambiae lar- vae, male sugar-fed adults, female sugar-fed adults, and female blood-fed adults 3, 24, 48, 72, 96 hours and 15 days after a bloodmeal using Affymetrix GCOS software. Values from tissue-specific microarray analyses also were imported using GCOS to quantify genome-wide transcrip- tion in fat bodies, midgut, and ovaries at 24 hours after bloodfeeding [3,4]. Functional gene annotation was imported from the Ano-Xcel database [5] to populate angaGEDUCI with keywords and annotation from the ENSEMBL, NCBI non-redundant, GO, PFAM, and SMART databases. Promoter sequences were selected as regions 1.5 kilobases (kb) in length adjacent to the 5'-ends of transcription start sites of genes using genomic data from ENSEMBL (Assembly: AgamP3, Feb 2006; Genebuild: VectorBase, Feb 2006; Database version: 37.3). Transcrip- tion factor binding sites from several classes of organisms were imported from the Transcription Factors Database (TFD) available publicly at ftp://ftp.ncbi.nih.gov/reposi tory/TFD/datasets/. Of the 7,066 sites listed in TFD, 6639 (94.0%) are eight nucleotides or longer and 623 (8.82%) contain degenerate notation. Five-hundred and eleven sites in the database were identified in insects (7.23%), of which 499 (97.7%) are eight nucleotides or longer, and 34 (6.65%) contain degeneracy. Implementation The data have been stored as a MySQL relational database that is accessible directly through an Apache web server. A web-based data mining interface is used to manage que- ries to identify genes that meet specific expression, key- word, and sequence criteria (Figure 1). A sequence comparison program based on the Boyer-Moore algo- rithm [6] is built into the data-mining interface for com- parison of promoter regions of genes within a selected gene set. Data retrieval The main page of the database provides hyperlinks to: Fil- ter Database, Import Gene Set, Download Data, View Database, Submit Study, Documentation, and Contact. Selection of the Filter Database link opens the data-min- ing interface and allows users to focus on specific genes that satisfy input criteria based on: 1) stage- and tissue- specific expression, 2) annotated keywords, 3) DNA sequences present in promoter, 3' untranslated regions (UTR), or coding regions, or 4) presence of specific tran- scription factor binding sites (Figure 1). Queries are con- ducted by stepwise entry of input criteria with each query imposed on the previous so that all genes currently dis- played meet all preceding query criteria as well as the cri- terion that was last entered. Once a gene set of interest has been selected, users then can use the analysis menu in the interface to search for conserved DNA motifs within the promoters of the gene set, view expression profiles, build a distribution of annotated keywords, or export the set for future retrieval (Figure 2). Detailed annotation and expression data for each gene also can be viewed at any time by selecting the gene identifier link to invoke the description of a gene entry. Description of a gene entry Each gene has a corresponding data page that can be accessed by selecting the gene identifier link during data retrieval. Gene entry pages display data from microarray expression analyses for stage- and tissue-specific expres- sion and functional annotation as gathered by Ano-Xcel from ENSEMBL, NCBI non-redundant, GO, PFAM, and SMART databases (Figure 3). A link to the Vectorbase database that contains additional, centralized gene data also is provided on each entry page. User-contributed notes and a form for sharing notes for a gene entry are found below the annotation of each gene. To encourage data sharing, note submission does not require user pre- registration. Comparing promoters to identify conserved DNA sequence motifs After clustering genes into gene sets that show similar pat- terns of expression, the data-mining interface analysis menu can be used to search for common DNA motifs that may act as regulatory sequences in coordinating these expression patterns. Two parameters must be selected to begin the analysis: 1) motif match length: the desired con- served sequence motif length to search for in the analysis, 2) mismatches: the number of base mismatches allowed between two nearly-conserved sequence motifs without disqualification. Page 2 of 11 (page number not for citation purposes)