W156 Nucleic Acids Research, 2007, Vol. 35, Web Server issue in each library (Supplementary Figure 3). The libraries are grouped by their tissue type. Due to space considerations, only libraries with matched ESTs are displayed on the web, but the full list is available for download. The EST detail page can also be bookmarked. For text-based searching, when multiple gene matches are found, the server displays the list of all matched genes with basic information, such as gene names and genomic locations, so that users can click one of the genes for further analysis. For sequence-based searching, the program ﬁrst tries to match the input sequence with our pre-deﬁned gene collection of the same species using BLAST (460 bp match with 498% identity, and the top hit chosen). If a match is found in the same species, the program directly reports the matched gene’s expression data. If the matched sequence is from a species diﬀerent from that of the input sequence, the program queries a backend table to identify its orthologous gene for subsequent result display. In rare cases where the input sequence fails to match any pre- deﬁned genes, the program resorts to a secondary BLAST search against the EST sequence database directly, and matched ESTs are used to compute expression results on the ﬂy. In this case, we used the method described previously (7), and no gene annotation will be available for display. Batch analysis and data download To facilitate large-scale analysis, we implemented a batch analysis function and allow download of all backend data. For batch analysis, a text ﬁeld is provided for pasting in a list of gene identiﬁers, which can be a mix of gene symbols and diﬀerent types of accession numbers. For example, the input can be a list of Aﬀymetrix microarray probe IDs supplemented with additional gene names. Upon submis- sion, the program produces paginated result pages showing expression results for each of the input gene in a concatenated tabular format. Links to detailed informa- tion and graphical displays are provided for each gene. These tabular data, along with detailed breakdown of EST library information, can be downloaded in text ﬁles for further study. Figure 2. Screenshot of GeneHub-GEPIS web input interface. Users can perform either text- or sequence-based search for a targeted organism, with an option to limit the search to a speciﬁed chromosome.