CATchUP – A web database for spatiotemporally regulated genes

For proper control of biological activity, some key genes are highly expressed in a particular spatiotemporal domain. Mining of such spatiotemporally expressed genes using large-scale gene expression data derived from a broad range of experimental sources facilitates our understanding of genome-scale functional gene networks. However, comprehensive information on spatiotemporally expressed genes is lacking in plants. To collect such information, researchers at Meiji University devised a new index, δdmax, which is the maximum difference in relative gene expression levels between sample runs which are neighboring when sorted by the levels. Employing this index, they  comprehensively evaluated transcripts using large-scale RNA sequencing (RNA-Seq) data stored in the Sequence Read Archive for eight plant species: Arabidopsis thaliana (Arabidopsis), Solanum lycopersicum (tomato), Solanum tuberosum (potato), Oryza sativa (rice), Sorghum bicolor (sorghum), Vitis vinifera (grape), Medicago truncatula (Medicago), and Glycine max (soybean). Based on the frequency distribution of the δdmax values, approximately 70,000 transcripts showing 0.3 or larger δdmax values were extracted for the eight species. Information on these genes including the δdmax values, functional annotations, conservation among species, and experimental conditions where the genes show high expression levels are provided in a new database, CATchUP. The CATchUP database assists in identifying genes specifically expressed under particular conditions with powerful search functions and an intuitive graphical user interface.

Site map of CATchUP

The top page of the CATchUP (left panel) provides keyword search functions (inside green box). When a keyword search for genes (1) or experimental conditions (2) is submitted, retrieved information is displayed on a result page. The result page for a gene search provides a list of retrieved candidate transcripts and hyperlinks to detail pages for information on experimental conditions (3) and orthologous groups (4). The result page for an experimental condition search provides a list of retrieved experimental conditions and hyperlinks to detail pages for information on experimental conditions (5). On the top page, the ‘Ontology list’ function is accessible by clicking ‘Ontology’ (circled in red) (6). The ‘Ontology list’ provides lists of generalized terms for experimental conditions, namely Plant Ontology and Plant Environmental Ontology and hyperlinks to search result pages displaying experimental conditions annotated with the selected ontology term (7). On the top page, the ‘Conditions’ function is also accessible by clicking ‘Conditions’ (circled in blue) (8). ‘Conditions’ provides lists of ungeneralized terms for experimental conditions. Whereas this function provides no hyperlinks, the terms are useful as keywords in a search for experimental conditions by copying and pasting them.

Availability – CATchUP is available at: http://plantomics.mind.meiji.ac.jp/CATchUP