GEsture: an online hand-drawing tool for gene expression pattern search

Abstract

Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a ‘desirable’ or ‘user-defined’ pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with a gene expression curve as input from time series datasets. We presented three examples that illustrate the capacity of GEsture in gene hunting while following users’ requirements. GEsture also provides visualization tools (such as expression pattern figure, heat map and correlation network) to display the searching results. The result outputs may provide useful information for researchers to understand the targets, function and biological processes of the involved genes.

TimesVector-Web: A Web Service for Analysing Time Course Transcriptome Data with Multiple Conditions

“…Nevertheless, only a few tools provide a web-based time course gene expression analysis platform. GEsture [ 8 ] is a web-based tool that helps to search for user specified gene expression patterns from time course gene expression data. Hence, instead of performing clustering in a traditional way, the results depends on the user specified search pattern.…”