Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data

Abstract

Summary. Three-dimensional gene expression PointCloud data generated by the Berkeley Drosophila Transcription Network Project (BDTNP) provides quantitative information about the spatial and temporal expression of genes in early Drosophila embryos at cellular resolution. The BDTNP team visualizes and analyzes PointCloud data using the software application PointCloudXplore (PCX). To maximize the impact of novel, complex data sets, such as PointClouds, the data needs to be accessible to biologists and comprehensible to developers of analysis functions. We address this challenge by linking PCX and Matlab R 6 via a dedicated interface, thereby providing biologists seamless access to advanced data analysis functions and giving bioinformatics researchers the opportunity to integrate their analysis directly into the visualization application. To demonstrate the usefulness of this approach, we computationally model parts of the expression pattern of the gene even skipped using a genetic algorithm implemented in Matlab and integrated into PCX via our Matlab interface.

Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data

“…PCX addresses this need by providing an interface to MATLAB (The Math- Works Inc., Natick, MA, USA), allowing researchers to integrate custom analysis capabilities with PCX and providing biologists faster and more convenient access to advanced analysis functions [22]. With its interface to MATLAB, PCX supports fast prototyping and testing of new ideas, thus facilitating communication between bioinformatics researchers and experimental biologists.…”