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

Conference · Wed Mar 30 04:00:00 EDT 2011

OSTI ID:1050634

Ruebel, Oliver; Keranen, Soile V.E.; Biggin, Mark; Knowles, David W; Weber, Gunther H; Hagen, Hans; Hamann, Bernd; Bethel, E Wes

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 Point-Cloud 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 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.

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
• Sponsoring Organization: Computational Research Division; Genomics Division; Life Sciences Division
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 1050634
• Report Number(s): LBNL-4891E
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
97 MATHEMATICS AND COMPUTING
ALGORITHMS
DATA ANALYSIS
DROSOPHILA
EMBRYOS
GENES
GENETICS
MEDICINE
RESOLUTION
TRANSCRIPTION
three-dimensional gene expression
integrating visualization and data analysis
Matlab integration
network modeling
genetic algorithm