GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments.
BACKGROUND
High-throughput methods that allow for measuring the expression of thousands of genes or proteins simultaneously have opened new avenues for studying biochemical processes. While the noisiness of the data necessitates an extensive pre-processing of the raw data, the high dimensionality requires effective statistical analysis methods that facilitate the identification of crucial biological features and relations. For these reasons, the evaluation and interpretation of expression data is a complex, labor-intensive multi-step process. While a variety of tools for normalizing, analysing, or visualizing expression profiles has been developed in the last years, most of these tools offer only functionality for accomplishing certain steps of the evaluation pipeline.


RESULTS
Here, we present a web-based toolbox that provides rich functionality for all steps of the evaluation pipeline. Our tool GeneTrailExpress offers besides standard normalization procedures powerful statistical analysis methods for studying a large variety of biological categories and pathways. Furthermore, an integrated graph visualization tool, BiNA, enables the user to draw the relevant biological pathways applying cutting-edge graph-layout algorithms.


CONCLUSIONS
Our gene expression toolbox with its interactive visualization of the pathways and the expression values projected onto the nodes will simplify the analysis and interpretation of biochemical pathways considerably.
Keller
Andreas
A
Center for Bioinformatics, Saarland University, Saarbrücken, Germany. ack@bioinf.uni-sb.de
Backes
Christina
C
Al-Awadhi
Maher
M
Gerasch
Andreas
A
Küntzer
Jan
J
Kohlbacher
Oliver
O
Kaufmann
Michael
M
Lenhof
Hans-Peter
HP
D003196:Computer Graphics; D003627:Data Interpretation, Statistical; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software