Name
Title | ||
|---|---|---|
A Two-Step Clustering For 3-D Gene Expression Data Reveals The Main Features Of The Arabidopsis Stress Response |
Abstract | ||
|---|---|---|
We developed an integrative approach for discovering gene modules, i.e. genes that are tightly correlated under several experimental conditions and applied it to a threedimensional Arabidopsis thaliana microarray dataset. The dataset consists of approximately 23000 genes responding to 9 abiotic stress conditions at 6-9 different points in time. Our approach aims at finding relatively small and dense modules lending themselves to a specific biological interpretation. In order to detect gene modules within this dataset, we employ a two-step clustering process. In the first step, a k-means clustering on one condition is performed, which is subsequently used in the second step as a seed for the clustering of the remaining conditions. To validate the significance of the obtained modules, we performed a permutation analysis and determined a null hypothesis to compare the module scores against, providing a p-value for each module. Significant modules were mapped to the Gene Ontology (GO) in order to determine the participating biological processes.As a result, we isolated modules showing high significance with respect to the p-values obtained by permutation analysis and GO mapping. In these modules we identified a number of genes that are either part of a general stress response with similar characteristics under different conditions (coherent modules), or part of a more specific stress response to a single stress condition (single response modules). We also found genes clustering within several conditions, which are, however, not part of a coherent module. These genes have a distinct temporal response under each condition. We call the modules they are contained in individual response modules (IR). |
Year | DOI | Venue |
|---|---|---|
2007 | 10.2390/biecoll-jib-2007-54 | JOURNAL OF INTEGRATIVE BIOINFORMATICS |
Keywords | Field | DocType |
stress response | Arabidopsis,Abiotic stress,Fight-or-flight response,Data mining,Stress conditions,Computer science,Permutation,Gene expression,Gene Modules,Bioinformatics,Cluster analysis | Journal |
Volume | Issue | ISSN |
4 | 1 | 1613-4516 |
Citations | PageRank | References |
3 | 0.39 | 9 |
Authors | ||
7 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Martin Strauch | 1 | 53 | 2.65 |
| Jochen Supper | 2 | 106 | 8.69 |
| Christian Spieth | 3 | 119 | 12.87 |
| Dierk Wanke | 4 | 63 | 2.81 |
| Joachim Kilian | 5 | 3 | 0.39 |
| Klaus Harter | 6 | 62 | 2.46 |
| Andreas Zell | 7 | 1419 | 137.58 |