Research
Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress
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* Corresponding authors: Simon M Dittami dittami@sb-roscoff.fr - Thierry Tonon tonon@sb-roscoff.fr
1 UPMC Univ Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, 29680 Roscoff, France
2 CNRS, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, 29680 Roscoff, France
3 CEA, DSV, Institut de Génomique, Génoscope, rue Gaston Crémieux, CP5706, 91057 Evry, France
4 CNRS, UMR 8030 Génomique métabolique des genomes, rue Gaston Crémieux, CP5706, 91057 Evry, France
5 Université d'Evry, UMR 8030 Génomique métabolique des genomes, 91057 Evry, France
6 SIG-FR 2424 CNRS UPMC, Station Biologique, 29680 Roscoff, France
7 Center for Biotechnology (CeBiTec), University of Bielefeld, 33594 Bielefeld, Germany
8 German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
9 VIB Department of Plant Systems Biology, Ghent University, 9052 Ghent, Belgium
Genome Biology 2009, 10:R66 doi:10.1186/gb-2009-10-6-r66
Published: 16 June 2009Additional files
Additional data file 1:
The tested stress conditions correspond to the conditions used for the microarray experiment (1,470 mM NaCl, 12.5% seawater, and 1 mM H2O2), but the duration of the stress treatments was 24 hours rather than 6 hours.
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Additional data file 2:
P indicates the probability of this pathway being actually over-represented in the two datasets (5% FDR and 10% FDR). The column FDR refers to the FDR that was applied when identifying the significantly regulated transcripts used for this analysis.
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Additional data file 3:
All genes are grouped according to their putative function.
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Additional data file 4:
Q represents the q-value, that is, the expected proportion of false positives incurred when the pathway is considered significant. It is given for the two datasets containing genes considered to be significantly regulated at FDRs of 5% and 10%. Pathways significant at q-values < 0.05 are highlighted in boldface; pathways not known to be present in E. siliculosus and thus representing possible artifacts of the automatic annotation are shown in grey.
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Additional data file 5:
The column FDR refers to the FDR that was applied when identifying the significantly regulated transcripts used for this analysis.
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Additional data file 6:
The first tab contains a graphical representation of identified groups of unknown stress response genes. The roman numerals on the left (I-VI) refer to the network graphs to their right, each representing a group of unknown stress response genes. In the network graphs, brown nodes represent sequences only found in E. siliculosus, while green nodes represent genes found in other organisms also. Edges represent the sequence similarity between two genes (e-value of the BLAST output). The cluster each gene was assigned to by the k-means clustering (Figure 5) is given in boldface. Furthermore, the expression profile of each gene in the three stress conditions (hyposaline-, hypersaline-, and oxidative stress) is given on the right. Yellow indicates that a gene was over-expressed in a particular condition, while black indicates no change, and blue indicates that a particular gene was repressed. The other two tabs contain additional information, such as corresponding genome equivalent, amino acid sequence, subcellular localization of each protein, the results of the transmembrane domain search, and the expression profile for both the genes shown in the first tab and the other stress response genes that could not be assigned to the different groups.
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Additional data file 7:
C5-epimerase-genes represented on the microarray and their expression profiles.
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Additional data file 8:
Accession numbers of all sequences used in the design of the Ectocarpus siliculosus microarray.
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