Research
A genomic approach to investigate developmental cell death in woody tissues of Populus trees
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* Corresponding author: Hannele Tuominen hannele.tuominen@plantphys.umu.se
1 Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-901 87 Umeå, Sweden
2 Department of Biochemistry, Umeå University, SE-901 87 Umeå, Sweden
3 Department of Biotechnology, KTH - Royal Institute of Technology, AlbaNova University Center, SE-10691, Stockholm, Sweden
Genome Biology 2005, 6:R34 doi:10.1186/gb-2005-6-4-r34
Published: 22 March 2005Additional files
Additional File 1:
The complete list of fiber death library-specific transcripts and the corresponding gene expression data from the microarray analysis. The list shows clusters and singletons unique to the fiber death library within the POPULUSDB, the number of EST sequences in each cluster, annotation, closest Arabidopsis gene and the BLASTX value (E), and the corresponding gene expression from the microarray analysis. The log2 expression ratio (M) is calculated between gene expression in sample B (fiber-cell death) and sample A (early fiber development). A statistically significant difference in gene expression is predicted for transcripts having P<0.001 (t-test) and B>0 (Bayesian statistics [55]).
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Additional File 2:
The complete gene expression data in xylem fibers undergoing cell death using the 25k Populus cDNA array and the POPULUSDB. Transcripts and the corresponding library distribution in POPULUSDB are listed in descending order of expression ratio from the microarray analysis. The log2 expression ratio (M) is calculated between gene expression in sample B (fiber-cell death) and sample A (early fiber development). A statistically significant difference in gene expression is predicted for transcripts having P<0.001 (t-test) and B>0 (Bayesian statistics [55]). The annotations and the E values were derived from BLASTX analysis against the Arabidopsis proteome or the Swiss-Prot database according to an annotation pipeline described in [50]. The PU numbers define the unigene clone numbers on the array.
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Additional File 3:
Comparison of the microarray data from xylem tissues of Populus and Arabidopsis. The Populus genes were selected that were statistically significantly more than two times upregulated in the fiber cell death sample (late maturing fibers; B) compared to the early fiber development (A). The automatically assigned Arabidopsis homologs [14] were listed for these Populus genes (column 'Populus B/A'), and compared to Arabidopsis genes that were previously shown to be upregulated at least two times during secondary growth compared to primary growth of the inflorescence stems (column 'Treatment') or in xylem tissues compared to bark of the hypocotyls (column 'Xylem') [41]. The list shows the genes that were shared by the Populus dataset and at least one of the Arabidopsis datasets. '1' denotes the presence, and '0' the absence of a particular gene in a dataset. The annotations were derived from the Arabidopsis Information Resource (TAIR) 28/01/2005. The PU numbers, corresponding to the unigene clones of the selected Populus genes, are shown for each homologous Arabidopsis gene.
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Additional File 4:
A table showing GenBank accession(s) for the EST sequences(s) in each POPULUSDB unigene cluster and singleton. A table showing GenBank accession(s) for the EST sequences(s) in each POPULUSDB unigene cluster and singleton.
Format: XLS Size: 2.7MB Download file
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