Research article
Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue
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* Corresponding author: Marc Strickert stricker@ipk-gatersleben.de
- † Equal contributors
1 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany
2 Max-Planck-lnstitute of Molecular Plant Physiology, 14424 Potsdam, Germany
BMC Bioinformatics 2007, 8:165 doi:10.1186/1471-2105-8-165
Published: 22 May 2007Additional files
Additional file 1:
Additional HiT-MDS-2 embeddings of the expression data set containing 4824 genes, using different exponents p. Different exponents used in the data similarity measure (1 - r(xi, xj))p highlight specific correlation structures in the corresponding HiT-MDS-2 embeddings. Results for exponents p = 24, 4,1,0.25 are shown in panels a-d, respectively.
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Additional file 2:
List of 4824 genes with 64 centroids. The table contains gene expressions of 4824 high-quality genes covering 14 developmental stages, ODAF-26DAF, in steps of two days. Expression levels are log2-transformed quantile-normalized values. Genes are assigned to 64 centroids from neural gas clustering.
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Additional file 3:
Table of functional categories. The table contains genes with manually assigned major functional categories corresponding to Fig. 3 of the manuscript.
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Additional file 4:
HiT-MDS-2 embedding of gene expressions of 3031 filtered genes from developing barley endosperm at time points 4, 8, 16, 25 days after flowering. Expression levels are taken from Barley 1 Affymetrix chip. Like in Figure 2 of the manuscript, a sandglass shape is obtained for a correlation exponent of p = 8. Since only four time points are considered, the four-dimensional expression vectors are very faithfully represented in the scatter plot. The corresponding regulation patterns of up-, down- and intermediate regulation are displayed in an extra figure [see Additional file 5].
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Additional file 5:
Gene expression profiles obtained from Barley 1 Affymetrix gene chip connected to highlighted regions of the HiT-MDS-2 gene space plot [see Additional file 4]. High spatial specificity is observed in the exemplary clusters 1–8 covering interesting locations in the gene space. Patterns of up- and down-regulation fall into opposite poles. Cluster number 5 shows intermediate up-regulation with quite diverse characteristic, where Pearson correlation does not yield good discrimination between peaks in the second or third temporal stage. Cluster number 3 contains genes that become active just at the last stage (day 25 after flowering).
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Additional file 6:
Gene expression profiles corresponding to the six sub-clusters 2a, 2b, 3a, 3b, 4a and 4b referred in Figure 3 of the manuscript. The expression profiles reflect z-score normalized log2 values. In addition to individual gene expression curves displayed in blue, their mean and standard deviation are depicted by red lines. Highest variability is observed for intermediate regulation events in cluster 2a; yet, the overall quality of coexpression in the six clusters is represented well.
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