Abstract
BackgroundMicro- and macroarray technologies help acquire thousands of gene expression patterns covering important biological processes during plant ontogeny. Particularly, faithful visualization methods are beneficial for revealing interesting gene expression patterns and functional relationships of coexpressed genes. Such screening helps to gain deeper insights into regulatory behavior and cellular responses, as will be discussed for expression data of developing barley endosperm tissue. For that purpose, high-throughput multidimensional scaling (HiT-MDS), a recent method for similarity-preserving data embedding, is substantially refined and used for (a) assessing the quality and reliability of centroid gene expression patterns, and for (b) derivation of functional relationships of coexpressed genes of endosperm tissue during barley grain development (0–26 days after flowering).ResultsTemporal expression profiles of 4824 genes at 14 time points are faithfully embedded into two-dimensional displays. Thereby, similar shapes of coexpressed genes get closely grouped by a correlation-based similarity measure. As a main result, by using power transformation of correlation terms, a characteristic cloud of points with bipolar sandglass shape is obtained that is inherently connected to expression patterns of pre-storage, intermediate and storage phase of endosperm development.ConclusionThe new HiT-MDS-2 method helps to create global views of expression patterns and to validate centroids obtained from clustering programs. Furthermore, functional gene annotation for developing endosperm barley tissue is successfully mapped to the visualization, making easy localization of major centroids of enriched functional categories possible.
Highlights
Micro- and macroarray technologies help acquire thousands of gene expression patterns covering important biological processes during plant ontogeny
Data of developing barley endosperm tissue In order to demonstrate its benefits, the presented HiTMDS-2 algorithm has been applied to an expression data set obtained from a 12 k seed array (11786 genes) of
We noticed very interesting patterns showing dominant expression values in the pre-storage phase with drastic decrease in the intermediate stage, followed by an increase of expression levels during the storage phase (Fig. 2, cluster group 5). These results indicate that the non-linear data embedding technique of high-throughput multidimensional scaling (HiT-multidimensional scaling (MDS))-2 is a useful tool for identifying the major global patterns occurring during temporal development; informative minor patterns that could be missed in noisy subsets of gene expression data show up as scattered point sets
Summary
Micro- and macroarray technologies help acquire thousands of gene expression patterns covering important biological processes during plant ontogeny. Faithful visualization methods are beneficial for revealing interesting gene expression patterns and functional relationships of coexpressed genes Such screening helps to gain deeper insights into regulatory behavior and cellular responses, as will be discussed for expression data of developing barley endosperm tissue. High-throughput multidimensional scaling (HiT-MDS), a recent method for similarity-preserving data embedding, is substantially refined and used for (a) assessing the quality and reliability of centroid gene expression patterns, and for (b) derivation of functional relationships of coexpressed genes of endosperm tissue during barley grain development (0–26 days after flowering). The low-dimensional output space should be Euclidean – this allows a visual interpretation of close points as representing similar input data, and distant points as indicating dissimilarities Since, for such view, high similarity is expressed by small values and vice versa, this inverse interpretation is sometimes referred to as dissimilarity in the literature
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