Abstract
We present a methodology to analyze zebrafish knock-out experiment replicated time series microarray data. The knock-out experiment aimed to elucidate the transcriptomal regulators underlying the glycocalyx-regulation of vasculogenesis by performing global gene expression analysis of NDST mutants and wild-type siblings at three distinct time points during development. Cluster analysis and the construction of a genetic interaction network allows to identify groups of genes acting in the process of early stage vasculogenesis. We report the following findings: we found a large number of gene clusters, particularly glycans, during the three developmental steps of the zebrafish organism. In each step, genes connectivity changes according to two different powerlaws. The clusters are highlighted in such a way, that it is possible to see the dynamics of the interactions through the time points recorded in the microarray experiment. Vegf-related genes seem not to be involved at transcriptomics level, suggesting alternative regulative pathways do exist to modulate transcriptomal signatures in developing zebrafish. Our results show that there are several glycan-related genes which may be involved in early processes such as vasculogenesis.
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Sorathiya, A., Jucikas, T., Piecewicz, S., Sengupta, S., Liò, P. (2009). Searching for Glycomics Role in Stem Cell Development. In: Masulli, F., Tagliaferri, R., Verkhivker, G.M. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2008. Lecture Notes in Computer Science(), vol 5488. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02504-4_18
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DOI: https://doi.org/10.1007/978-3-642-02504-4_18
Publisher Name: Springer, Berlin, Heidelberg
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