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Application of machine learning and visualization of heterogeneous datasets to uncover relationships between translation and developmental stage expression of C. elegans mRNAs

¹ Department of Computer Science, Louisiana State University
² Department of Biochemistry and Molecular Biology
³ Center for Bioinformatics and Computational Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana

The relationships between genes in neighboring clusters in a self-organizing map (SOM) and properties attributed to them are sometimes difficult to discern, especially when heterogeneous datasets are used. We report a novel approach to identify correlations between heterogeneous datasets. One dataset, derived from microarray analysis of polysomal distribution, contained changes in the translational efficiency of Caenorhabditis elegans mRNAs resulting from loss of specific eIF4E isoform. The other dataset contained expression patterns of mRNAs across all developmental stages. Two algorithms were applied to these datasets: a classical scatter plot and an SOM. The outputs were linked using a two-dimensional color scale. This revealed that an mRNA’s eIF4E-dependent translational efficiency is strongly dependent on its expression during development. This correlation was not detectable with a traditional one-dimensional color scale.

eIF4E; self-organizing map; color scale; mRNA-specific translational control; Caenorhabditis elegans

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