Self-Organizing Map Methodology for Sorting Differential Expression Data of MMP-9 Inhibition

St Clair, R.; Teti, M.; Knapinska, A.; Fields, G.; Hahn, W.; Barenholtz, E.

doi:10.1101/586628

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bioRxiv · 10.1101/586628

Self-Organizing Map Methodology for Sorting Differential Expression Data of MMP-9 Inhibition

St Clair, R.·Teti, M.·Knapinska, A.·Fields, G.·Hahn, W.·Barenholtz, E.

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Abstract

An unsupervised machine-learning model, based on a self-organizing map (SOM), was employed to extract suggested target genes from DESeq2 differential expression analysis data. Such methodology was tested on matrixmetalloproteinase 9 (MMP-9) inhibitors. The model generated information on several novel gene hits that may be regulated by MMP-9, suggesting the self-organizing map method may serve as a useful analytic tool in degradomics research for further differential expression data analysis. Original data was generated from a previous study, which consisted of quantitative measures in changes of levels of gene expression from 32,000 genes in four different conditions of stimulated T-cells treated with an MMP-9 inhibitor. Since intracellular target of MMP-9 are not yet well characterized, the functional enrichment analysis program, WebGestalt, was used for validation of the SOM identified regulated genes. The proposed data analysis method indicated MMP-9s prominent role in biological regulatory and metabolic processes as major categories of regulation of the predicted genes. Both fields suggest extensive intracellular targets for MMP-9-triggered regulation, which are new interests in MMP-9 research. The methodology presented here is useful for similar knowledge and discovery from quantitative datasets and a proposed extension of DESeq2 or similar data analysis.

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St Clair, R., Teti, M., Knapinska, A., Fields, G., Hahn, W., Barenholtz, E.. 2019-03-24. Self-Organizing Map Methodology for Sorting Differential Expression Data of MMP-9 Inhibition. https://doi.org/10.1101/586628

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