Novel in silico end-to-end platform tested on mesenchymal stromal cells (hMSC) revealed dysregulated MAB21L2 and CXCL6 in primary osteoporosis
AbstractThe dramatic drop in genome sequencing costs has led to vast stores of data, but the fragmentation of bioinformatic tools to analyze the data continues to elude many biologists. Mendel is a new R-based platform that allows biologists to focus on biology without the burden of learning software engineering. It is the first system to provide users the full range of an end-to-end experience, starting from uploading sequencing data through full-fledged differential analyses and functional annotation. Mendel has been tested on the transcriptome of human mesenchymal stromal cells (hMSC), using Affymetrix U133 Plus 2.0 RNA probe data from 5 primary osteoporosis and 5 control subjects. Importantly, the test also enhanced our current understanding of the disease, revealing additional and novel over-expressed genes MAB21L2 and XIST, and discovering a new series of downregulated genes CXCL6 and CMPK2. Mendel also reveals pathways, such as that for COL1A1/COL10A1, whose upregulation delays post-translation heterotrimer folding, leading to abnormal ɑ-chain collagens and helices, the latter of which are either degraded by the ERAD pathway or secreted into the ECM, leading to matrix mineralization, osteoblast development, and cell-cell crosstalk. Keywords: Bioinformatics, differential gene analysis, expression profiling, gene ontology, osteoporosis
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