Re Analyses Of Existing Human Ivd Degeneration Datasets Essay

1133 Words Apr 20th, 2016 5 Pages
4.2.3 Bioinformatic re-analyses of existing human IVD degeneration datasets: The publication and public availability of numerous human IVD gene expression datasets has enabled the use of bioinformatic tools to re-analyze data with emerging technologies to provide new insights that may have been missed in previous analyses. Bioinformatic strategies allow for the functional annotation of differentially expressed genes (DEGs) between experimental groups and analyses for protein-protein interactions (PPI), leading to a better understanding of the biological systems and pathways involved in IVD degeneration. One such study published in 2013 [56] re-analyzed dataset GSE15227 initially published by Gruber et al. [46] which used 3D-cultured AF cells from 15 patients across Thompson grades II-IV. They found 2 DEGs at an adjusted P-value threshold of 0.05 between Grade II and III discs, and 8 DEGs between Grade II and IV discs. Furthermore, when this group mapped PPI networks for each of their respective comparisons, it allowed them to identify hub genes which are central to the network, forming the most connections with other proteins in the network. MAP2K6 was found to be the hub gene for the Grade II vs. Grade III comparison, with other MAP family members such as MAP2K3 and MAPK being highly connected as well. RHOBTB2 was determined to be the hub gene for the Grade II vs. Grade IV comparison, with other Ras homologous (Rho) family members such as RHOB and RHOQ also being highly…

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