canonical pathways ipa

Infection and RNA-seq analysis of a zebrafish tlr2 mutant shows a broad function of this toll-like receptor in transcriptional and metabolic control and defense to Mycobacterium marinum infection. IPA allows you to compare analysis results from multiple experimental groups to identify similarities, differences, and trends. Ingenuity pathway analysis indicated that inflammation and immune response, cytokine signaling, cellular growth and movement, as well as tissue development and function were significantly activated following sciatic nerve injury. J. Neurosci. Cell. 8600 Rockville Pike At relatively later time points post peripheral nerve injury, the most significant canonical pathways and cellular functions were found to be tissue development and function. 43:e47. 31, 407–415. Gene expression profiling of the rat sciatic nerve in early Wallerian degeneration after injury. Accessibility Changes in pathways, networks and transcriptional factors were identified using Ingenuity Pathway Analysis (IPA). Following sciatic nerve transection, a diverse array of biological processes, including stimulus detection and response, inflammatory and immune response, cell migration, cell proliferation, cell death, axonal regeneration and guidance, and myelination, were significantly activated in the proximal nerve stump (Li S. et al., 2013). 2010 May;59(Pt 5):528-533. doi: 10.1099/jmm.0.016006-0. In this study we used microarray and bioinformatic analysis to examine dynamic molecular changes in the distal nerve stump following peripheral nerve injury. Analysis using Ingenuity Pathway Analysis (IPA) software revealed that 466 network and 423 functions-pathways eligible genes were up-regulated, and 363 network and 342 functions-pathways … The differentially expressed genes involved in Nervous System Development and Function are listed in Supplementary Table 5. Peripheral nerve injury and repair. Epub 2019 Dec 16. Myelin is an important inhibiting factor for neurite growth and nerve repair (Bähr and Przyrembel, 1995; David et al., 1995). In this study, we applied microarray to identify differentially expressed genes in the distal nerve stumps after sciatic nerve transection, and further used IPA program as the main bioinformatic tool to analyze microarray data. Starting from 6 h post injury, a larger number of canonical pathways were activated, which were mainly related to inflammation and immune response, cytokine signaling, diseases, nuclear receptor signaling, and intracellular and second messenger signaling. Certainly, the gene expression patterns and activated biological processes in the distal nerve stump showed different characteristics compared to those in the proximal nerve stump. Improved understanding of pathogenesis from protein interactions in Mycobacterium tuberculosis. Nerves are fragile tissues that are susceptible to traumatic injuries, such as penetration, crushing, and stretch tractions (Campbell, 2008). 36:17-36:50 Overlapping Network results. MS12015043); and a Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). Annu. Our results may help to illuminate the molecular aspects of Wallerian degeneration and to develop potential therapeutic targets for peripheral nerve repair. Neurosci. Schwann cells and endoneurial extracellular matrix molecules as potential cues for sorting of regenerated axons: a review. 11, 1165–1171. J. Autophagic myelin destruction by Schwann cells during Wallerian degeneration and segmental demyelination. The interferon signalling and hepatic fibrosis/hepatic stellate cell activation pathways were among the top 5 canonical pathways in all strains. doi: 10.4103/1673-5374.187059, Raimondo, S., Fornaro, M., Tos, P., Battiston, B., Giacobini-Robecchi, M. G., and Geuna, S. (2011). 24, 1254–1267. This site needs JavaScript to work properly. Red color indicates the increased expression whereas green color indicates the decreased expression as compared to control (expression at 0 h). The sequences of primer pairs were listed in Supplementary Table 1. doi: 10.1002/neu.480230507, Campbell, W. W. (2008). The expression patterns of SHH, solute carrier family 6 member 17 (SLC6A17), and ret proto-oncogene RET were also in agreement with microarray results. Res. Supplementary Table 5. 87, 27–46. Supplementary Figure 1. doi: 10.1002/mus.24082, Li, S., Liu, Q., Wang, Y., Gu, Y., Liu, D., Wang, C., et al. 2019 May;12(3):795-804. doi: 10.1038/s41385-019-0156-2. National Library of Medicine IPA provides two powerful tools to understand the pathway analysis results: the networks and canonical pathways that showed several pathways related to an adaptative immune response. At 0.5, 1, 6, 12, and 24 h, 4 days, and 1, 2, 3, and 4 weeks after surgery, rats were sacrificed by decapitation. Consistent with the results of canonical pathway analysis, following sciatic nerve transection, the number of categories of diseases and functions first increased and then progressively declined. J. Neuroinflammation 8:110. doi: 10.1186/1742-2094-8-110, Geuna, S., Raimondo, S., Ronchi, G., Di Scipio, F., Tos, P., Czaja, K., et al. 30, 153–179. (2014). 40, 99–107. List of the gene networks at 0.5, 1, 6, 12, and 24 h, 4 days, and 1, 2, 3, and 4 weeks post sciatic nerve transection. From 4 days post nerve injury, the scores of top networks were even higher and networks with a score value higher than 30 are presented in Table 1.

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