Cell. The interferon signalling and hepatic fibrosis/hepatic stellate cell activation pathways were among the top 5 canonical pathways in all strains. doi: 10.1371/journal.pone.0033664, Lee, S. K., and Wolfe, S. W. (2000). IPA Core Analysis Pathway Analysis Identifies enriched canonical pathways and scores directional changes based on gene expression Upstream Regulator Analysis Predicts what regulators caused changes in gene expression and the directional state of regulator Diseases and Functions Analysis doi: 10.1016/j.expneurol.2007.06.009, Dubový, P. (2004). canonical-pathway Sizes: 150x83 / 300x166 / 600x332 / 900x498 / 2362x1306 / doi: 10.1371/journal.pone.0143491, Yu, B., Zhou, S., Wang, Y., Qian, T., Ding, G., Ding, F., et al. Rev. 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. doi: 10.1093/nar/gkv007, Shubayev, V. I., Angert, M., Dolkas, J., Campana, W. M., Palenscar, K., and Myers, R. R. (2006). doi: 10.1007/s12264-013-1340-0, Yi, S., Yuan, Y., Chen, Q., Wang, X., Gong, L., Liu, J., et al. Supplementary Figure 1. Neurophysiol. doi: 10.1111/j.1471-4159.2005.03635.x, Braun, S., Croizat, B., Lagrange, M. C., Warter, J. M., and Poindron, P. (1996). eCollection 2021. Accordingly, the expression change of myelin-related genes might reflect that Schwann cells play different roles at different time periods during Wallerian degeneration. J. Neurosci. 2011 Dec;66(4):531-7. doi: 10.3412/jsb.66.531. 6, 391–407. Briefly, outcomes from microarray analysis were first uploaded into Qiagen's IPA system for core analysis and then overlaid with the global molecular network in the Ingenuity pathway knowledge base (IPKB). Cell Sci. Differential gene expression in proximal and distal nerve segments of rats with sciatic nerve injury during Wallerian degeneration. Neural Regen. 2021 Feb 4;12:612675. doi: 10.3389/fmicb.2021.612675. doi: 10.1016/j.mcn.2005.10.011, Sta, M., Cappaert, N. L., Ramekers, D., Baas, F., and Wadman, W. J. ＊PMCでIngenuity Pathway Analysisを検索をした結果 ナレッジ＆データベース 遺伝子、タンパク質、組織、細胞、ドラッグ、疾患などに関する、約760万（2020年10月現在）にもおよぶ生物学的機能、相互作用に関する情報が収集されたデータベースです。 Neurosci., 06 December 2016 Transcriptional profiling of the injured sciatic nerve of mice carrying the Wld(S) mutant gene: identification of genes involved in neuroprotection, neuroinflammation, and nerve regeneration. J. A p-value less than 0.05 was considered as significantly different. Different from the central nervous syst… Int. doi: 10.1016/j.clinph.2008.03.018, Chen, P., Piao, X., and Bonaldo, P. (2015). To investigate peripheral nerve injury-induced molecular changes during Wallerian degeneration, microarray analysis was performed to detect the expression levels of more than 30,000 genes at 0, 0.5, 1, 6, 12, and 24 h, 4 days, and 1, 2, 3, and 4 weeks in the distal nerve stumps post sciatic nerve transection. J. Neuropathol. Obtained cDNA was used as a template for amplification and qPCR was performed using SYBR Green Premix Ex Taq (TaKaRa) with specific primer pairs on an Applied Biosystems Stepone real-time PCR System. 193, 267–275. Briefly, rats were anesthetized by an injection of mixed narcotics (85 mg/kg trichloroacetaldehyde monohydrate, 42 mg/kg magnesium sulfate, and 17 mg/kg sodium pentobarbital). Mvubu NE, Pillay B, Gamieldien J, Bishai W, Pillay M. Dev Comp Immunol. 125, 2675–2683. Top enriched diseases and functions following sciatic nerve transection. J. Neurochem. Different from the central nervous system that can hardly regenerate by itself, the peripheral nervous system has a certain ability to regenerate on its own (Raimondo et al., 2011; Gu et al., 2014). Nihon Saikingaku Zasshi. Am. 24, 1254–1267. QIAGEN Ingenuity Pathway Analysis helps you perform insightful data analysis and interpretation to understand your experimental results … Scordo JM, Olmo-Fontánez AM, Kelley HV, Sidiki S, Arcos J, Akhter A, Wewers MD, Torrelles JB. Lett. Canonical pathways with a p-value < 10−3 (1E-03) are labeled in red color while canonical pathways with a p-value > 10−3 (1E-03) are labeled in white color. 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. 36:51-37:19 My Lists, My Pathways, and Molecules tab At 1 h post injury, significant activated cellular functions were generally related to inflammation and immune response, tissue development, and numerous diseases. IPA allows you to compare analysis results from multiple experimental groups to identify similarities, differences, and trends. Ann. In the current study, we made rat sciatic nerve transection, collected the distal nerve stump samples at different time points, re-analyzed previous obtained microarray data (Yao et al., 2012, 2013) by using the R software and the limma package and uploaded the massive microarray data into the IPA program for a systematic bioinformatic analysis. Biological processes, such as response to stimulus, inflammatory response, immune response, cell proliferation, migration, and apoptosis, axon guidance, myelination, signal transduction, and protein kinase activity, were also investigated (Jiang et al., 2014). Baclofen modulates the expression and release of neurotrophins in schwann-like adipose stem cells. The authors thank Professor Jie Liu for his help in manuscript preparation. Ingenuity® Pathway Analysis (IPA) software was used to conduct pathway enrichment based on the recruited gene datasets mentioned above. 29, 321–332. Neurol. (1995). 15:25-22:35 Core Analysis Canonical Pathway results. Figure 2. 2010 May;59(Pt 5):528-533. doi: 10.1099/jmm.0.016006-0. Stored distal nerve stumps were used for total RNA isolation. doi: 10.1007/s12031-012-9813-6, Frostick, S. P., Yin, Q., and Kemp, G. J. J. Mol. In contrast, many of these biological processes were also detected in the distal nerve stump after peripheral nerve injury, as revealed by this study. 11, 1165–1171. Neural tissue engineering options for peripheral nerve regeneration. Figure 5. The ratio is calculated as follows: The number of molecules in a given pathway that meet cutoff criteria, divided by total number of molecules that make up that pathway and that are in the reference set (see Defining the Reference Set). miR-221 and miR-222 promote Schwann cell proliferation and migration by targeting LASS2 after sciatic nerve injury. The gene list was loaded, and the source of the organism was filtered as only “Homo Sapiens”, so that the analysis of interactions and pathways was limited to humans. Why is Wallerian degeneration in the CNS so slow? 23:32-28:27 Upstream Analysis results. 54, 487–496. 以IPA建構Pathway 9, 1186–1194. Mol. The IPA system (version 42012434, Ingenuity Systems; Qiagen China Co., Ltd.) was used for subsequent bioinformatics analysis, which included canonical pathway analysis, disease and function, regulator effects, upstream regulators and molecular networks. Changes in pathways, networks and transcriptional factors were identified using Ingenuity Pathway Analysis (IPA). doi: 10.5435/00124635-200007000-00005, Li, M., Guo, W., Zhang, P., Li, H., Gu, X., and Yao, D. (2013). Clin. At 1 h post nerve transection, canonical pathways related to immune response and cytokine signaling were activated. 23, 521–536. J. Mol. Curr. Anat. 30, 209–233. Neural Regenerat. Chapter 3: histology of the peripheral nerve and changes occurring during nerve regeneration.
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