Abstract
There is increasing need for accurate Alzheimer’s disease (AD) related genes prediction to inform study design, but available genes estimates are limited. In this study, the subnetwork extraction algorithms were applied to extract subnetworks and mine candidate genes based on a combined network, which was constructed by integrating the information of protein-protein interactions and gene-gene co-expression network. We obtained seven candidate genes with high possibility during AD progression. The application of subnetwork extraction algorithms based on combined network would provide a new insight into predicting the AD-related genes.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Alzheimer’s Disease International, World Alzheimer Report 2016. London: Alzheimer’s Disease International (2016)
Nicolas, G., Charbonnier, C., Campion, D.: From common to rare variants: the genetic component of Alzheimer disease. Hum. Hered. 81(3), 129–141 (2016). doi:10.1159/000452256
Vidal, M., Cusick Michael, E., Barabási, A.-L.: Interactome networks and human disease. Cell 144(6), 986–998 (2011). doi:10.1016/j.cell.2011.02.016
Sun, G.P., Jiang, T., Xie, P.F., et al.: Identification of the disease-associated genes in periodontitis using the co-expression network. Mol. Biol. (Mosk) 50(1), 143–150 (2016). doi:10.7868/s0026898416010195
Zheng, S., Zhao, Z.: GenRev: exploring functional relevance of genes in molecular networks. Genomics 99(3), 183-188. doi:10.1016/j.ygeno.2011.12.005
Webster, J.A., Gibbs, J.R., Clarke, J., et al.: Genetic control of human brain transcript expression in Alzheimer disease. Am. J. Hum. Genet. 84(4), 445–458 (2009). doi:10.1016/j.ajhg.2009.03.011
Franceschini, A., Szklarczyk, D., Frankild, S., et al.: STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41(Database issue), D808–D815 (2013). doi:10.1093/nar/gks1094
Amberger, J.S., Bocchini, C.A., Schiettecatte, F., et al.: OMIM.org: Online Mendelian Inheritance in Man (OMIM(R)), an online catalog of human genes and genetic disorders. Nucleic Acids Res. 43(Database issue), D789–D798 (2015). doi:10.1093/nar/gku1205
Bertram, L., McQueen, M.B., Mullin, K., et al.: Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database. Nat. Genet. 39(1), 17–23 (2007). doi:10.1038/ng1934
Bai, Z., Han, G., Xie, B., et al.: AlzBase: an integrative database for gene dysregulation in Alzheimer’s disease. Mol. Neurobiol. 53(1), 310–319 (2016). doi:10.1007/s12035-014-9011-3
Consortium TU, UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45(D1), D158–D169 (2017). doi:10.1093/nar/gkw1099
Langfelder PHorvath S, WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 9, 559 (2008). doi:10.1186/1471-2105-9-559
Mills, J.D., Nalpathamkalam, T., Jacobs, H.I., et al.: RNA-Seq analysis of the parietal cortex in Alzheimer’s disease reveals alternatively spliced isoforms related to lipid metabolism. Neurosci. Lett. 536, 90–95 (2013). doi:10.1016/j.neulet.2012.12.042
Windisch, M., Hutter-Paier, B., Rockenstein, E., et al.: Development of a new treatment for Alzheimer’s disease and Parkinson’s disease using anti-aggregatory beta-synuclein-derived peptides. J. Mol. Neurosci. 19(1–2), 63–69 (2002). doi:10.1007/s12031-002-0012-8
Obulesu, M., Lakshmi, M.J.: Apoptosis in Alzheimer’s disease: an understanding of the physiology, pathology and therapeutic avenues. Neurochem Res. 39(12), 2301–12 (2014). doi:10.1007/s11064-014-1454-4
Hoerndli, F.J., Pelech, S., Papassotiropoulos, A., et al.: Aβ treatment and P301L tau expression in an Alzheimer’s disease tissue culture model act synergistically to promote aberrant cell cycle re-entry. Eur. J. Neurosci. 26(1), 60–72 (2007). doi:10.1111/j.1460-9568.2007.05618.x
Olmos-Alonso, A., Schetters, S.T., Sri, S., et al.: Pharmacological targeting of CSF1R inhibits microglial proliferation and prevents the progression of Alzheimer’s-like pathology. Brain 139(Pt 3), 891–907 (2016). doi:10.1093/brain/awv379
Spencer, K.L., Olson, L.M., Schnetz-Boutaud, N., et al.: Dissection of chromosome 16p12 linkage peak suggests a possible role for CACNG3 variants in age-related macular degeneration susceptibility. Invest. Ophthalmol. Vis. Sci. 52(3), 1748–1754 (2011). doi:10.1167/iovs.09-5112
Kurozumi, A., Goto, Y., Matsushita, R., et al.: Tumor-suppressive microRNA-223 inhibits cancer cell migration and invasion by targeting ITGA3/ITGB1 signaling in prostate cancer. Cancer Sci. 107(1), 84–94 (2016). doi:10.1111/cas.12842
Acknowledgments
This work was supported by National Natural Science Foundation of China (61672037 and 21601001), the Initial Foundation of Doctoral Scientific Research in Anhui University (J01001319), and Anhui Provincial Outstanding Young Talent Support Plan (No. gxyqZD2017005).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this paper
Cite this paper
Wang, X., Yan, H., Zhang, D., Zhao, L., Bin, Y., Xia, J. (2017). Investigating Alzheimer’s Disease Candidate Genes Based on Combined Network Using Subnetwork Extraction Algorithms. In: Huang, DS., Jo, KH., Figueroa-García, J. (eds) Intelligent Computing Theories and Application. ICIC 2017. Lecture Notes in Computer Science(), vol 10362. Springer, Cham. https://doi.org/10.1007/978-3-319-63312-1_49
Download citation
DOI: https://doi.org/10.1007/978-3-319-63312-1_49
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-63311-4
Online ISBN: 978-3-319-63312-1
eBook Packages: Computer ScienceComputer Science (R0)