1. Sechenov First Moscow State Medical University of the Russian Ministry of Health (Sechenov University), Moscow, Russia; Novosibirsk State University, Novosibirsk, Russia 2. Novosibirsk State University, Novosibirsk, Russia 3. Financial University under the Government of the Russian Federation, Moscow, Russia 4. Sechenov First Moscow State Medical University of the Russian Ministry of Health (Sechenov University), Moscow, Russia 5. Sechenov First Moscow State Medical University of the Russian Ministry of Health (Sechenov University), Moscow, Russia; Engelgardt Institute of Molecular Biology RAS, Moscow, Russia
Accumulation of genetic data in the field of Parkinson's disease research culminated in identifying risk factors and confident prediction of the disease occurrence. To find new gene-targets for diagnostics and therapy we have to reconstruct gene network of the disease, to cluster genes in the network, to reveal key (hub) genes with largest number of interactions in the network. Using the on-line bioinformatics tools OMIM, PANTHER, g:Profiler, GeneMANIA, and STRING-DB, we have analyzed the current array of data related to Parkinson's disease, calculated the categories of gene ontologies for a large list of genes, visualized them, and built gene networks containing the identified key objects and their relationships. However, translating the results into biological understanding is still a promising major challenge. The analysis of the genes associated with the disease, the assessment of their place in the gene network (connectivity) allows us to evaluate them as target genes for medicinal effects.
Download PDF:
Keywords: bioinformatics, reconstruction of gene networks, gene ontology
Supplementary materials:
Citation:
Orlov Y.L., Galieva A.G., Orlova N.G., Ivanova E.N., Mozyleva Y.A., Anashkina A.A. (2021) Reconstruction of gene network associated with Parkinson disease for gene targets search. Biomeditsinskaya Khimiya, 67(3), 222-230.
Orlov Y.L. et al. Reconstruction of gene network associated with Parkinson disease for gene targets search // Biomeditsinskaya Khimiya. - 2021. - V. 67. -N 3. - P. 222-230.
Orlov Y.L. et al., "Reconstruction of gene network associated with Parkinson disease for gene targets search." Biomeditsinskaya Khimiya 67.3 (2021): 222-230.
Orlov, Y. L., Galieva, A. G., Orlova, N. G., Ivanova, E. N., Mozyleva, Y. A., Anashkina, A. A. (2021). Reconstruction of gene network associated with Parkinson disease for gene targets search. Biomeditsinskaya Khimiya, 67(3), 222-230.
Warde-Farley D., Donaldson S.L., Comes O., Zuberi K., Badrawi R., Chao P., Franz M., Grouios C., Kazi F., Lopes C.T., Maitland A., Mostafavi S., Montojo J., Shao Q., Wright G., Bader G.D., Morris Q. (2010) Nucleic Acids Res., 38(Web Server issue), W214-W220. CrossRef Scholar google search
Hale C.M., Cheng Q., Ortuno D., Huang M., Nojima D., Kassner P.D., Wang S., Ollmann M.M., Carlisle H.J. (2016) Autophagy, 12(4), 713-726. CrossRef Scholar google search
Nalls M.A., Pankratz N., Lill C.M., Do C.B., Hernandez D.G., Saad M., de Stefano A.L., Kara E., Bras J., Sharma M. et al. (2014) Nat. Genet., 46(9), 989-993. CrossRef Scholar google search
Chang D., Nalls M.A., Hallgrímsdóttir I.B., Hunkapiller J., van der Brug M., Cai F., International Parkinson's Disease Genomics Consortium; 23andMe Research Team; Kerchner G.A., Ayalon G., Bingol B., Sheng M., Hinds D., Behrens T.W., Singleton A.B., Bhangale T.R., Graham R.R. (2017) Nat. Genet., 49(10), 1511-1516. CrossRef Scholar google search
Harel A., Inger A., Stelzer G., Strichman-Almashanu L., Dalah I., Safran M., Lancet D. (2009) BMC Bioinformatics, 10, 348. CrossRef Scholar google search
Zimprich A., Biskup S., Leitner P., Lichtner P., Farrer M., Lincoln S., Kachergus J., Hulihan M., Uitti R.J., Calne D.B., Stoessl A.J., Pfeiffer R.F., Patenge N., Carbajal I.C., Vieregge P., Asmus F., Müller-Myhsok B., Dickson D.W., Meitinger T., Strom T.M., Wszolek Z.K., Gasser T. (2004) Neuron, 44(4), 601-607. CrossRef Scholar google search
Skipper L., Wilkes K., Toft M., Baker M., Lincoln S., Hulihan M., Ross O.A., Hutton M., Aasly J., Farrer M. (2004) Am. J. Hum. Genet., 75(4), 669-677. CrossRef Scholar google search
Niethammer M., Tang C.C., Vo A., Nguyen N., Spetsieris P., Dhawan V., Ma Y., Small M., Feigin A., During M.J., Kaplitt M.G., Eidelberg D. (2018) Sci. Transl. Med., 10(469), eaau0713. CrossRef Scholar google search
Biernacka J.M., Chung S.J., Armasu S.M., Anderson K.S., Lill C.M., Bertram L., Ahlskog J.E., Brighina L., Frigerio R., Maraganore D.M. (2016). Parkinsonism Relat. Disord., 32, 25-30. CrossRef Scholar google search
Rappaport N., Twik M., Plaschkes I., Nudel R., Iny Stein T., Levitt J., Gershoni M., Morrey C.P., Safran M., Lancet D. (2017) Nucleic Acids Res., 45(D1), D877-D887. CrossRef Scholar google search
