Features of functional annotation of rheumatoid arthritis susceptibility genes by Cytoscape
https://doi.org/10.20538/1682-0363-2020-3-101-104
Abstract
Aim. To evaluate the functional annotation of genes associated with rheumatoid arthritis with different parameters of the ClueGO Cytoscape tool.
Materials and methods. Genes of susceptibility to rheumatoid arthritis were extracted from publicly available database GWAS (catalog of associations of single nucleotide polymorphisms with diseases). The Gene Ontology (GO), the functional annotation of genes, was performed using Cytoscape ClueGO. The features of the functional annotation using the plugin ClueGO Cytoscape were analyzed.
Results. Depending on the initial parameters specified in the plugin, the grouping of terms according to the gene ontology was carried out with a different degree of generalization. A smaller minimum number of genes in a group allows to form a larger number of groups, which makes it possible to obtain more detailed functional characteristics.
Conclusion. The results obtained with different grouping options can be useful for further studies of genetic mechanisms of rheumatoid arthritis.
About the Author
N. Yu. Chasovskikh
Siberian State Medical University
Russian Federation
2, Moscow Trakt, Tomsk, 634050, Russian Federation
Russian Federation
2, Moscow Trakt, Tomsk, 634050, Russian Federation
References
1. Blake A., Christie K.R., Dolan M.E. Gene Ontology Consortium: going forward. Nucleic Acids Research. 2015; 43 (1): 1049–1056. DOI: 10.1093/nar/gku1179.
2. Ashburner M., Ball C., Blake J., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000; 25 (1): 25–29. DOI: 10.1093/nar/gku1179.
3. Bindea G., Mlecnik B., Hackl H., Charoentong P., Tosolini M., Kirilovsky A., Fridman W.H., Pagès F., Trajanoski Z., Galon J. ClueGO: a Cytoscape plug-into decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009; 25 (8): 1091–1093. DOI: 10.1093/bioinformatics/btp101.
4. Hindorff L.A., Sethupathy P., Junkins H.A., Ramos E.M., Mehta J.P., Collins F.S., Manolio T.A. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. PNAS. 2009; 106 (23): 9362–9367. DOI: 10.1073/pnas.0903103106.
5. Welter D., MacArthur J., Morales J., Burdett T., Hall P., Junkins H., Klemm A., Flicek P., Manolio T., Hindorff L., Parkinson H. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Research. 2014; 42 (1): 1001–1006. DOI: 10.1093/nar/gkt1229.
6. A catalog of published genome-wide association studies. URL: http://www.genome.gov/gwastudies/.
7. Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B. 1995; 57 (1): 289–300. DOI: 10.2307/2346101.
8. Udachkina E.V., Novikova D.S., Popkova T.V., Nasonov E.L. Te role of interleukin 6 in development of atherosclerosis in rheumatoid arthritis. Modern Reumatology. 2013; 7 (3): 25–32 (in Russ.).
9. Tanaka T., Narazaki M., Kishimoto T. IL-6 in inflammation, immunity, and disease. Cold Spring Harb. Perspect. Biol. 2014; 6 (10): a016295. DOI: 10.1101/cshperspect.a016295.
10. Ross S.H., Cantrell D.A. Signaling and function of interleukin-2 in T lymphocytes. Annu. Rev. Immunol. 2018; (36): 411–433. DOI: 10.1146/annurev-immunol-042617-053352.
11. Novikov A.A., Aleksandrova E.N., Diatroptova M.A., Nasonov E.L. The role of cytokines in the pathogenesis of rheumatoid arthritis. Research and Practical Rheumatology. 2010; 48 (2): 71–82 (in Russ.).
12. Vignali D.A., Kuchroo V.K. IL-12 family cytokines: immunological playmakers. Nat. Immunol. 2012; 13 (8): 722–728. DOI: 10.1038/ni.2366.
Review
For citations:
Chasovskikh N.Yu. Features of functional annotation of rheumatoid arthritis susceptibility genes by Cytoscape. Bulletin of Siberian Medicine. 2020;19(3):101-104. https://doi.org/10.20538/1682-0363-2020-3-101-104
Views:
730
Email this article 