The paper presents different ways to graphically interpret gene ontology (GO) terms for a small proteome of 20 proteins with high osmotic activity (OAP) from the blood serum of the Atlantic cod Gadus morhua. Term analysis was carried out in two ways — 1) using the topGO package (v2.46.0, Alexa & Rahnenfuhrer, 2021), and visualization using the ggplot2 package; 2) using the UniProt database and graphical visualization of the results in Excel 2016. The results obtained showed that the main part of cod OAP consists of extracellular “true” plasma proteins, among which fetuin, hemopexin and apolipproteins were identified. OAB are involved in the biological processes of hematopoiesis, proteolysis and development, as well as the regulation of metabolic processes. Their molecular functions include transport, hydrolase activity and inhibition of proteinase activity. When using the topGO and ggplot2 packages, the program code was unable to correctly graphically display all the data obtained due to the small sample of proteins. Data processing through DB UniProt gives a correct idea of the functions and participation of proteins in biological processes.
Atlantic cod, blood serum, osmotically active proteins, electrophoresis, MALDI, gene ontology, bioinformatics
1. Bazarova Z.M., Toropygin I.Yu., Vasil'ev A.S. i dr. Poisk i identifikaciya osmoticheski aktivnyh belkov v syvorotke krovi atlanticheskoy treski Gadus morhua // Trudy Instituta biologii vnutrennih vod im. I.D. Papanina RAN, 2022. Vyp. 99(102). S. 88–92. DOI:https://doi.org/10.47021/0320-3557-2022-88-92.
2. Alexa A., Rahnenfuhrer J. (2021) Gene set enrichment analysis with topGO // http://www.mpi-sb.mpg.de/∼alexa
3. Anderson N.L., Polanski M., Pieper R. et al. The human plasma proteome: a nonredundant list developed by combination of four separate sources // Molecular & Cellular Proteomics. 2004. Vol. 3. P. 311–326. DOI:https://doi.org/10.1074/mcp.M300127-MCP200.
4. Andreeva A.M. Structural Organization of Plasma Proteins as a Factor of Capillary Filtration in Pisces // Inland Water Biology. 2020. Vol. 13. № 4. P. 664–673. DOI:https://doi.org/10.1134/S1995082920060036.
5. Andreeva A.M., Bazarova Z.M., Toropygin I.Yu. et al. Serum Osmotically Active Proteins in the Atlantic Cod Gadus morhua // Journal of Evolutionary Biochemistry and Physiology. 2023. Vol. 59. P. 325–336. DOI:https://doi.org/10.31857/S004445292302002X.
6. Bohne-Kjersem A., Skadsheim A., Goksoyr A., Grosvik B.E. Candidate biomarker discovery in plasma of juvenile cod (Gadus morhua) exposed to crude North Sea oil, alkyl phenols and polycyclic aromatic hydrocarbons (PAHs) // Marine Environmental Research. 2009. Vol. 68(5), Iss. 5. P. 268–277. DOI:https://doi.org/10.1016/j.marenvres.2009.06.016.
7. Concha M.I., Smith V.J., Castro K. et al. Apolipoproteins AI and A-II are potentially important effectors of innate immunity in the teleost fish Cyprinus carpio // European journal of biochemistry. 2004. Vol. 271, Iss. 14. P. 2984–2990. DOI:https://doi.org/10.1111/j.1432-1033.2004.04228.x.
8. He Y., Yu H., Zhao H. et al. Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella) // BMC Genomics. 2021. Vol. 22. 620. DOI:https://doi.org/10.1186/s12864-021-07924-4.
9. Kaneko K., Nishii S., Izumi Y. et al. Proteomic Analysis after Sequential Extraction of Matrix Proteinsin Urinary Stones Composed of Calcium Oxalate Monohydrate and Calcium Oxalate Dihydrate // Analytical Sciences. 2015. Vol. 31(9). P. 935–942. DOI:https://doi.org/10.2116/analsci.31.935.
10. Liu M., Yan X., Zhang M., Li X., Li S., Jing M. Influence of Human Papillomavirus Infection on the Natural History of Cervical Intraepithelial Neoplasia 1: A Meta-Analysis // BioMed Research International. 2017. Vol. 2017. 8971059. DOI:https://doi.org/10.1155/2017/8971059.
11. Noel E.S., Reis M., Arai Z., Ober E.A. Analysis of the Albumin/α-Fetoprotein/Afamin/Group specific component gene family in the context of zebrafish liver differentiation // Gene Expression Patterns. 2010. Vol. 10(6). P. 237–243. DOI:https://doi.org/10.1016/j.gep.2010.05.002.
12. Tang T., Huang Y., Peng C., Liao Y., Lv Y., Shi Q., Gao B. A Chromosome-Level Genome Assembly of the Reef Stonefish (Synanceia verrucosa) Provides Novel Insights into Stonustoxin (sntx) Genes // Molecular Biology and Evolution. 2023. Vol. 40(10). msad215. DOI:https://doi.org/10.1093/molbev/msad215.
13. Elektronnyy resurs. URL: http://www.springer.com/series/6991
14. Elektronnyy resurs. URL: http://eggnog-mapper.embl.de/
15. Elektronnyy resurs. URL: http://www.matrixscience.com
16. Elektronnyy resurs. URL: https://vniiz.org/science/publication/article-383/conf90-article-17
17. Elektronnyy resurs. URL: https://www.codecamp.ru/blog/kolmogorov-smirnov-test-r/
18. Elektronnyy resurs. URL: https://r-statistics.co/Top50-Ggplot2-Visualizations-MasterList-R-Code.html
