База знаний RatDEGdb по дифференциально экспрессирующимся генам крысы как модельного объекта биомедицинских исследований

Животные модели, используемые в биомедицинских исследованиях, в настоящее время охватывают практически весь известный спектр заболеваний человека. База знаний RatDEGdb по дифференциально экспрессирующимся генам (ДЭГ) крысы как модельного объекта в биомедицинских исследованиях представляет собой коллекцию опубликованных данных по экспрессии генов у крыс разных линий, предназначенных для изучения артериальной гипертонии, болезней пожилого возраста, психопатологических состояний и других заболеваний человека. Текущий выпуск RatDEGdb содержит 25 101 ДЭГ, представляющих 14 320 уникальных генов крысы, которые изменяют уровень транскрипции в 21 ткани 10 генетических линий крысы в качестве моделей 11 заболеваний человека согласно 45 оригинальным научным статьям. Новшество RatDEGdb по сравнению с другими биомедицинскими базами данных заключается в курируемой аннотации отклонений ДЭГ крысы как модельного объекта с использованием независимых клинических данных об однонаправленных изменениях экспрессии гомологичных генов, выявленных у людей при различных патологиях. Собранные ДЭГ крыс были аннотированы однонаправленными изменениями экспрессии гомологичных им генов человека у больных людей относительно здоровых. К настоящему времени выпуск RatDEGdb содержит 94 873 такие аннотации для 321 гена человека при 836 заболеваниях согласно 959 оригинальным научным статьям, найденным в текущем выпуске базы данных PubMed. Представленная база знаний может быть интересна в первую очередь специалистам по генетике человека, молекулярным биологам, клиницистам и генетическим консультантам, а также специалистам в области биофармацевтики, биоинформатики и персонализированной геномики. RatDEGdb является общедоступной  (https://www.sysbio.ru/RatDEGdb).

1. Aikawa H., Nonaka I., Woo M., Tsugane T., Esaki K. Shaking rat Kawasaki (SRK): a new neurological mutant rat in the Wistar strain. Acta Neuropathol. 1988;76:366-372. DOI 10.1007/BF00686973

2. Albert F.W., Somel M., Carneiro M., Aximu-Petri A., Halbwax M., Thalmann O., Blanco-Aguiar J.A., Plyusnina I.Z., Trut L., Villafuerte R., Ferrand N., Kaiser S., Jensen P., Paabo S. A comparison of brain gene expression levels in domesticated and wild animals. PLoS Genet. 2012;8(9):e1002962. DOI 10.1371/journal.pgen.1002962

3. Ashraf U.M., Mell B., Jose P.A., Kumarasamy S. Deep transcriptomic profiling of Dahl salt-sensitive rat kidneys with mutant form of Resp18. Biochem. Biophys. Res. Commun. 2021;572:35-40. DOI 10.1016/j.bbrc.2021.07.071

4. Barykina N.N., Chepkasov I.L., Alekhina T.A., Kolpakov V.G. Selection of Wistar rats for predisposition to catalepsy. Genetika. 1983; 19(12):2014­2021

5. Bay V., Happ D.F., Ardalan M., Quist A., Oggiano F., Chumak T., Hansen K., Ding M., Mallard C., Tasker R.A., Wegener G. Flinders sensitive line rats are resistant to infarction following transient occlusion of the middle cerebral artery. Brain Res. 2020;1737:146797. DOI 10.1016/j.brainres.2020.146797

6. Belyaev D.K., Borodin P.M. The influence of stress on variation and its role in evolution. Biologisches Zentralblatt. 1982;101(6):705-714

7. Bi J., Huang Y., Liu Y. Effect of NOP2 knockdown on colon cancer cell proliferation, migration, and invasion. Transl. Cancer Res. 2019; 8(6):2274-2283. DOI 10.21037/tcr.2019.09.46

8. Bustin S.A., Benes V., Garson J.A., Hellemans J., Huggett J., Kubista M., Mueller R., Nolan T., Pfaffl M.W., Shipley G.L., Vandesompele J., Wittwer C.T. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 2009;55(4):611-622. DOI 10.1373/clinchem.2008.112797

9. Carter C.S., Richardson A., Huffman D.M., Austad S. Bring back the rat! J. Gerontol. A Biol. Sci. Med. Sci. 2020;75(3):405-415. DOI 10.1093/gerona/glz298

10. Chadaeva I.V., Ponomarenko M.P., Rasskazov D.A., Sharypova E.B., Kashina E.V., Matveeva M.Y., Arshinova T.V., Ponomarenko P.M., Arkova O.V., Bondar N.P., Savinkova L.K., Kolchanov N.A. Candidate SNP markers of aggressiveness­related complications and co­ morbidities of genetic diseases are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters. BMC Genomics. 2016;17(Suppl.14):995. DOI 10.1186/s12864-016-3353­3

11. Chadaeva I., Ponomarenko P., Rasskazov D., Sharypova E., Kashina E., Kleshchev M., Ponomarenko M., Naumenko V., Savinkova L., Kolchanov N., Osadchuk L., Osadchuk A. Natural selection equally supports the human tendencies in subordination and domination: a genome­wide study with in silico confirmation and in vivo validation in mice. Front. Genet. 2019;10:73. DOI 10.3389/fgene.2019.00073

12. Chadaeva I., Ponomarenko P., Kozhemyakina R., Suslov V., Bogomolov A., Klimova N., Shikhevich S., Savinkova L., Oshchepkov D., Kolchanov N., Markel A., Ponomarenko M. Domestication explains two-thirds of differential-gene-expression variance between domestic and wild animals; the remaining one-third reflects intraspecific and interspecific variation. Animals. 2021;11(9):2667. DOI 10.3390/ani11092667

13. Choi J., Lee S., Won J., Jin Y., Hong Y., Hur T.Y., Kim J.H., Lee S.R., Hong Y. Pathophysiological and neurobehavioral characteristics of a propionic acid­mediated autism­like rat model. PLoS One. 2018; 13(2):e0192925. DOI 10.1371/journal.pone.0192925

14. Cucielo M.S., Cesario R.C., Silveira H.S., Gaiotte L.B., Dos Santos S.A.A., de Campos Zuccari D.A.P., Seiva F.R.F., Reiter R.J., de Almeida Chuffa L.G. Melatonin reverses the warburg-type metabolism and reduces mitochondrial membrane potential of ovarian cancer cells independent of MT1 receptor activation. Molecules. 2022;27(14):4350. DOI 10.3390/molecules27144350

15. Du H., Xiao G., Xue Z., Li Z., He S., Du X., Zhou Z., Cao L., Wang Y., Yang J., Wang X., Zhu Y. QiShenYiQi ameliorates salt-induced hypertensive nephropathy by balancing ADRA1D and SIK1 expression in Dahl salt­sensitive rats. Biomed. Pharmacother. 2021;141: 111941. DOI 10.1016/j.biopha.2021.111941

16. Fedoseeva L.A., Dymshits G.M., Markel A.L., Jakobson G.S. Renin system of the kidney in ISIAH rats with inherited stress-induced arterial hypertension. Bull. Exp. Biol. Med. 2009;147(2):177-180. DOI

17. 1007/s10517-009-0465-7

18. Fedoseeva L.A., Riazanova M.A., Antonov E.V., Dymshits G.M., Markel A.L. Expression of the renin angiotensin system genes in the kidney and heart of ISIAH hypertensive rats. Biochem. Moscow Suppl. Ser. B. 2011;5(1):37-43. DOI 10.1134/s1990750811010069

19. Fedoseeva L.A., Klimov L.O., Ershov N.I., Alexandrovich Y.V., Efimov V.M., Markel A.L., Redina O.E. Molecular determinants of the adrenal gland functioning related to stress­sensitive hypertension in ISIAH rats. BMC Genomics. 2016a;17(Suppl.14):989. DOI 10.1186/s12864-016-3354-2

20. Fedoseeva L.A., Ryazanova M.A., Ershov N.I., Markel A.L., Redina O.E. Comparative transcriptional profiling of renal cortex in rats with inherited stress­induced arterial hypertension and normotensive Wistar Albino Glaxo rats. BMC Genet. 2016b;17(Suppl.1):12. DOI 10.1186/s12863-015-0306-9

21. Fedoseeva L.A., Klimov L.O., Ershov N.I., Efimov V.M., Markel A.L., Orlov Y.L., Redina O.E. The differences in brain stem transcriptional profiling in hypertensive ISIAH and normotensive WAG rats. BMC Genomics. 2019;20(Suppl.3):297. DOI 10.1186/s12864-019-5540­5

22. Gaitanis J., Nie D., Hou T., Frye R. Developmental regression followed by epilepsy and aggression: a new syndrome in autism spectrum disorder? J. Pers. Med. 2023;13(7):1049. DOI 10.3390/jpm 13071049

23. Gayday E.A., Gayday D.S. Genetic diversity of experimental mice and rats: history of origin, methods of production and check. Laboratornye Zhivotnye Dlya Nauchnykh Issledovaniy = Laboratory Ani­ mals for Scientific Research. 2019;4:78-85. DOI 10.29296/2618723X-2019-04-09 (in Russian)

24. Gholami K., Loh S.Y., Salleh N., Lam S.K., Hoe S.Z. Selection of suitable endogenous reference genes for qPCR in kidney and hypothalamus of rats under testosterone influence. PLoS One. 2017;12(6): e0176368. DOI 10.1371/journal.pone.0176368

25. Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Soder­ gren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., … Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F; Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004;428(6982):493-521. DOI 10.1038/nature02426

26. Gonzalez-Arto M., Hamilton T.R., Gallego M., Gaspar-Torrubia E., Aguilar D., Serrano-Blesa E., Abecia J.A., Perez-Pe R., MuinoBlanco T., Cebrian-Perez J.A., Casao A. Evidence of melatonin synthesis in the ram reproductive tract. Andrology. 2016;4(1):163-171. DOI 10.1111/andr.12117

27. Govindarajulu M., Patel M.Y., Wilder D.M., Long J.B., Arun P. Blast exposure dysregulates nighttime melatonin synthesis and signaling in the pineal gland: a potential mechanism of blast­induced sleep disruptions. Brain Sci. 2022;12(10):1340. DOI 10.3390/brainsci12101340

28. Greenhouse D.D., Festing M.F.W., Hasan S., Cohen A.L. Inbred strains of rats and mutants. In: Hedrich H.J. (Ed.) Genetic Monitoring of Inbred Strains of Rats. Stuttgart: Gustav Fischer Verlag, 1990; 410­480

29. Gryksa K., Schmidtner A.K., Masís-Calvo M., Rodríguez-Villagra O.A., Havasi A., Wirobski G., Maloumby R., Jägle H., Bosch O.J., Slattery D.A., Neumann I.D. Selective breeding of rats for high (HAB) and low (LAB) anxiety-related behaviour: a unique model for comorbid depression and social dysfunctions. Neurosci. Biobehav. Rev. 2023;152:105292. DOI 10.1016/j.neubiorev.2023.105292

30. Gulevich R., Kozhemyakina R., Shikhevich S., Konoshenko M., Herbeck Y. Aggressive behavior and stress response after oxytocin administration in male Norway rats selected for different attitudes to humans. Physiol. Behav. 2019;199:210-218. DOI 10.1016/j.physbeh.2018.11.030

31. Herbeck Yu.E., Os’kina I.N., Gulevich R.G., Plyusnina I.Z. Effects of maternal methyl­supplemented diet on hippocampal glucocorticoid receptor mRNA expression in rats selected for behavior. Cytol. Genet. (Moscow.). 2010;44(2):108-113. DOI 10.3103/S0095452710020064

32. Ideno J., Mizukami H., Honda K., Okada T., Hanazono Y., Kume A., Saito T., Ishibashi S., Ozawa K. Persistent phenotypic correction of central diabetes insipidus using adeno-associated virus vector expressing arginine­vasopressin in Brattleboro rats. Mol. Ther. 2003; 8(6):895-902. DOI 10.1016/j.ymthe.2003.08.019

33. Ilchibaeva T.V., Kondaurova E.M., Tsybko A.S., Kozhemyakina R.V., Popova N.K., Naumenko V.S. Brain-derived neurotrophic factor (BDNF) and its precursor (proBDNF) in genetically defined fear-induced aggression. Behav. Brain Res. 2015;290:45-50. DOI 10.1016/j.bbr.2015.04.041

34. Ilchibaeva T.V., Tsybko A.S., Kozhemyakina R.V., Naumenko V.S. Expression of apoptosis genes in the brain of rats with genetically defined fear-induced aggression. Mol. Biol. (Moscow). 2016;50(5): 814-820. DOI 10.7868/S0026898416030071

35. Kang S., Gair S.L., Paton M.J., Harvey E.A. Racial and ethnic differences in the relation between parenting and preschoolers’ externalizing behaviors. Early Educ. Dev. 2023;34(4):823-841. DOI 10.1080/10409289.2022.2074202

36. Klimov L.O., Fedoseeva L.A., Ryazanova M.A., Dymshits G.M., Markel A.L. Expression of renin-angiotensin system genes in brain structures of ISIAH rats with stress-induced arterial hypertension. Bull. Exp. Biol. Med. 2013;154(3):357-660. DOI 10.1007/s10517-013-1950-6

37. Klimov L.O., Ershov N.I., Efimov V.M., Markel A.L., Redina O.E. Genome­wide transcriptome analysis of hypothalamus in rats with inherited stress­induced arterial hypertension. BMC Genet. 2016; 17(Suppl.1):13. DOI 10.1186/s12863-015-0307-8

38. Klimov L.O., Ryazanova M.A., Fedoseeva L.A., Markel A.L. Effects of brain renin-angiotensin system inhibition in ISIAH rats with inherited stress­induced arterial hypertension. Vavilovskii Zhur nal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2017; 21(6):735-741. DOI 10.18699/VJ17.29-o (in Russian)

39. Klimova N.V., Chadaeva I.V., Shichevich S.G., Kozhemyakina R.V. Differential expression of 10 genes in the hypothalamus of two generations of rats selected for a reaction to humans. Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2021;25(2):208-215. DOI 10.18699/VJ21.50-o

40. Kolosova N.G., Stefanova N.A., Korbolina E.E., Fursova A.Z., Kozhevnikova O.S. Senescence-accelerated OXYS rats: a genetic mo del of premature aging and age­related diseases. Adv. Gerontol. 2014;4:294-298. DOI 10.1134/S2079057014040146

41. Kolpakov V.G., Kulikov A.V., Alekhina T.A., Chuguy V.F., Petrenko O.I., Barykina N.N. Catatonia or depression: the GC rat strain as an animal model of psychopathology. Russ. J. Genet. 2004;40(6): 672-678. DOI 10.1023/B:RUGE.0000033315.79449.d4

42. Kondaurova E.M., Ilchibaeva T.V., Tsybko A.S., Kozhemyakina R.V., Popova N.K., Naumenko V.S. 5-HT1A receptor gene silencers Freud-1 and Freud-2 are differently expressed in the brain of rats with genetically determined high level of fear­induced aggression or its absence. Behav. Brain Res. 2016;310:20-25. DOI 10.1016/j.bbr.2016.04.050

43. Kozhevnikova O.S., Korbolina E.E., Ershov N.I., Kolosova N.G. Rat retinal transcriptome: effects of aging and AMD-like retinopathy. Cell Cycle. 2013;12(11):1745-1761. DOI 10.4161/cc.24825

44. Lau Y.F., Zhang J. Expression analysis of thirty one Y chromosome genes in human prostate cancer. Mol. Carcinog. 2000;27(4):308­321. DOI 10.1002/(sici)1098-2744(200004)27:4<308::aid-mc9>3.0.co;2-r

45. Li G., Lv D., Yao Y., Wu H., Wang J., Deng S., Song Y., Guan S., Wang L., Ma W., Yang H., Yan L., Zhang J., Ji P., Zhang L., Lian Z., Liu G. Overexpression of ASMT likely enhances the resistance of transgenic sheep to brucellosis by influencing immune-related signaling pathways and gut microbiota. FASEB J. 2021;35(9):e21783. DOI 10.1096/fj.202100651r

46. Li W., Wang X., Fan W., Zhao P., Chan Y.C., Chen S., Zhang S., Guo X., Zhang Y., Li Y., Cai J., Qin D., Li X., Yang J., Peng T., Zychlinski D., Hoffmann D., Zhang R., Deng K., Ng K.M., Menten B., Zhong M., Wu J., Li Z., Chen Y., Schambach A., Tse H.F., Pei D., Esteban M.A. Modeling abnormal early development with induced pluripotent stem cells from aneuploid syndromes. Hum. Mol. Genet. 2012;21(1):32-45. DOI 10.1093/hmg/ddr435

47. Liddelow S.A., Dziegielewska K.M., Ek C.J., Habgood M.D., Bauer H., Bauer H.C., Lindsay H., Wakefield M.J., Strazielle N., Kratzer I., Mollgard K., Ghersi-Egea J.F., Saunders N.R. Mechanisms that determine the internal environment of the developing brain: a transcriptomic, functional and ultrastructural approach. PLoS One. 2013;8(7):e65629. DOI 10.1371/journal.pone.0065629

48. Liu W., Huang Z., Xia J., Cui Z., Li L., Qi Z., Liu W. Gene expression profile associated with Asmt knockout-induced depression-like behaviors and exercise effects in mouse hypothalamus. Biosci. Rep. 2022;42(7):bsr20220800. DOI 10.1042/bsr20220800

49. Liu X., Zhan Y., Xu W., Liu L., Liu X., Da J., Zhang K., Zhang X., Wang J., Liu Z., Jin H., Zhang B., Li Y. Characterization of transcriptional landscape in bone marrow­derived mesenchymal stromal cells treated with aspirin by RNA­seq. PeerJ. 2022;10:e12819. DOI 10.7717/peerj.12819

50. Liu Y., Xiang J., Liao Y., Peng G., Shen C. Identification of tryptophan metabolic gene­related subtypes, development of prognostic models, and characterization of tumor microenvironment infiltration in gliomas. Front. Mol. Neurosci. 2022;15:1037835. DOI 10.3389/fnmol.2022.1037835

51. Lu Z. PubMed and Beyond: A Survey of Web Tools for Searching Biomedical Literature. Database (Oxford). 2011;2011:baq036. DOI 10.1093/database/baq036

52. Lv J.W., Zheng Z.Q., Wang Z.X., Zhou G.Q., Chen L., Mao Y.P., Lin A.H., Reiter R.J., Ma J., Chen Y.P., Sun Y. Pan-cancer genomic analyses reveal prognostic and immunogenic features of the tumor melatonergic microenvironment across 14 solid cancer types. J. Pi­ neal Res. 2019;66(3):e12557. DOI 10.1111/jpi.12557

53. Markel A.L. Development of a new strain of rats with inherited stressinduced arterial hypertension. In: Sassard J. (Ed.) Genetic Hypertension. London: John Libbey Eurotext Ltd., 1992;218:405-407

54. Markel A.L., Maslova L.N., Shishkina G.T., Mahanova N.A., Jacobson G.S. Developmental influences on blood pressure regulation in ISIAH rats. In: McCarty R., Blizard D.A., Chevalier R.L. (Eds.) Development of the Hypertensive Phenotype: Basic and Clinical Studies. In the series Handbook of Hypertension. Amsterdam: Elsevier, 1999;493-526

55. Martín-Carro B., Donate-Correa J., Fernández-Villabrille S., MartínVírgala J., Panizo S., Carrillo-López N., Martínez-Arias L., Navarro-González J.F., Naves-Díaz M., Fernández-Martín J.L., Alonso-Montes C., Cannata-Andía J.B. Experimental models to study diabetes mellitus and its complications: limitations and new opportunities. Int. J. Mol. Sci. 2023;24(12):10309. DOI 10.3390/ijms 241210309

56. Melke J., Goubran Botros H., Chaste P., Betancur C., Nygren G., Anckar säter H., Rastam M., Ståhlberg O., Gillberg I.C., Delorme R., Chabane N., Mouren­Simeoni M.C., Fauchereau F., Durand C.M., Chevalier F., Drouot X., Collet C., Launay J.M., Leboyer M., Gillberg C., Bourgeron T. Abnormal melatonin synthesis in autism spectrum disorders. Mol. Psychiatry. 2008;13(1):90-98. DOI 10.1038/sj.mp.4002016

57. Modlinska K., Pisula W. The Norway rat, from an obnoxious pest to a laboratory pet. eLife. 2020;9:e50651. DOI 10.7554/eLife.50651

58. Moskaliuk V.S., Kozhemyakina R.V., Bazovkina D.V., Terenina E., Khomenko T.M., Volcho K.P., Salakhutdinov N.F., Kulikov A.V., Naumenko V.S., Kulikova E. On an association between fear-induced aggression and striatal­enriched protein tyrosine phosphatase (STEP) in the brain of Norway rats. Biomed. Pharmacother. 2022; 147:112667. DOI 10.1016/j.biopha.2022.112667

59. Moskaliuk V.S., Kozhemyakina R.V., Khomenko T.M., Volcho K.P., Salakhutdinov N.F., Kulikov A.V., Naumenko V.S., Kulikova E.A. On associations between fear-induced aggression, Bdnf transcripts, and serotonin receptors in the brains of Norway rats: an influence of antiaggressive drug TC­2153. Int. J. Mol. Sci. 2023;24(2):983. DOI 10.3390/ijms24020983

60. Naumenko V.S., Kozhemjakina R.V., Plyusnina I.Z., Popova N.K. Expression of serotonin transporter gene and startle response in rats with genetically determined fear­induced aggression. Bull. Exp. Biol. Med. 2009;147(1):81-83. DOI 10.1007/s10517-009-0441-2

61. Oshchepkov D., Ponomarenko M., Klimova N., Chadaeva I., Bragin A., Sharypova E., Shikhevich S., Kozhemyakina R. A rat model of human behavior provides evidence of natural selection against underexpression of aggressiveness-related genes in humans. Front. Genet. 2019;10:1267. DOI 10.3389/fgene.2019.01267

62. Oshchepkov D., Chadaeva I., Kozhemyakina R., Zolotareva K., Khandaev B., Sharypova E., Ponomarenko P., Bogomolov A., Klimova N.V., Shikhevich S., Redina O., Kolosova N.G., Nazarenko M., Kolchanov N.A., Markel A., Ponomarenko M. Stress reactivity, susceptibility to hypertension, and differential expression of genes in hypertensive compared to normotensive patients. Int. J. Mol. Sci. 2022a;23(5):2835. DOI 10.3390/ijms23052835

63. Oshchepkov D., Chadaeva I., Kozhemyakina R., Shikhevich S., Sharypova E., Savinkova L., Klimova N.V., Tsukanov A., Levitsky V.G., Markel A.L. Transcription factors as important regulators of changes in behavior through domestication of gray rats: quantitative data from RNA sequencing. Int. J. Mol. Sci. 2022b;23(20):12269. DOI 10.3390/ijms232012269

64. Paxinos G., Watson C. The Rat Brain in Stereotaxic Coordinates. London: Acad. Press, Elsevier Inc., 2013. Penning L.C., Vrieling H.E., Brinkhof B., Riemers F.M., Rothuizen J., Rutteman G.R., Hazewinkel H.A. A validation of 10 feline reference genes for gene expression measurements in snap-frozen tissues. Vet. Immunol. Immunopathol. 2007;120(3-4):212-222. DOI 10.1016/j.vetimm.2007.08.006

65. Perepechaeva M.L., Grishanova A.Y., Rudnitskaya E.A., Kolosova N.G. The mitochondria-targeted antioxidant SkQ1 downregulates aryl hydrocarbon receptor-dependent genes in the retina of OXYS rats with AMD­like retinopathy. J. Ophthalmol. 2014;2014:530943. DOI 10.1155/2014/530943

66. Popova N.K., Naumenko V.S., Plyusnina I.Z. Involvement of brain serotonin 5-HT1A receptors in genetic predisposition to aggressive behavior. Neurosci. Behav. Physiol. 2007;37(6):631-635. DOI

67. Plekanchuk V.S., Ryazanova M.A. Expression of glutamate receptor genes in the hippocampus and frontal cortex in GC rat strain with genetic catatonia. J. Evol. Biochem. Phys. 2021;57(1):156-163. DOI 10.1134/S0022093021010154

68. Plyusnina I., Oskina I. Behavioral and adrenocortical responses to open-field test in rats selected for reduced aggressiveness toward humans. Physiol. Behav. 1997;61(3):381-385. DOI 10.1016/S0031-9384(96)00445-310.1007/s11055-007-0062-z

69. Popova N.K., Naumenko V.S., Kozhemyakina R.V., Plyusnina I.Z. Functional characteristics of serotonin 5-HT2A and 5-HT2C receptors in the brain and the expression of the 5-HT2A and 5-HT2C receptor genes in aggressive and non­aggressive rats. Neurosci. Behav. Physiol. 2010;40(4):357-361. DOI 10.1007/s11055-010-9264-x

70. Ryazanova M.A., Fedoseeva L.A., Ershov N.I., Efimov V.M., Markel A.L., Redina O.E. The gene-expression profile of renal medulla in ISIAH rats with inherited stress-induced arterial hyperten sion. BMC Genet. 2016;17(Suppl.3):151. DOI 10.1186/s12863-016-0462-6

71. Ryazanova M.A., Prokudina O.I., Plekanchuk V.S., Alekhina T.A. Expression of catecholaminergic genes in the midbrain and prepulse inhibition in rats with a genetic catatonia. Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2017;21(7): 798-803. DOI 10.18699/VJ17.296 (in Russian)

72. Ryazanova M.A., Plekanchuk V.S., Prokudina O.I., Makovka Y.V., Alekhina T.A., Redina O.E., Markel A.L. Animal models of hypertension (ISIAH rats), catatonia (GC rats), and audiogenic epilepsy (PM rats) developed by breeding. Biomedicines. 2023;11(7):1814. DOI 10.3390/biomedicines11071814

73. Sengupta P. The laboratory rat: relating its age with human’s. Int. J. Prev. Med. 2013;4(6):624-630

74. Schmidt I. Metabolic diseases: the environment determines the odds, even for genes. News Physiol. Sci. 2002;17:115-121. DOI 10.1152/nips.01380.2001

75. Shikhevich S., Chadaeva I., Khandaev B., Kozhemyakina R., Zolotareva K., Kazachek A., Oshchepkov D., Bogomolov A., Klimova N.V., Ivanisenko V.A., Demenkov P., Mustafin Z., Markel A., Savinkova L., Kolchanov N.A., Kozlov V., Ponomarenko M. Differentially expressed genes and molecular susceptibility to human agerelated diseases. Int. J. Mol. Sci. 2023;24(4):3996. DOI 10.3390/ijms24043996

76. Singh G., Bhat B., Jayadev M.S.K., Madhusudhan C., Singh A. mutTCPdb: a comprehensive database for genomic variants of a tropical country neglected disease-tropical calcific pancreatitis. Database (Oxford ). 2018;2018:bay043. DOI 10.1093/database/bay043

77. Stefanova N.A., Kolosova N.G. The rat brain transcriptome: from infancy to aging and sporadic Alzheimer’s disease­like pathology. Int. J. Mol. Sci. 2023;24(2):1462. DOI 10.3390/ijms24021462

78. Stefanova N.A., Maksimova K.Y., Rudnitskaya E.A., Muraleva N.A., Kolosova N.G. Association of cerebrovascular dysfunction with the development of Alzheimer’s disease-like pathology in OXYS rats. BMC Genomics. 2018;19(Suppl.3):75. DOI 10.1186/s12864-0184480­9

79. Stefanova N.A., Ershov N.I., Maksimova K.Y., Muraleva N.A., Tyumentsev M.A., Kolosova N.G. The rat prefrontal-cortex transcriptome: effects of aging and sporadic Alzheimer’s disease-like pathology. J. Gerontol. A Biol. Sci. Med. Sci. 2019;74(1):33-43. DOI 10.1093/gerona/gly198

80. Stelzer G., Rosen N., Plaschkes I., Zimmerman S., Twik M., Fishilevich S., Stein T.I., Nudel R., Lieder I., Mazor Y., Kaplan S., Dahary D., Warshawsky D., Guan-Golan Y., Kohn A., Rappaport N., Safran M., Lancet D. The GeneCards suite: from gene data mining to disease genome sequence analyses. Curr. Protoc. Bioinformatics. 2016;54:1.30.1-1.30.33. DOI 10.1002/cpbi.5

81. Stenson P.D., Mort M., Ball E.V., Shaw K., Phillips A., Cooper D.N. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum. Genet. 2014;133(1):1­9. DOI 10.1007/s00439-013-1358-4

82. Sun S., Wang Y., Maslov A.Y., Dong X., Vijg J. SomaMutDB: a database of somatic mutations in normal human tissues. Nucleic Acids Res. 2022;50(D1):D1100-D1108. DOI 10.1093/nar/gkab914

83. Suzuki H., Han S.D., Lucas L.R. Increased 5-HT1B receptor density in the basolateral amygdala of passive observer rats exposed to aggression. Brain Res. Bull. 2010;83(1-2):38-43. DOI 10.1016/j.brainresbull.2010.06.007

84. Tain Y.L., Huang L.T., Chan J.Y., Lee C.T. Transcriptome analysis in rat kidneys: importance of genes involved in programmed hypertension. Int. J. Mol. Sci. 2015;16(3):4744-4758. DOI 10.3390/ijms16034744

85. Talarowska M., Szemraj J., Zajączkowska M., Galecki P. ASMT gene expression correlates with cognitive impairment in patients with recurrent depressive disorder. Med. Sci. Monit. 2014;20:905-912. DOI 10.12659/MSM.890160

86. Taylor J.R., Morshed S.A., Parveen S., Mercadante M.T., Scahill L., Peterson B.S., King R.A., Leckman J.F., Lombroso P.J. An animal model of Tourette’s syndrome. Am. J. Psychiatry. 2002;159(4):657-660. DOI 10.1176/appi.ajp

87. Tharmalingam S., Khurana S., Murray A., Lamothe J., Tai T.C. Whole transcriptome analysis of adrenal glands from prenatal glucocorticoid programmed hypertensive rodents. Sci. Rep. 2020;10(1): 18755. DOI 10.1038/s41598-020-75652-y

88. Trent S., Dean R., Veit B., Cassano T., Bedse G., Ojarikre O.A., Humby T., Davies W. Biological mechanisms associated with increased perseveration and hyperactivity in a genetic mouse model of neurodevelopmental disorder. Psychoneuroendocrinology. 2013; 38(8):1370-1380. DOI 10.1016/j.psyneuen.2012.12.002

89. Wall V.L., Fischer E.K., Bland S.T. Isolation rearing attenuates social interaction-induced expression of immediate early gene protein products in the medial prefrontal cortex of male and female rats. Physiol. Behav. 2012;107(3):440-450. DOI 10.1016/j.physbeh.2012.09.002

90. Watanabe Y., Yoshida M., Yamanishi K., Yamamoto H., Okuzaki D., No jima H., Yasunaga T., Okamura H., Matsunaga H., Yamanishi H. Genetic analysis of genes causing hypertension and stroke in spontaneously hypertensive rats: gene expression profiles in the kidneys. Int. J. Mol. Med. 2015;36(3):712-724. DOI 10.3892/ijmm.2015. 2281

91. Wu H.M., Zhao C.C., Xie Q.M., Xu J., Fei G.H. TLR2-melatonin feedback loop regulates the activation of NLRP3 inflammasome in murine allergic airway inflammation. Front. Immunol. 2020;11:172.

92. DOI 10.3389/fimmu.2020.00172

93. Xiao G., Wang T., Zhuang W., Ye C., Luo L., Wang H., Lian G., Xie L. RNA sequencing analysis of monocrotaline-induced PAH reveals dysregulated chemokine and neuroactive ligand receptor pathways. Aging (Albany NY ). 2020;12(6):4953-4969. DOI 10.18632/aging.102922

94. Xie F., Wang L., Liu Y., Liu Z., Zhang Z., Pei J., Wu Z., Zhai M., Cao Y. ASMT regulates tumor metastasis through the circadian clock system in triple­negative breast cancer. Front. Oncol. 2020;10:537247. DOI 10.3389/fonc.2020.537247

95. Yang H., Zhang Z., Ding X., Jiang X., Tan L., Lin C., Xu L., Li G., Lu L., Qin Z., Feng X., Li M. RP58 knockdown contributes to hypoxia-ischemia-induced pineal dysfunction and circadian rhythm disruption in neonatal rats. J. Pineal Res. 2023;75(1):e12885. DOI 10.1111/jpi.12885

96. Ye J., Coulouris G., Zaretskaya I., Cutcutache I., Rozen S., Madden T.L. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics. 2012;13:134. DOI 10.1186/1471-2105-13-134

97. Yoshida M., Watanabe Y., Yamanishi K., Yamashita A., Yamamoto H., Okuzaki D., Shimada K., Nojima H., Yasunaga T., Okamura H., Matsunaga H., Yamanishi H. Analysis of genes causing hypertension and stroke in spontaneously hypertensive rats: gene expression profiles in the brain. Int. J. Mol. Med. 2014;33(4):887-896. DOI 10.3892/ijmm.2014.1631

98. Yuan X., Wu Q., Liu X., Zhang H., Xiu R. Transcriptomic profile analysis of brain microvascular pericytes in spontaneously hypertensive rats by RNA­Seq. Am. J. Transl. Res. 2018;10(8):2372-2386. PMID 30210677

99. Zhang H.F., Wang J.H., Wang Y.L., Gao C., Gu Y.T., Huang J., Wang J.H., Zhang Z. Salvianolic acid A protects the kidney against oxidative stress by activating the Akt/GSK-3β/Nrf2 signaling pathway and inhibiting the NF-κB signaling pathway in 5/6 nephrectomized rats. Oxid. Med. Cell. Longev. 2019;2019:2853534. DOI 10.1155/2019/2853534

100. Zhang Z., Silveyra E., Jin N., Ribelayga C.P. A congenic line of the C57BL/6J mouse strain that is proficient in melatonin synthesis. J. Pineal Res. 2018;65(3):e12509. DOI 10.1111/jpi.12509