A bioinformatics model of human diseases on the basis of differentially expressed genes (Of domestic versus wild animals) that are orthologs of human genes associated with reproductive‐potential changes

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A bioinformatics model of human diseases on the basis of differentially expressed genes (Of domestic versus wild animals) that are orthologs of human genes associated with reproductive‐potential changes. / Vasiliev, Gennady; Chadaeva, Irina; Rasskazov, Dmitry и др.

в: International Journal of Molecular Sciences, Том 22, № 5, 2346, 01.03.2021, стр. 1-17.

Результаты исследований: Научные публикации в периодических изданиях › статья › Рецензирование

BibTeX

@article{eaf648ad2738402eafd43b558d224899,

title = "A bioinformatics model of human diseases on the basis of differentially expressed genes (Of domestic versus wild animals) that are orthologs of human genes associated with reproductive‐potential changes",

abstract = "Earlier, after our bioinformatic analysis of single‐nucleotide polymorphisms of TATA-binding protein‐binding sites within gene promoters on the human Y chromosome, we suggested that human reproductive potential diminishes during self‐domestication. Here, we implemented bioinformatics models of human diseases using animal in vivo genome‐wide RNA‐Seq data to com-pare the effect of co‐directed changes in the expression of orthologous genes on human reproductive potential and during the divergence of domestic and wild animals from their nearest common an-cestor (NCA). For example, serotonin receptor 3A (HTR3A) deficiency contributes to sudden death in pregnancy, consistently with Htr3a underexpression in guinea pigs (Cavia porcellus) during their divergence from their NCA with cavy (C. aperea). Overall, 25 and three differentially expressed genes (hereinafter, DEGs) in domestic animals versus 11 and 17 DEGs in wild animals show the direction consistent with human orthologous gene‐markers of reduced and increased reproductive potential. This indicates a reliable association between DEGs in domestic animals and human orthologous genes reducing reproductive potential (Pearson{\textquoteright}s χ2 test p < 0.001, Fisher{\textquoteright}s exact test p <0.05, binomial distribution p < 0.0001), whereas DEGs in wild animals uniformly match human orthologous genes decreasing and increasing human reproductive potential (p > 0.1; binomial dis-tribution), thus enforcing the norm (wild type).",

keywords = "Animal model of human disease, Differentially expressed gene, Domestication, In vivo verifi-cation, Reproductive potential, RNA‐seq",

author = "Gennady Vasiliev and Irina Chadaeva and Dmitry Rasskazov and Petr Ponomarenko and Ekaterina Sharypova and Irina Drachkova and Anton Bogomolov and Ludmila Savinkova and Mikhail Ponomarenko and Nikolay Kolchanov and Alexander Osadchuk and Dmitry Oshchepkov and Ludmila Osadchuk",

note = "Funding Information: Manuscript writing was supported by Russian government project #0259?2021?0009 (for M.P.). The data curation was supported by project #28.12487.2018/12.1 from the Ministry of Science and Higher Education of the Russian Federation (for G.V.). The conceptualization and supervision of the investigation were supported by the Russian Federal Science & Technology Program for the Development of Genetic Technologies (for N.K., D.R., P.P., I.C., E.S., I.D., L.S., and D.O.). The methodology and software development were supported by project #19?15?00075 from the Russian Science Foundation (for A.O., L.O., and A.B.). We are grateful to Nikolai Shevchuk (Shevchuk Editing Co., Brooklyn, NY, USA) for useful discussions of the work and assistance in adapting it to the requirements of the English language for scientific publications. Publisher Copyright: {\textcopyright} 2021 by the author. Licensee MDPI, Basel, Switzerland. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

year = "2021",

month = mar,

day = "1",

doi = "10.3390/ijms22052346",

language = "English",

volume = "22",

pages = "1--17",

journal = "International Journal of Molecular Sciences",

issn = "1661-6596",

publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",

number = "5",

}

RIS

TY - JOUR

T1 - A bioinformatics model of human diseases on the basis of differentially expressed genes (Of domestic versus wild animals) that are orthologs of human genes associated with reproductive‐potential changes

AU - Vasiliev, Gennady

AU - Chadaeva, Irina

AU - Rasskazov, Dmitry

AU - Ponomarenko, Petr

AU - Sharypova, Ekaterina

AU - Drachkova, Irina

AU - Bogomolov, Anton

AU - Savinkova, Ludmila

AU - Ponomarenko, Mikhail

AU - Kolchanov, Nikolay

AU - Osadchuk, Alexander

AU - Oshchepkov, Dmitry

AU - Osadchuk, Ludmila

N1 - Funding Information: Manuscript writing was supported by Russian government project #0259?2021?0009 (for M.P.). The data curation was supported by project #28.12487.2018/12.1 from the Ministry of Science and Higher Education of the Russian Federation (for G.V.). The conceptualization and supervision of the investigation were supported by the Russian Federal Science & Technology Program for the Development of Genetic Technologies (for N.K., D.R., P.P., I.C., E.S., I.D., L.S., and D.O.). The methodology and software development were supported by project #19?15?00075 from the Russian Science Foundation (for A.O., L.O., and A.B.). We are grateful to Nikolai Shevchuk (Shevchuk Editing Co., Brooklyn, NY, USA) for useful discussions of the work and assistance in adapting it to the requirements of the English language for scientific publications. Publisher Copyright: © 2021 by the author. Licensee MDPI, Basel, Switzerland. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2021/3/1

Y1 - 2021/3/1

N2 - Earlier, after our bioinformatic analysis of single‐nucleotide polymorphisms of TATA-binding protein‐binding sites within gene promoters on the human Y chromosome, we suggested that human reproductive potential diminishes during self‐domestication. Here, we implemented bioinformatics models of human diseases using animal in vivo genome‐wide RNA‐Seq data to com-pare the effect of co‐directed changes in the expression of orthologous genes on human reproductive potential and during the divergence of domestic and wild animals from their nearest common an-cestor (NCA). For example, serotonin receptor 3A (HTR3A) deficiency contributes to sudden death in pregnancy, consistently with Htr3a underexpression in guinea pigs (Cavia porcellus) during their divergence from their NCA with cavy (C. aperea). Overall, 25 and three differentially expressed genes (hereinafter, DEGs) in domestic animals versus 11 and 17 DEGs in wild animals show the direction consistent with human orthologous gene‐markers of reduced and increased reproductive potential. This indicates a reliable association between DEGs in domestic animals and human orthologous genes reducing reproductive potential (Pearson’s χ2 test p < 0.001, Fisher’s exact test p <0.05, binomial distribution p < 0.0001), whereas DEGs in wild animals uniformly match human orthologous genes decreasing and increasing human reproductive potential (p > 0.1; binomial dis-tribution), thus enforcing the norm (wild type).

AB - Earlier, after our bioinformatic analysis of single‐nucleotide polymorphisms of TATA-binding protein‐binding sites within gene promoters on the human Y chromosome, we suggested that human reproductive potential diminishes during self‐domestication. Here, we implemented bioinformatics models of human diseases using animal in vivo genome‐wide RNA‐Seq data to com-pare the effect of co‐directed changes in the expression of orthologous genes on human reproductive potential and during the divergence of domestic and wild animals from their nearest common an-cestor (NCA). For example, serotonin receptor 3A (HTR3A) deficiency contributes to sudden death in pregnancy, consistently with Htr3a underexpression in guinea pigs (Cavia porcellus) during their divergence from their NCA with cavy (C. aperea). Overall, 25 and three differentially expressed genes (hereinafter, DEGs) in domestic animals versus 11 and 17 DEGs in wild animals show the direction consistent with human orthologous gene‐markers of reduced and increased reproductive potential. This indicates a reliable association between DEGs in domestic animals and human orthologous genes reducing reproductive potential (Pearson’s χ2 test p < 0.001, Fisher’s exact test p <0.05, binomial distribution p < 0.0001), whereas DEGs in wild animals uniformly match human orthologous genes decreasing and increasing human reproductive potential (p > 0.1; binomial dis-tribution), thus enforcing the norm (wild type).

KW - Animal model of human disease

KW - Differentially expressed gene

KW - Domestication

KW - In vivo verifi-cation

KW - Reproductive potential

KW - RNA‐seq

UR - http://www.scopus.com/inward/record.url?scp=85101526363&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/e6bd1e57-d7ef-3a53-a54d-a8139628cfdd/

U2 - 10.3390/ijms22052346

DO - 10.3390/ijms22052346

M3 - Article

C2 - 33652917

AN - SCOPUS:85101526363

VL - 22

SP - 1

EP - 17

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 5

M1 - 2346

ER -

ID: 28014086