TY - JOUR

T1 - MiceDEGdb: a knowledge base on differentially expressed mouse genes as a model object in biomedical research

AU - Podkolodnaya, O. A.

AU - Chadaeva, I. V.

AU - Filonov, S. V.

AU - Podkolodnyy, N. L.

AU - Rasskazov, D. A.

AU - Tverdokhleb, N. N.

AU - Zolotareva, K. A.

AU - Bogomolov, A. G.

AU - Kondratyuk, E. Yu

AU - Oshchepkov, D. Yu

AU - Ponomarenko, M. P.

N1 - The work was supported by State Budget Projects FWNR-2022-0020 and FWNM-2025-0005. Authors express their gratitude to the multi-access center Bioinformatics for access to computational resources.

PY - 2025

Y1 - 2025

N2 - The fundamental understanding of many biological processes that unfold in a human body has become possible due to experimental studies on animal models. The backbone of modern biomedical research is the use of mouse models for studying important pathophysiological mechanisms, assessing new therapeutic approaches and making decisions on acceptance or rejection of new candidate medicines in preclinical trials. The use of mice is advantageous because they have small size, are easy to keep and to genetically modify. Mice make up more than 90 % of the rodents used for pharmaceutical research. We present the pilot version of MiceDEGdb, a knowledge base on the genes that are differentially expressed in the mouse used as a model object in biomedical research. MiceDEGdb is a collection of published data on gene expression in mouse strains used for studying age-related diseases, such as hypertension, periodontal disease, bone fragility, renal fibrosis, smooth muscle remodeling, heart failure and circadian rhythm disorder. The pilot release of MiceDEGdb contains 21,754 DEGs representing 9,769 unique Mus musculus genes the transcription levels whereof were found as being changed in 25 RNA-seq experiments involving eight tissues – gum, bone, kidney, right ventricle, aortic arch, hippocampus, skeletal muscle and uterus – in six genetic mouse strains (C57BL/6J, Ren1cCre|ZsGreen, B6.129S7(Cg)-Polgtm1Prol/J, BPN/3J, BPH/2J and Kunming) used as models of eight human diseases – all these data were based on information in 10 original articles. MiceDEGdb is novel in that it features a curated annotation of changes in the expression levels of mouse DEGs using independent biomedical publications about same-direction changes in the expression levels of human homologs in patients with one disease or the other. In its pilot release, MiceDEGdb documented 85,092 such annotations for 318 human genes in 895 diseases, as suggest to 912 scientific articles referenced by their PubMed ID. The information contained in MiceDEGdb may be of interest to geneticists, molecular biologists, bioinformatics scientists, clinicians, pharmacologists and genetic advisors in personalized medicine. MiceDEGdb is freely available at https://www.sysbio.ru/MiceDEGdb.

AB - The fundamental understanding of many biological processes that unfold in a human body has become possible due to experimental studies on animal models. The backbone of modern biomedical research is the use of mouse models for studying important pathophysiological mechanisms, assessing new therapeutic approaches and making decisions on acceptance or rejection of new candidate medicines in preclinical trials. The use of mice is advantageous because they have small size, are easy to keep and to genetically modify. Mice make up more than 90 % of the rodents used for pharmaceutical research. We present the pilot version of MiceDEGdb, a knowledge base on the genes that are differentially expressed in the mouse used as a model object in biomedical research. MiceDEGdb is a collection of published data on gene expression in mouse strains used for studying age-related diseases, such as hypertension, periodontal disease, bone fragility, renal fibrosis, smooth muscle remodeling, heart failure and circadian rhythm disorder. The pilot release of MiceDEGdb contains 21,754 DEGs representing 9,769 unique Mus musculus genes the transcription levels whereof were found as being changed in 25 RNA-seq experiments involving eight tissues – gum, bone, kidney, right ventricle, aortic arch, hippocampus, skeletal muscle and uterus – in six genetic mouse strains (C57BL/6J, Ren1cCre|ZsGreen, B6.129S7(Cg)-Polgtm1Prol/J, BPN/3J, BPH/2J and Kunming) used as models of eight human diseases – all these data were based on information in 10 original articles. MiceDEGdb is novel in that it features a curated annotation of changes in the expression levels of mouse DEGs using independent biomedical publications about same-direction changes in the expression levels of human homologs in patients with one disease or the other. In its pilot release, MiceDEGdb documented 85,092 such annotations for 318 human genes in 895 diseases, as suggest to 912 scientific articles referenced by their PubMed ID. The information contained in MiceDEGdb may be of interest to geneticists, molecular biologists, bioinformatics scientists, clinicians, pharmacologists and genetic advisors in personalized medicine. MiceDEGdb is freely available at https://www.sysbio.ru/MiceDEGdb.

KW - DEG

KW - RNA-seq

KW - age frustration

KW - circadian rhythm

KW - infectious diseases

KW - knowledge base

KW - mouse Mus musculus

KW - mouse models of disease

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-86000576057&origin=inward&txGid=b1555bb5d55815cc5ee762907789c20c

UR - https://www.mendeley.com/catalogue/68f32615-aea3-3fb2-ba54-7c64b504e0e0/

U2 - 10.18699/vjgb-25-18

DO - 10.18699/vjgb-25-18

M3 - Article

VL - 29

SP - 153

EP - 161

JO - Вавиловский журнал генетики и селекции

JF - Вавиловский журнал генетики и селекции

SN - 2500-0462

IS - 1

ER -