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BioTreasury:a community-based repository enabling indexing and rating of bioinformatics tools

Science China(Life Sciences) 2024年第2期67卷 221-229页

作者： Qi Zhao Xin Zhou Jingxing Wu Jieyi Cai Xiaoqiong Bao Lin Tang Chaoye Wang Chunlei Liu Yukai Wang Yuyan Teng Mohan Zheng Weiping Mu Zhixiang Zuo Yubin Xie Xiaotong Luo Jian Ren School of Life Sciences State Key Laboratory of Oncology in South ChinaCancer CenterGuangdong Provincial Clinical Research Center for CancerSun Yat-sen UniversityGuangzhou 510060China Institute of Precision Medicine The First Affiliated HospitalSun Yat-sen UniversityGuangzhou 510080China Guangdong Institute of Gastroenterology Department of General SurgeryGuangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat-sen UniversityGuangzhou 510275China

The exponential growth of bioinformatics tools in recent years has posed challenges for scientists in selecting the most suitable one for their data analysis ***,to aid scientists in making informed choices,a community-based platform that indexes and rates bioinformatics tools is urgently *** this study,we introduce Bio Treasury(http://***),an integrated communitybased repository that provides an interactive platform for users and developers to share their experiences in various bioinformatics *** Treasury offers a comprehensive collection of well-indexed bioinformatics software,tools,and databases,totaling over 10,000 *** the past two years,we have continuously improved and maintained Bio Treasury,adding several exciting features,including creating structured homepages for every tool and user,a hierarchical category of bioinformatics tools and classifying tools using large language model(LLM).Bio Treasury streamlines the tool submission process with intelligent ***,Bio Treasury provides a wide range of social features,for example,enabling users to participate in interactive discussions,rate tools,build and share tool collections for the *** believe Bio Treasury can be a valuable resource and knowledge-sharing platform for the biomedical *** empowers researchers to effectively discover and evaluate bioinformatics tools,fostering collaboration and advancing bioinformatics research.

关键词： bioinformatics tools index tool database rating system large language model tool collections shari

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Network analyses:Inhibition of androgen receptor signaling reduces inflammation in the lung through AR-MAF-IL6 signaling axes

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Genes & Diseases 2024年第3期11卷 140-143页

作者： Albert R.Wang Andrew M.Baschnagel Zijian Ni Sean R.Brennan Hypatia K.Newton Darya Buehler Christina Kendziorski Randall J.Kimple Gopal lyer Department of Human Oncology University of Wisconsin School of Medicine and Public HealthUniversity of WisconsinMadisonWI 53705USA Department of Biomedical Engineering University of Wisconsin-MadisonMadisonWI 53705USA University of Wisconsin Carbone Cancer center MadisonWI 53705USA Department of biostatistics and Medical Informatics University of Wisconsin-MadisonMadisonWI 53706USA Department of Biology Tufts UniversityMedfordMA 02155USA Department of Pathology and Laboratory Medicine University of Wisconsin School of Medicine and Public HealthUniversity of WisconsinMadisonWI 53705USA

Androgen receptor(AR)is a major transcription factor that plays a role in inflammatory response including interleukin-6(IL6)signaling.1 While AR regulation through paracrine loop signaling in prostate tissue is well-studied,its impact through an IL6 autocrine loop in the lung has not been wellstudied despite the organ's response to respiratory viral *** inhibition and RNA knockdown of AR identified a bZIP transcription factor MAF to be a common target of inflammation using these perturbations in lung cells.

关键词： inflammation lung respiratory

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MicroRNAs in thyroid cancer with focus on medullary thyroid carcinoma:potential therapeutic targets and diagnostic/prognostic markers and web based tools

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Oncology research 2024年第6期32卷 1011-1019页

作者： ELHAM SHAKIBA SETI BOROOMAND SIMA KHERADMAND KIA MEHDI HEDAYATI Department of Biochemistry Faculty of Biological SciencesNorth Tehran BranchIslamic Azad UniversityTehran***Iran Department of Pathology and Laboratory Medicine Vancouver General HospitalVancouverV5Z 1M9Canada Department of Blood Cell research Laboratory for Red Blood Cell DiagnosticsSanquinAmsterdam1006 ANThe Netherlands Cellular and Molecular Endocrine research center Research Institute for Endocrine SciencesShahid Beheshti University of Medical SciencesTehran***Iran

This review aimed to describe the inculpation of microRNAs(miRNAs)in thyroid cancer(TC)and its subtypes,mainly medullary thyroid carcinoma(MTC),and to outline web-based tools and databases for bioinformatics analysis of miRNAs in ***,the capacity of miRNAs to serve as therapeutic targets and biomarkers in TC management will be *** review is based on a literature search of relevant articles on the role of miRNAs in TC and its subtypes,mainly ***,web-based tools and databases for bioinformatics analysis of miRNAs in TC were identified and *** can perform as oncomiRs or antioncoges,relying on the target mRNAs they *** replacement therapy using miRNA mimics or antimiRs that aim to suppress the function of certain miRNAs can be applied to correct miRNAs aberrantly expressed in diseases,particularly in *** are involved in the modulation of fundamental pathways related to cancer,resembling cell cycle checkpoints and DNA repair *** are also rather stable and can reliably be detected in different types of biological materials,rendering them favorable diagnosis and prognosis biomarkers as *** have emerged as promising tools for evaluating medical outcomes in TC and as possible therapeutic *** contribution of miRNAs in thyroid cancer,particularly MTC,is an active area of research,and the utility of web applications and databases for the biological data analysis of miRNAs in TC is becoming increasingly important.

关键词： Thyroid cancer MicroRNAs Biomarker bioinformatics analysis Medullary thyroid carcinoma(MTC) OncomiRs Antioncoges

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Survival and risk analysis of patients with COVID-19 in Iran

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Journal of Acute Disease 2024年第2期13卷 60-66页

作者： Mottaghipoor F Heidari Z Sami R Memarzadeh H Saghaeiannejad Isfahani S Department of Management and Health Information Technology Isfahan University of Medical SciencesIsfahanIran Department of biostatistics and Epidemiology Isfahan University of Medical SciencesIsfahanIran Department of Internal Medicine School of MedicineIsfahan University of Medical SciencesIsfahanIran Software Engineering Isfahan University of Medical SciencesIsfahanIran Health Information Technology research center Isfahan University of Medical SciencesIsfahanIran

Objective:To evaluate the risk factors of death caused by COVID-19 in ***:This study was a retrospective cohort study from February 20,2020,to August 22,2022,in the hospitals in Isfahan,*** data were collected through a researcher-made *** determine the risk factors of the death,logistic regression and Cox regression models were *** each variable,the odds ratio and 95%confidence interval were also ***:1885 Patients were *** age of deceased persons was significantly higher than that of the surviving *** risk of death for the age group above 60 years was about 14 times higher than that of people aged 19-35 years[95%CI:14.41(2.02-102.99),P<0.01].Hypertension[95%CI:1.92(1.47-2.5),P<0.01],diabetes[95%CI:1.62(1.23-2.13),P<0.001],and chronic obstructive pulmonary disease[95%CI:1.92(1.47-2.50),P<0.01]were also risk factors of ***:This study reveals that the mortality rate due to COVID-19 is associated with old age,longer hospitalization in the ICU,increased length of stay,and comorbidities of high blood pressure,diabetes,and chronic pulmonary disease.

关键词： Cause Death Survival COVID-19 Risk factors Iran

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Development,validation,and transportability of several machine-learned,non-exercise-based VO_(2max)prediction models for older adults

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Journal of Sport and Health Science 2024年第5期13卷 611-620页

作者： Benjamin T.Schumacher Michael J.LaMonte Andrea Z.LaCroix Eleanor M.Simonsick Steven P.Hooker Humberto Parada Jr. John Bellettiere Arun Kumar Herbert Wertheim School of Public Health and Human Longevity Science University of California San DiegoLa JollaCA 92093USA Department of Epidemiology and Environmental Health School of Public Health and Health ProfessionsUniversity at BuffaloState University of New YorkBuffaloNY 14214USA Translational Gerontology Branch Intramural Research ProgramNational Institute on AgingNational Institutes of HealthBaltimoreMD 21225USA College of Health and Human Services San Diego State UniversitySan DiegoCA 92182USA Division of Epidemiology and biostatistics School of Public HealthSan Diego State UniversitySan DiegoCA 92182USA University of California San Diego Moores Cancer center La JollaCA 92093USA Computer Science and Engineering and Halicioglu Data Science Institute University of California San DiegoLa JollaCA 92093USA

Background:There exist few maximal oxygen uptake(VO_(2max))non-exercise-based prediction equations,fewer using machine learning(ML),and none specifically for older *** direct measurement of VO_(2max)is infeasible in large epidemiologic cohort studies,we sought to develop,validate,compare,and assess the transportability of several ML VO_(2max)prediction ***:The Baltimore Longitudinal Study of Aging(BLSA)participants with valid VO2_(max)tests were included(n=1080).Least absolute shrinkage and selection operator,linear-and tree-boosted extreme gradient boosting,random forest,and support vector machine(SVM)algorithms were trained to predict VO_(2max)*** developed these algorithms for:(a)the overall BLSA,(b)by sex,(c)using all BLSA variables,and(d)variables common in aging ***,we quantified the associations between measured and predicted VO_(2max)and ***:The age was 69.0±10.4 years(mean±SD)and the measured VO_(2max)was 21.6±5.9 mL/kg/*** absolute shrinkage and selection operator,linear-and tree-boosted extreme gradient boosting,random forest,and support vector machine yielded root mean squared errors of 3.4 mL/kg/min,3.6 mL/kg/min,3.4 mL/kg/min,3.6 mL/kg/min,and 3.5 mL/kg/min,*** quartiles of measured VO_(2max)showed an inverse gradient in mortality *** VO_(2max)variables yielded similar effect estimates but were not robust to ***:Measured VO_(2max)is a strong predictor of *** ML can improve the accuracy of prediction as compared to simpler approaches but estimates of association with mortality remain sensitive to *** studies should seek to reproduce these results so that VO_(2max),an important vital sign,can be more broadly studied as a modifiable target for promoting functional resiliency and healthy aging.

关键词： Cardiorespiratory fitness Prediction algorithms Epidemiology Mortality

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Identification and Validation of SLC9A2 as A Potential Tumor Suppressor in Colorectal Cancer:Integrating bioinformatics Analysis with Experimental Confirmation

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Current Medical Science 2024年第3期44卷 529-544页

作者： Yan-min LIU Tie-cheng YANG Xiao-chang FANG Li-jie YANG Li-wen SHI Hua-qiao WANG Ting-ting DOU Lin SHU Tian-Liang CHEN Jun HU Xiao-ming YU Xuan-fei LI Department of Gastroenterology the Central Hospital of WuhanKey Laboratory for Molecular Diagnosis of Hubei ProvinceTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430014China Department of Gastrointestinal Surgery Zhongnan Hospital of Wuhan UniversityWuhan430071China Clinical Medical research center of Peritoneal Cancer of Wuhan Wuhan430071China Hubei Provincial Clinical research center for Cancer Hubei Key Laboratory of Tumor Biological Behavi Wuhan430071China Department of General Surgery Taihe HospitalHubei University of MedicineShiyan442000China Department of Gastrointestinal Surgery Huangshi Central HospitalAffiliated Hospital of Hubei Polytechnic UniversityWuhan435001China

Objective To uncover the mechanisms underlying the development of colorectal cancer(CRC),we applied bioinformatic analyses to identify key genes and experimentally validated their possible roles in CRC onset and *** We performed Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis on differentially expressed genes(DEGs),constructed a protein-protein interaction(PPI)network to find the top 10 hub genes,and analyzed their expression in colon adenocarcinoma(COAD)and rectum adenocarcinoma(READ).We also studied the correlation between these genes and immune cell infiltration and prognosis and validated the expression of SLC9A2 in CRC tissues and cell lines using qRT-PCR and Western *** experiments were conducted in vitro to investigate the effects of SLC9A2 on tumor growth and *** We found 130 DEGs,with 45 up-regulated and 85 down-regulated in *** analysis indicated that these DEGs were primarily enriched in functions related to the regulation of cellular pH,zymogen granules,and transmembrane transporter *** pathway analysis revealed that the DEGs played pivotal roles in pancreatic secretion,rheumatoid arthritis,and the IL-17 signaling *** identified 10 hub genes:CXCL1,SLC26A3,CXCL2,MMP7,MMP1,SLC9A2,SLC4A4,CLCA1,CLCA4,and *** enrichment analysis showed that these hub genes were predominantly involved in the positive regulation of *** expression analysis revealed that CXCL1,CXCL2,MMP1,and MMP7 were highly expressed in CRC,whereas CLCA1,CLCA4,SLC4A4,SLC9A2,SLC26A3,and ZG16 were expressed at lower *** analysis revealed that 5 key genes were significantly associated with the prognosis of *** mRNA and protein expression levels of SLC9A2 were markedly reduced in CRC tissues and cell ***,SLC9A2 overexpression in SW480 cells led to a notable inhibition of cell proliferation,migration,and *** blotting analysis revealed tha

关键词： SLC9A2 colorectal cancer bioinformatic analysis biomarkers immune infiltrate

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Impact of phytoconstituents on oral health practices:a post COVID-19 observation

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Food Science and Human Wellness 2024年第5期13卷 2386-2400页

作者： Harsh Kumar Reena Singh Daljeet Singh Dhanjal Chirag Chopra Natália Cruz-Martins Gheyath K.Nasrallah Amin F.Majdalawieh Sivakumar Manickam Shahida Anusha Siddiqui Dinesh Kumar Indu Sharma Varun Sharma School of Bioengineering&Food Technology Shoolini University of Biotechnology and Management SciencesSolan 173229India School of Bioengineering and Biosciences Lovely Professional UniversityPunjab 144402India Faculty of Medicine University of PortoPorto 4200-319Portugal Institute for research and Innovation in Health(i3S) University of PortoPorto 4200-135Portugal Institute of research and Advanced Training in Health Sciences and Technologies(CESPU) RuaCentral de GandraGandra 4585-116Portugal TOXRUN-Toxicology research Unit University Institute of Health SciencesCESPUCRLGandra 4585-116Portugal Biomedical research center Qatar UniversityDoha 2713Qatar Department of Biomedical Science College of Health SciencesQatar UniversityDoha 2713Qatar Department of Biology Chemistryand Environmental SciencesCollege of Arts and SciencesAmerican University of SharjahSharjah 26666United Arab Emirates Petroleum and Chemical Engineering Faculty of EngineeringUniversiti Teknologi BruneiBandar Seri Begawan BE1410Brunei Campus Straubing for Biotechnology and Sustainability Technical University of MunichStraubing 94315Germany Genetic Heritage Group New York UniversityAbu Dhabi 129188United Arab Emirates bioinformatics Division NMC Genetics India Pvt.Ltd.Gurugram 122001India

Appropriate oral hygiene significantly reduces the possibility of oral ***,dental caries and periodontal diseases are major oral health issues causing chronic diseases due to poor oral ***,herbal compounds have gained interest in maintaining oral *** of burdock root(Arctium),noni fruit(Morinda citrifolia),and neem leaf(Azadirachta indica)are now used as intracanal medicaments in endodontics and *** amboinicus species and other plants produces essential oil likeβ-caryophyllene,p-cymene,andγ-terpinene can exhibit antibacterial activity;highlighting phytoconstituents plays a vital role in oral *** COVID-19 pandemic highlighted the importance of hygiene and sanitization,to curb *** cavity is among the gateways for virus entry into *** is a potential reservoir of SARS-CoV-2,and there is an increased risk of infection if there is any fissure in the *** enables entry of virus into the vascular system through gingival or periodontal pocket,possibly reaching lung periphery then to lung vessels by interacting with endothelial surface receptors triggering pulmonary vasoconstriction and lung damage due to endothelial *** review aims to draw attention to the possible route of SARS-CoV-2 infection via the oral cavity and the importance of oral hygiene against COVID-19.

关键词： COVID-19 SARS-CoV-2 Oral Hygiene Microbiota Phytochemicals

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Small extrachromosomal circular DNA in amyotrophic lateral sclerosis matter

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Neural Regeneration research 2025年第5期20卷 1411-1413页

作者： Marcos J.Arauzo-Bravo Daniela Gerovska Matthias Schwab Alexandra Kretz Computational Biology and Systems Biomedicine Biodonostia Health Research InstituteSan SebastianSpain Basque Foundation for Science IKERBASQUEBilbaoSpainMax Planck Institute for Molecular BiomedicineComputational Biology and Bioinformatics GroupMünsterNorth Rhine-WestphaliaGermany Department of Cell Biology and Histology Faculty of Medicine and NursingUniversity of Basque Country(UPV/EHU)LeioaSpain Department of Neurology Jena University HospitalJenaThuringiaGermany

Comprehensive studies identify motor neuron spectrum disorders including amyotrophic lateral sclerosis(ALS)as globally rising fatal disorders with the highest prevalence in aging populations,influenced by ethnicity and ancestry(GBD 2016 Motor Neuron Disease Colla borators,2018).While~10% of diagnoses involve a family history(fALS),most cases are considered sporadic(sALS).However,population-based studies suggest that even cases without a common index mutation impart heritability(Ryan et al.,2019),indicating a crucial role of rare and as yet unknown genetic denominators.

关键词： amyotrophic sclerosis

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Cardiovascular risk burden,dementia risk and brain structural imaging markers:a study from UK Biobank

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General Psychiatry 2024年第1期37卷 94-102页

作者： Yaying Cao Gaohong Zhu Chengwu Feng Jing Chen Wei Gan Yuan Ma Yonghua Hu Klodian Dhana Trudy Voortman Jie Shen Ting Li Yan Zheng Changzheng Yuan Geng Zong Department of Food Nutrition and Health School of Medicine and HealthHarbin Institute of TechnologyHarbinHeilongjiangChina CAS Key Laboratory of Nutrition Metabolism and Food SafetyShanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghaiChina Department of Nuclear Medicine First Affiliated Hospital of Kunming Medical UniversityKunmingYunnanChina Neurology Department Zhongshan Hospital Affliated with Fudan UniversityShanghaiChina Medical research Council Population Health research Unit University of OxfordOxfordUK Department of Genetics Novo Nordisk Research Centre OxfordOxfordUK Harvard University T H Chan School of Public Health BostonMassachusettsUSA Department of Epidemiology and biostatistics School of Public HealthPeking UniversityBeijingChina Department of Internal Medicine Rush University Medical CenterChicagolinoisUSA Department of Epidemiology rasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands Division of Human Nutrition and Health Wageningen University&ResearchWageningenThe Netherlands School of Public Health the Second Afliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina First Afiliated Hospital of Kunming Medical University KunmingYunnanChina State Key Laboratory of Genetic Engineering School f ife SCciencesFudan UniversityShanghaiChina Ministry of Education Key Laboratory of Public Health Safety School of Public HealthFudan UniversityShanghaiChina The Key Laboratory of Inteligent Preventive Medicine of Zhejang Province HangzhouZhejiangChina Shanghai Jiao Tong University Affiliated Sixth People's Hospital ShanghaiChina

Background Cardiovascular risk burden is associated with dementia risk and neurodegeneration-related brain structure,while the role of genetics and incident cardiovascular disease(CVD)remains *** To examine the association of overall cardiovascular risk burden with the risk of major dementia subtypes and volumes of related brain regions in a large sample,and to explore the role of genetics and CVD *** A prospective study among 354 654 participants free of CVD and dementia(2006-2010,mean age 56.4 years)was conducted within the UK Biobank,with brain magnetic resonance imaging(MRl)measurement availablefor 15104participants since *** risk burden was evaluated by the Framingham General Cardiovascular Risk Score(FGCRS).Dementia diagnosis was ascertained from inpatient and death register *** Overamedian 12.0-yearfollow-up,3998 all-cause dementia cases were *** FGCRS was associated with increasedall-cause dementia risk after adjusting for demographic,major lifestyle,clinical factors and the polygenic risk score(PRS)of Alzheimer's *** the high versus low tertile of FGCRS,the odds ratios(ORs)and 95%confidence intervals(Cls)were 1.26(1.12 to 1.41)for all-cause dementia,1.67(1.33 to 2.09)for Alzheimer's disease and 1.53(1.07 to 2.16)for vascular dementia(all p_(treng)<0.05).Incident stroke and coronary heart disease accounted for 14%(95%Cl:9% to 21%)of the association between FGCRS and all-cause *** were not detected for FGCRS and PRS on the risk of any dementia *** observed an 83%(95%Cl:47%to 128%)higher all-cause dementia risk comparing the high-high versus low-low FGCRS-PRS *** brain volumes,higher FGCRS was associated with greater log-transformed white matter hyperintensities,smaller cortical volume and smaller grey matter *** Our findings suggest that the positive association of cardiovascular risk burden with dementia risk also applies to major dementia subtypes.T

关键词： Cardiovascular diagnosis burden

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A systematic study of Erzhu Erchen decoction against damp-heat internalized type 2 diabetes based on data mining and experimental verification

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Traditional Medicine research 2024年第2期9卷 27-41页

作者： Peng-Yu Wang Jian-Fen Shen Shuo Zhang Qing Lan Guan-Di Ma Tong Wang You-Zhi Zhang School of Pharmacy Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei ProvinceXianning Medical CollegeHubei University of Science and TechnologyXianning 437100China Department of Central Laboratory The First Affiliated Hospital of Jiaxing UniversityJiaxing 314000China

Background:Erzhu Erchen decoction(EZECD),which is based on Erchen decoction and enhanced with Atractylodes lancea and Atractylodes macrocephala,is widely used for the treatment of dampness and heat(The clinical manifestations of Western medicine include thirst,inability to drink more,diarrhea,yellow urine,red tongue,et al.)internalized ***,the mechanism of EZECD on damp-heat internalized Type 2 diabetes(T2D)remains *** employed data mining,pharmacology databases and experimental verification to study how EZECD treats damp-heat internalized ***:The main compounds or genes of EZECD and damp-heat internalized T2D were obtained from the pharmacology ***,the overlapped targets of EZECD and damp-heat internalized T2D were performed by the Gene Ontology,kyoto encyclopedia of genes and genomes *** the compound-disease targets-pathway network were constructed to obtain the hub ***,the hub genes and core related pathways were mined with weighted gene co-expression network analysis based on Gene Expression Omnibus database,the capability of hub compound and genes was valid in AutoDock ***,and violin plot and gene set enrichment analysis were performed to explore the role of hub genes in damp-heat internalized ***,the interactions of hub compound and genes were explored using Comparative Toxicogenomics Database and quantitative polymerase chain ***:First,herb-compounds-genes-disease network illustrated that the hub compound of EZECD for damp-heat internalized T2D could be ***,the hub genes were CASP8,CCL2,and AHR according to weighted gene co-expression network *** docking showed that quercetin could bind with the hub ***,gene set enrichment analysis and Gene Ontology represented that CASP8,or CCL2,is negatively involved in insulin secretion response to the TNF or lipopolysaccharide process,and AHR or CCL2 positively regulated li

关键词： data mining damp-heat internalized type 2 diabetes Erzhu Erchen decoction network pharmacology bioinformatics

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