Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19코로나19에 적용한 scMLnet을 사용하여 단일 세포 RNA 시퀀싱 데이터에서 유전자 발현의 미세 환경 조절 추론Article Published on 2021-03-222022-09-11 Journal: Briefings in Bioinformatics [Category] 유전자 메커니즘, [키워드] ACE2 ACE2 expression activated addition anti-cytokine therapies anti-cytokine therapy applied approach Cell cellular cellular microenvironment correlated COVID-19 COVID-19 infection COVID-19 patient COVID-19 severity cytokine Cytokines dataset EGF expression of SARS-CoV-2 Extracellular facilitate functional Gene Expression gene regulatory network human lung cell human lung cells IFN-γ Infection Inflammatory cytokine Inflammatory cytokines Intercellular communication mechanism methodology microenvironment multilayer network predicted provided receptor ACE2 Regulation reported SARS-CoV-2 SARS-COV-2 infection SARS-CoV-2 receptor scMLnet scRNA-seq sequencing data Signaling signaling pathway significantly Single-cell RNA sequencing single-cell RNA-seq Single-cell RNA-sequencing targeted therapy TNF-α [DOI] 10.1093/bib/bbaa327 PMC 바로가기 [Article Type] Article
Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids인간 기관지 오르가노이드의 SARS-CoV-2 감염 중 관련 허브 유전자 발현의 탐색 및 검증Genome Database Published on 2021-03-162022-09-10 Journal: Human Genomics [Category] 유전자 메커니즘, [키워드] 3D structure model acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 affected analyzed Bioinformatics analysis bronchial organoid CCL2 CCL5 coronavirus COVID-19 CXCL1 CXCL10 CXCL8 Cytokines DEGs differentially expressed gene Differentially expressed genes downloaded downregulated gene EGF exploration expressed expression feasibility FGF2 FN1 Gene Expression Gene ontology Genes genomes GEO Health help high mortality hub genes Human bronchial organoids human bronchus ICAM1 identify IL1B IL6 immune response in vitro model Infection infection mechanism infection rate Interaction KEGG Kyoto Microarray MMP9 mRNA mRNA expression Novel coronavirus Novel coronavirus infection pandemic Pathogenesis pathway Pathways patients PBMC PBMCs Potential treatment PPI prognostic protein-protein interaction Protein–protein interaction R software respiratory Result SARS-CoV-2 SARS-COV-2 infection selected severe acute respiratory syndrome Coronavirus significantly suggested System three-dimensional structure Treatment upregulated gene were used [DOI] 10.1186/s40246-021-00316-5 PMC 바로가기 [Article Type] Genome Database
COVID-19 engages clinical markers for the management of cancer and cancer-relevant regulators of cell proliferation, death, migration, and immune responseCOVID-19는 암 관리 및 세포 증식, 사멸, 이동 및 면역 반응의 암 관련 조절자를 위한 임상 마커를 사용합니다.Article Published on 2021-03-042022-08-31 Journal: Scientific Reports [Category] SARS, 바이오마커, 치료법, [키워드] biological processe biological processes Cancer cancer patient Cancer patients Cancer therapy Cell cell proliferation clinical clinical decision clinical marker clinical markers clinical observations COVID-19 death Diagnosis diagnostic Diversity EGF endothelial engage Engagement epidemiological epithelial FGF immune response immune system immune system cells infected with SARS-CoV-2 initiated Intersection management marker mechanism Migration modifications network network analysis observation pathway Pathways predicted Prognosis provide rationale regulator Regulatory Regulatory networks retrieved SARS-CoV-2 smooth muscle Support Symptom TGFβ Treatment Tumor tumor suppressors tumorigenesis understanding VEGF virus was used [DOI] 10.1038/s41598-021-84780-y PMC 바로가기 [Article Type] Article
Unique inflammatory profile is associated with higher SARS-CoV-2 acute respiratory distress syndrome (ARDS) mortality독특한 염증 프로파일은 더 높은 SARS-CoV-2 급성 호흡 곤란 증후군(ARDS) 사망률과 관련이 있습니다.Article Published on 2021-03-012022-09-12 Journal: American Journal of Physiology - Regulatory, Integrative and Comparative Physiology [Category] MERS, SARS, 진단, [키워드] acute respiratory distress ARDS association calibrated caused chemokines circulating circulating leukocyte circulating leukocytes Complication conducted correlation COVID19 Critical Cytokines death EGF Gene Expression group had no Hyperinflammatory IL1RA IL8 Infection Inflammatory inflammatory mediator information leukocyte mechanically ventilated patient Mortality outcome pandemic Patient patients with COVID19 phenotype plasma prospective cohort study Protein RANTES regulated SARS-CoV-2 statistically significant syndrome to define transcriptionally transcriptomic unique [DOI] 10.1152/ajpregu.00324.2020 PMC 바로가기 [Article Type] Article
CXCL10 could drive longer duration of mechanical ventilation during COVID-19 ARDSResearch Published on 2020-11-022022-11-01 Journal: Critical Care [Category] COVID-19, [키워드] acute respiratory distress syndrome alarmin alveolar alveolar cell ARDS ARDS patients Biomarker Bronchoalveolar lavage CCL5 CD40 ligand cell-free mitochondrial DNA clinical Concentration concentrations confounders correlated correlation COVID-19 COVID-19 ARDS patient COVID-19 ARDS patients CXCL-10 CXCL1 CXCL10 CXCL2 DNA dysregulated immune response EGF elevated epithelial lining etiology evaluated feature GM-CSF granzyme B host response IL-10 IL-1β IL-8 immune response Inflammatory inflammatory mediator involved lung mechanical ventilation mitochondrial mitochondrial DNA no difference Non-COVID-19 outcome Pathogenesis plasma predict required Result SARS-CoV-2 significantly systemic inflammation targeting Therapeutic approach TRAIL two groups unique Ventilator-free days Viral load were measured [DOI] 10.1186/s13054-020-03328-0 PMC 바로가기 [Article Type] Research
Associations of viral ribonucleic acid (RNA) shedding patterns with clinical illness and immune responses in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) infectionOriginal Article Published on 2020-07-272022-10-31 Journal: Clinical & Translational Immunology [Category] COVID-19, [키워드] age Analysis Clinical characteristics coronavirus 2 correlated COVID‐19 infection COVID‐19 patient COVID‐19 patients COVID‐19 cytokine Cytokine analysis Cytokines demographic Duration early immune response EGF electronic medical records explain Factor hospitalised identify IL‐17A immune immune response immune responses immunoassay Infection initial Intermittent interquartile range Invasive mechanical ventilation IQR Kaplan–Meier laboratory data male median multiplex objective Patient plasma Plasma level Prevent RANTES recovered patients respiratory Result retrospective cohort RNA RT‐PCR SARS‐CoV‐2 SARS‐CoV‐2 subset survival symptomatic symptomatic patient T‐cell T‐cell response Viral load viral ribonucleic acid Viral RNA Viral RNA shedding was used were measured [DOI] 10.1002/cti2.1160 PMC 바로가기 [Article Type] Original Article
Genome-wide computational prediction of miRNAs in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) revealed target genes involved in pulmonary vasculature and antiviral innate immunityOriginal Article Published on 2020-06-012022-10-30 Journal: Molecular Biology Research Communications [Category] COVID-19, [키워드] acute respiratory syndrome analysed Analysis Antiviral Apoptosis BMPR2 cellular components China Community Complete coronavirus COVID-19 EGF etiology Evidence FGF receptor function Gene ontology gene silencing Genome genome sequence help human gene Human genome Innate immunity involved mature miRNA microRNA miRNA outbreak p53 pathway Pathways pre-miRNA pre-miRNAs predict predicted receptor signaling Research retrieved RNA genome RNA viruses SARS-CoV-2 Signaling target target gene Target genes the disease vasculature VEGF signaling virus pathogenesis [DOI] 10.22099/mbrc.2020.36507.1487 PMC 바로가기 [Article Type] Original Article
Introducing APOA1 as a key protein in COVID-19 infection: a bioinformatics approachOriginal Article Published on 2020-01-012022-10-31 Journal: Gastroenterology and Hepatology From Bed to Bench [Category] COVID-19, [키워드] adverse effect Analysis apoA1 app applied approach approved assigned bioinformatics biological process biological processe Biomarker Biomarkers candidate central nodes complementary complex contribute coronavirus disease COVID-19 COVID-19 patient Cytoscape software database demonstrated diagnostic down-regulation dysregulated dysregulation EGF expressed healthy hidden Interaction introduced molecular nervous system nine Patient PPI Protein protein complex protein complexes protein interaction mapping protein-protein interaction proteomics severity of COVID-19 the disease therapeutic therapeutic target Urine urine proteome was used were used PMC 바로가기 [Article Type] Original Article
Comparative and kinetic analysis of viral shedding and immunological responses in MERS patients representing a broad spectrum of disease severityArticle Published on 2016-05-052022-10-29 Journal: Scientific Reports [Category] Coronavirus, MERS, [키워드] affecting Analysis analyzed antibody antiviral therapy Blood level chemokine Clinical data Comparative correlated correlation cytokine Deceased disease disease severity early phase effective EGF Factor febrile illness four group hospital IL-10 IL-15 Immunity Immunological response increases in kinetic kinetic analysis knowledge lymphocyte response lymphopenia MERS MERS patient MERS-CoV infection Mild Monocytes Mortality neutrophil outcomes Patient patients Pneumonia prognostic representing required response responses severity specimen Spread TGF-β the patient treated viral loads viral shedding Virological [DOI] 10.1038/srep25359 PMC 바로가기 [Article Type] Article