Bioinformatics in bioscience and bioengineering: Recent advances, applications, and perspectives

Uesaka, Kazuma; Oka, Hideyuki; Kato, Ryuji; Kanie, Kei; Kojima, Takaaki; Tsugawa, Hiroshi; Toda, Yosuke; Horinouchi, Takaaki

doi:10.1016/j.jbiosc.2022.08.004

Cited by 20 publications

(16 citation statements)

References 64 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Its continuous development provides powerful tools and methods for life science and medical research. [13,14] Currently, the relationship between Lipocalin-2 (LCN2), elastase, neutrophil expressed (ELANE), and sepsis is not well understood. The study aims to use bioinformatics techniques to explore the core genes between sepsis and normal tissues, and to conduct correlation analysis.…”

Section: Enze Pain Management Medical Research Project Tianjin Health...mentioning

confidence: 99%

LCN2 and ELANE overexpression induces sepsis

Wang,

Han,

Dong

et al. 2024

Medicine

View full text Add to dashboard Cite

Sepsis is a syndrome characterized by a systemic inflammatory response due to the invasion of pathogenic microorganisms. The relationship between Lipocalin-2 (LCN2), elastase, neutrophil expressed (ELANE) and sepsis remains unclear. The sepsis datasets GSE137340 and GSE154918 profiles were downloaded from gene expression omnibus generated from GPL10558. Batch normalization, differentially expressed Genes (DEGs) screening, weighted gene co-expression network analysis (WGCNA), functional enrichment analysis, Gene Set Enrichment Analysis (GSEA), immune infiltration analysis, construction and analysis of protein–protein interaction (PPI) networks, Comparative Toxicogenomics Database (CTD) analysis were performed. Gene expression heatmaps were generated. TargetScan was used to screen miRNAs of DEGs. 328 DEGs were identified. According to Gene Ontology (GO), in the Biological Process analysis, they were mainly enriched in immune response, apoptosis, inflammatory response, and immune response regulation signaling pathways. In cellular component analysis, they were mainly enriched in vesicles, cytoplasmic vesicles, and secretory granules. In Molecular Function analysis, they were mainly concentrated in hemoglobin binding, Toll-like receptor binding, immunoglobulin binding, and RAGE receptor binding. In Kyoto Encyclopedia of Genes and Genomes (KEGG), they were mainly enriched in NOD-like receptor signaling pathway, Toll-like receptor signaling pathway, TNF signaling pathway, P53 signaling pathway, and legionellosis. Seventeen modules were generated. The PPI network identified 4 core genes (MPO, ELANE, CTSG, LCN2). Gene expression heatmaps revealed that core genes (MPO, ELANE, CTSG, LCN2) were highly expressed in sepsis samples. CTD analysis found that MPO, ELANE, CTSG and LCN2 were associated with sepsis, peritonitis, meningitis, pneumonia, infection, and inflammation. LCN2 and ELANE are highly expressed in sepsis and may serve as molecular targets.

show abstract

Section: Enze Pain Management Medical Research Project Tianjin Health...mentioning

confidence: 99%

LCN2 and ELANE overexpression induces sepsis

Wang,

Han,

Dong

et al. 2024

Medicine

View full text Add to dashboard Cite

show abstract

“…It not only accelerates the speed of scientific discovery, but also provides important support for drug research and development, medical diagnosis and personalized medicine. [12,13] However, the relationship between Il1r2, Tnfrsf12a, ischemic stroke and TMS is still unclear. Therefore, this paper intends to use bioinformatics technology to explore the core genes between ischemic stroke, TMS and normal tissues, and conduct enrichment analysis and pathway analysis.…”

Section: Introductionmentioning

confidence: 99%

“…It not only accelerates the speed of scientific discovery, but also provides important support for drug research and development, medical diagnosis and personalized medicine. [12,13]…”

Section: Introductionmentioning

confidence: 99%

Il1r2 and Tnfrsf12a in transcranial magnetic stimulation effect of ischemic stroke via bioinformatics analysis

Zhao,

Liu,

et al. 2024

Medicine

View full text Add to dashboard Cite

Ischemic stroke refers to ischemic necrosis or softening of localized brain tissue. Transcranial magnetic stimulation (TMS) is a painless, noninvasive and green treatment method, which acts on the central nervous system through a pulsed magnetic field to assist in the treatment of central nervous system injury diseases. However, the role of Il1r2 and Tnfrsf12a in this is unknown. The ischemic stroke datasets GSE81302 and TMS datasets GSE230148 were downloaded from Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis (WGCNA) was performed. The construction and analysis of protein-protein interaction (PPI) network and functional enrichment analysis were performed. Draw heat map gene expression. Through the Comparative Toxicogenomics Database (CTD) to find the most relevant and core gene diseases. TargetScan was used to screen miRNAs regulating DEGs. A total of 39 DEGs were identified. According to gene ontology (GO) analysis results, in biological process (BP) analysis, they were mainly enriched in the positive regulation of apoptosis process, inflammatory response, positive regulation of p38MAPK cascade, and regulation of cell cycle. In cellular component (CC) analysis, they were mainly enriched in the cell surface, cytoplasm, and extracellular space. In Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, they were mainly enriched in nf-κB signaling pathway, fluid shear stress and atherosclerosis, P53 signaling pathway, TNF signaling pathway, and apoptosis. Among the enrichment items of metascape, negative regulation of T cell activation, hematopoietic cell lineage, positive regulation of apoptotic process, fluid shear stress and atherosclerosis were observed in GO enrichment items. Five core genes (Socs3, Irf1, Il1r2, Ccr1, and Tnfrsf12a) were obtained, which were highly expressed in ischemic stroke samples. Il1r2 and Tnfrsf12a were lowly expressed in TMS samples. CTD analysis found that the core gene (Socs3, Irf1 and Il1r2, Ccr1, Tnfrsf12a) and ischemic stroke, atherosclerosis, hypertension, hyperlipidemia, thrombosis, stroke, myocardial ischemia, myocardial infarction, and inflammation. Il1r2 and Tnfrsf12a are highly expressed in ischemic stroke, but lowly expressed in TMS samples.

show abstract

“…Considering the complexity of randomized controlled trials, MR is an alternative method, which can use genetic variation as a tool to assess the causality of exposure to outcomes, reducing unmeasurable confusion and reverse causality 15 . Then the variation will be mapped to the related gene by eQTL analysis for further exploration 16,17 …”

Section: Introductionmentioning

confidence: 99%

Exploration of the causality of frailty index on psoriasis: A Mendelian randomization study

Lei,

Xing,

Chen

et al. 2024

Skin Research and Technology

View full text Add to dashboard Cite

BackgroundFrailty is associated with a variety of diseases, but the relationship between frailty and psoriasis remains unclear.MethodsFirst, we conducted a two‐sample Mendelian randomization based on genome‐wide association studies (GWAS) to investigate genetic causality between frailty index and common diseases in dermatology. Inverse variance weighted was used to estimate causality. Second, expression quantitative trait locus (eQTLs) analysis was conducted to identify the genes affected by Single nucleotide polymorphisms (SNPs). Third, we performed function and pathway enrichment, transcriptome‐wide association studies (TWAS) analysis based on eQTLs.ResultsIt was shown that the rise of frailty index could increase the risk of psoriasis (IVW, beta = 0.916, OR = 2.500, 95%CI:1.418‐4.408, p = 0.002) through Mendelian randomization (MR), and there was no heterogeneity and pleiotropy. There was no causality between the frailty index and other common diseases in dermatology. We found 31 eQTLs based on strongly correlated SNPs in the causality. TWAS analysis found that the expressions of four genes were closely related to psoriasis, including HLA‐DQA1, HLA‐DQA2, HLA‐DRB1 and HLA‐DQB1.ConclusionIt suggested that the frailty index had a significant positive causality on the risk of psoriasis, which was well documented by combined genomic, transcriptome, and proteome analyses.

show abstract

Bioinformatics in bioscience and bioengineering: Recent advances, applications, and perspectives

Cited by 20 publications

References 64 publications

LCN2 and ELANE overexpression induces sepsis

LCN2 and ELANE overexpression induces sepsis

Il1r2 and Tnfrsf12a in transcranial magnetic stimulation effect of ischemic stroke via bioinformatics analysis

Exploration of the causality of frailty index on psoriasis: A Mendelian randomization study

Contact Info

Product

Resources

About