Transcriptome, miRNA, and degradome sequencing reveal the leaf stripe (Pyrenophora graminea) resistance genes in Tibetan hulless barley by Yue Wang, Qian Hu, Youhua Yao, Yongmei Cui, Yixiong Bai, Likun An, Xin Li, Baojun Ding, Xiaohua Yao, Kunlun Wu

“…The results showed a total of 7,669 and 5,943 differentially expressed genes (DEGs) were found in resistant and susceptible Kunlun 14 and Z1141, respectively, with 8,916 DEGs found between Kunlun 14 and Z1141. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the 8,916 DEGs identified many significantly enriched categories and pathways, of which a plant–pathogen interaction pathway, containing a total of 102 genes (100 known genes and two novel genes), was found, that was very important for the study of the leaf stripe resistance mechanism. …”
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Protective effect and mechanism of Sufentanil on acute lung injury in septic mice by Hongqiao Hou, Bowen Jiang, Aiqing Zhu, Junjun Hou, Zhe Qu, Ruping Liu, Aiqun Li

“…To this end, a protein-protein interaction (PPI) network for common targets was first constructed with Swiss Target Prediction Database, GeneCards Database, Draw Venn Diagram Software, STRING 11.5 Database, Cytoscape 3.10.0 Software and Metascape Database, and then key targets were subject to enrichment analysis by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to obtain the key targets of Sufentanil for the treatment of pulmonary sepsis, and then verified by animal experiments. …”
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Identification of Potential miRNA-mRNA Regulatory Network Contributing to Parkinson’s Disease by Xi Yin, Miao Wang, Wei Wang, Tong Chen, Ge Song, Yixuan Niu, Ziying Jiang, Zhongbao Gao, Zhenfu Wang

“…Target genes of the DEmis were selected when they were predicted by three or four online databases and overlapped with DEGs from GSE100054. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then conducted by Database for Annotation, Visualization and Integrated Discovery (DAVID) and Metascape analytic tools. …”
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Synergistic interaction between wheat streak mosaic virus and Triticum mosaic virus modulates wheat transcriptome to favor disease severity by Haritha Nunna, Nathan A. Palmer, Gautam Sarath, Stephen N. Wegulo, Satyanarayana Tatineni, Satyanarayana Tatineni

“…Weighted gene co-expression network analysis resulted in 11 co-expression modules that broadly indicated gene expression profiles attributable to control, single, and double infections. Gene ontology, protein domain and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis revealed that genes specifically related to photosynthesis, growth, stress, senescence, and defense were differentially enriched. …”
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Identification of immune-associated genes with altered expression in the spleen of mice enriched with probiotic species using RNA-seq profiling by Anh Duc Truong, Ha Thi Thanh Tran, Nhu Thi Chu, Lanh Phan, Hoai Thi Phan, Thu Huong Dang, Hoang Vu Dang, La Anh Nguyen

“…In addition, the Kyoto encyclopedia of genes and genomes and gene ontology analyses revealed that the DEGs were predominantly enriched in defense responses to pathogens, including inflammatory bowel diseases, malaria, leukaemia virus 1, and herpes virus, as well as immune processes related to immune response and signal transduction. …”
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TOM40 as a prognostic oncogene for oral squamous cell carcinoma prognosis by Lifei Deng, Hong Ran, Dunhui Yang, Zhen Wang, Peng Zhao, Hengjie Huang, Yongjin Wu, Peng Zhang

“…A network of genes co-expressed with TOM40 was constructed and functionally annotated by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. …”
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Comprehensive bioinformatics analysis identifies hub genes associated with immune cell infiltration in early-onset schizophrenia by Shasha Wu, Tailian Xue, Yilin Li, Weikang Chen, Yan Ren

“…These genes were subjected to genome enrichment analysis (GSEA) and gene ontology (GO) analysis. Hub genes were identified through protein-protein interactions (PPIs) and the GeneMANIA database. …”
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Identification and Analysis of Potential Immune-Related Biomarkers in Endometriosis by Yanan He, Jixin Li, Yanjun Qu, Liyuan Sun, Xibo Zhao, Han Wu, Guangmei Zhang

“…To explore potential therapeutic targets for endometriosis, the Gene Expression Omnibus (GEO), Immunology Database and Analysis Portal (ImmPort), and TF databases were used to obtain data related to the recognition of differentially expressed genes (DEGs), differentially expressed IRGs (DEIRGs), and differentially expressed TFs (DETFs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the DETFs and DEIRGs. …”
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CircRNA-miRNA-mRNA regulatory network in high-altitude hypobaric hypoxia-induced hearing impairment and hearing acclimatization by Danzeng Awang, Kanzi Danzeng, Tianheng Wang, Quzong Deji, Mengting Huang, Hailong Ren, Xinzhu Liu, Binghan Zhao, Lanzi Gongga

“…The DEmRNAs in this network were functionally annotated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses based on Metascape. …”
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Discovery of mutated oncodriver genes associated with glioblastoma originated from stem cells of subventricular zone through whole exome sequence profile analysis, and drug repurpo... by Arnob Sarker, Burhan Uddin, Reaz Ahmmed, Sabkat Mahmud, Alvira Ajadee, Md. Al Amin Pappu, Md. Abdul Aziz, Md. Nurul Haque Mollah

“…Then molecular mechanisms of GBM development were investigated by these three overexpressed driver genes through gene ontology (GO), KEGG-pathways, Gene regulatory network (GRN) and mutation analysis. …”
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Exploration of metastasis-related signatures in osteosarcoma based on tumor microenvironment by integrated bioinformatic analysis by Shiyao Liao, Xing Gao, Kai Zhou, Yao Kang, Lichen Ji, Xugang Zhong, Jun Lv

“…DEGs with similar biological functions were grouped into the same module by Gene Ontology (GO) analysis and MCODE analysis. Prognostic DEGs were selected in two datasets through survival analysis. …”
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Identification of novel cytoskeleton protein involved in spermatogenic cells and sertoli cells of non-obstructive azoospermia based on microarray and bioinformatics analysis by Danial Hashemi Karoii, Hossein Azizi, Maryam Darvari, Ali Qorbanee, Dawan Jamal Hawezy

“…A combined analysis of Gene Ontology (GO) and STRING, were used to predict proteins’ molecular interactions and then to recognize master pathways. …”
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Identification of Breast Cancer Biomarkers by Constructing Protein-Protein Interaction and miRNAs-mRNAs Networks by Azizeh Asadzadeh, Bita Behboodian, Parsa Bernoos, Masoumeh Shojaei Barjouei

“…GEO2R was used to obtain differentially expressed mRNA (DEMs) and miRNAs (DEMIs) based on |logFC|>2 and adjusted P-value <0.05. Gene Ontology and KEGG Pathway Enrichment Analysis were performed by EnrichR. …”
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Network pharmacology-based screening of the active ingredients and mechanisms of Cymbaria daurica against diabetes mellitus by Ruyu Shi, Dongxue Chen, Mingyue Ji, Baochang Zhou, Ziyan Zhang, Chunhong Zhang, Minhui Li

“…Based on data mining techniques involving topological parameters, gene ontology, and pathway enrichment, we established a compound-target, protein-protein interaction, and target-pathway network to identify central targets and pathways. …”
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A Proteomic Study Based on Home Quarantine Model Identifies NQO1 and Inflammation Pathways Involved in Adenoid Hypertrophy by Chen P, Hou S, Pang X, Li L, Wei W

“…Differences in protein expression were analyzed using Gene Ontology, the Kyoto Encyclopedia of Genes and Genomes, Gene Set Enrichment Analysis, Protein-protein interaction, and immunohistochemistry analysis.Results: Long-term home quarantine had a profound impact on the proteomics of pediatric adenoids, with up-regulated and down-regulated proteins of 28 and 92 downregulated proteins, respectively. …”
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"ANAPUS KANTO": M. FOUCAULT NAUJOJI MORALĖS GENEALOGIJA by Jūratė Baranova

“…he finds echo of his own project "ontology of present". But Foucault's investigation of morals goes into opposite direction than Kant's. …”
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THE SOLANUM TUBEROSUM KNOWLEDGE BASE: THE SECTION ON MOLECULAR-GENETIC REGULATION OF METABOLIC PATHWAYS by T. V. Ivanisenko, O. V. Saik, P. S. Demenkov, V. K. Khlestkin, E. K. Khlestkina, N A. Kolchanov, V. А. Ivanisenko

“…SOLANUM TUBEROSUM is a computer platform for complex intellectual processing of large data bodies, including (1) automatic analysis of scientific publications and databases for extraction of information on genetics, markers, breeding, diagnostics, protection and storage technologies for potato, (2) formalized representation of extracted information in the knowledge base, (3) user access to these data, (4) analysis and visualization of query results. The ontology of the SOLANUM TUBEROSUM knowledge base contains dictionaries of molecular genetic objects (proteins, genes, metabolites, microRNAs, biomarkers); phenotypic characteristics of potato varieties; potato diseases and pests; biotic/abiotic environmental factors; potato agrobiotechnologies. …”
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Transcriptome responses to Ralstonia solanacearum infection in tetraploid potato by Zhuo Chen, Shunwei Shao, Xi Zhu, Yu Zhang, Zhendong Lan, Hui Jin

“…Transcriptome sequencing reveals 659 differentially expressed genes between the two varieties, with the ethylene responsive factor family containing the most differentially expressed genes. Gene ontology and KEGG analyses provided further insights into the genetic basis and molecular mechanisms underlying plant defense against R. solanacearum disease. …”
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Mechanism of <italic>Coptis chinensis</italic> in Treatment of Type 2 Diabetes Mellitus Based on Network Pharmacology and Molecular Docking by LIU Huiling, TAN Dingying, HUANG Min, CHEN Pingping, ZHANG Wang

“…In addition, molecular docking was conducted between the core targets and the active ingredients of <italic>Coptis chinensis</italic> to verify the binding ability between the active ingredients and the core targets.Results① A total of 14 active ingredients of <italic>Coptis chinensis</italic>, 189 targets for the treatment of type 2 diabetes mellitus were screened out, among which 136 potential targets were identified, including 20 core targets (degree≥12), 137 signaling pathways with significant significance. ② Gene Ontology (GO) functional enrichment analysis showed that, the biological processes (BP) involved in the predicted target of <italic>Coptis chinensis</italic> in the treatment of type 2 diabetes mellitus involved gland development, epithelial cell proliferation, regulation of DNA-binding transcription factor activity, oxidative stress and apoptosis response to lipopolysaccharide, etc. …”
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Identification of Anoikis-Related Genes in Chronic Kidney Disease Based on Bioinformatics Analysis Combined with Experimental Validation by Liu H, Mei M, Zhong H, Lin S, Luo J, Huang S, Zhou J

“…We aimed to establish the Anoikis-related gene signature in CKD by bioinformatics analysis.Methods: We retrieved 3 datasets from the Gene Expression Omnibus (GEO) database to obtain differentially expressed genes (DEGs), followed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) of them, which were intersected with Anoikis-related genes (ARGs) to derive Anoikis-related differentially expressed genes (ARDEGs). …”
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