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  1. 21481
    “…Expression patterns of upregulated genes and gene ontology enrichment analysis revealed that host infection strategies depends on plant cell wall degradation and modification, detoxification of compounds, transporter activities and toxin production. …”
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    Comparative genomics of plant pathogenic Diaporthe species and transcriptomics of Diaporthe caulivora during host infection reveal insights into pathogenic strategies of the genus
  2. 21482
    “…METHODS: The gene expression profiles of GSE43523 from nasal epithelial cells and GSE75011 from Th2-enriched CD4+ T cells in blood were downloaded from the Gene Expression Omnibus database. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses and protein–protein interaction (PPI) network analysis were conducted to investigate the functional changes of genes. …”
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    Identification of gene biomarkers with expression profiles in patients with allergic rhinitis
  3. 21483
    “…We ran sWES and WGS and applied our interactome-prioritization algorithm based on the network expansion of a seed group of GWMD-related genes derived from the Human Phenotype Ontology terms of each patient. RESULTS: We evaluated 126 patients (101 children and 25 adults) with ages ranging from 1 month to 74 years. …”
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    Diagnosis of Genetic White Matter Disorders by Singleton Whole-Exome and Genome Sequencing Using Interactome-Driven Prioritization
  4. 21484
    “…The intersecting targets of GpM and AD were identified and Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were carried out to analyze the mechanism of them. …”
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    Network pharmacology analysis reveals neuroprotection of Gynostemma pentaphyllum (Thunb.) Makino in Alzheimer’ disease
  5. 21485
    “…The functional analysis using gene ontology and Kyoto Encyclopedia of Genes and Genomes databases and a gene set enrichment analysis (GSEA) were conducted to examine the PCGF1-related biological processes and signaling pathways. …”
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    PCGF1 is a prognostic biomarker and correlates with tumor immunity in gliomas
  6. 21486
    “…In addition, it showed that more than 64 percentages of AktWRKY genes were differentially expressed during fungal infection in I02 and H05. Furthermore, Gene ontology (GO) analysis showed that AktWRKY genes were categorized into 26 functional groups under cellular components, molecular functions and biological processes, and a predicted protein interaction network was also constructed. …”
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    Characterization of the WRKY gene family in Akebia trifoliata and their response to Colletotrichum acutatum
  7. 21487
    “…A compound–target network, compound–target–disease network, protein–protein interaction network, compound–target–pathway network, gene ontology, and pathway enrichment for hypertension were applied to identify the potential active compounds, drug targets, and pathways. …”
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    Vasorelaxant Activities and its Underlying Mechanisms of Magnolia Volatile Oil on Rat Thoracic Aorta Based on Network Pharmacology
  8. 21488
    “…According to the topological algorithm, we identified the key lncRNAs which had both the higher node degrees and the higher numbers of lncRNA–miRNA pairs and total pairs in the ceRNA network. Meanwhile, Gene Ontology (GO) and pathway analysis were performed using databases such as DAVID, KOBAS and Cytoscape plug-in ClueGO respectively. …”
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    Revealing key lncRNAs in cytogenetically normal acute myeloid leukemia by reconstruction of the lncRNA–miRNA–mRNA network
  9. 21489
    “…These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. …”
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    The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases
  10. 21490
    “…On the one hand, it can be used to perform Gene Ontology and biological pathways enrichment analysis over gene sets. …”
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    ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS
  11. 21491
    “…The expression level of SLC2A1 in CRC was certified by cell experiments and immunohistochemical staining analysis. The Genome Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) analyses of SLC2A1 relative genes were completed by bioinformatics analysis. …”
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    SLC2A1 is a Diagnostic Biomarker Involved in Immune Infiltration of Colorectal Cancer and Associated With m6A Modification and ceRNA
  12. 21492
    “…METHODS: The GSE32863 and GSE75037 data sets were standardized and merged to screen for differentially expressed genes (DEGs). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted. …”
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    Machine learning-based screening of the diagnostic genes and their relationship with immune-cell infiltration in patients with lung adenocarcinoma
  13. 21493
    “…Reactome pathway database and Gene ontology (GO) was subsequently performed for the extracted genes of three bipartite networks and miRNAs, respectively. …”
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    mRNA–miRNA bipartite networks reconstruction in different tissues of bladder cancer based on gene co-expression network analysis
  14. 21494
    “…We identified 543, 759, 670, and 181 differentially expressed genes (DEGs) in the hypothalamus, pituitary, ovary stroma, and F5 follicle membrane, respectively. Gene Ontology (GO) analysis revealed that DEGs from four HPG axis-related tissues were enriched in the "cellular component" category. …”
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    Transcriptomic analyses of the HPG axis-related tissues reveals potential candidate genes and regulatory pathways associated with egg production in ducks
  15. 21495
    “…The “limma” package of R was used to screen differentially expressed genes, and the “clusterProfiler” package was used to perform enrichment analysis of the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. …”
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    Bioinformatics Analysis Identified the Hub Genes, mRNA–miRNA–lncRNA Axis, and Signaling Pathways Involved in Rheumatoid Arthritis Pathogenesis
  16. 21496
    “…Differentially enriched biological functions and processes were identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis. …”
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    Transcriptome Analysis Reveals miR-302a-3p Affects Granulosa Cell Proliferation by Targeting DRD1 in Chickens
  17. 21497
    “…In total, 719 DEGs were obtained and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for function enrichment analysis. …”
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    Identification of novel prognostic targets in glioblastoma using bioinformatics analysis
  18. 21498
    “…Moreover, the functional annotation analysis based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases showed that DE mRNAs and the target genes of the lncRNAs were significantly enriched in organ morphogenesis, response to stimulus, haem binding, the immune system, arginine and proline metabolism, and fatty acid biosynthesis. …”
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    Comparative analysis of long noncoding RNA and mRNA expression provides insights into adaptation to hypoxia in Tibetan sheep
  19. 21499
    “…To evaluate performance, we used gene set enrichment (GSE) testing on 87 independent ENCODE ChIP-seq datasets of 34 transcription factors (TFs) and assessed concordance of results with known TF Gene Ontology annotations, and other benchmarks. RESULTS: The top ranked 741 (40%) EnTDefs significantly outperform the common, naïve approach of linking distal regions to the nearest genes, and the top 10 EnTDefs perform well when applied to ChIP-seq data of other cell types. …”
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    Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data
  20. 21500
    “…Thus, when available, the UniProt ID is provided, the protein UniProt name, the gene name, the organism as well as annotated involvement in diseases, gene ontology data, and cross-references to the Reactome pathway database. …”
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    A new ChEMBL dataset for the similarity-based target fishing engine FastTargetPred: Annotation of an exhaustive list of linear tetrapeptides
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