“…These clusters were subjected to both functional and pathway analysis by using the Kyoto Encyclopedia of Genes and Genomes. Interestingly, on a global gene expression level, the family members clustered together, regardless of their disease status. …”
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“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to obtain the enrichment data of differently expressed genes (DEGs). …”
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“…Furthermore, the co-expressed genes of prognostic lncRNAs were screened using a Multi-Experiment Matrix online tool for construction of lncRNA-gene networks. Finally, Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology (GO) function enrichment analyses were performed on genes in the lncRNA-gene networks using KOBAS, GOATOOLS and ClusterProfiler. …”
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“…The common downregulated genes were significantly enriched in BPs, including ‘response to wounding’, ‘positive regulation of immune system process’, ‘immune response’, ‘acute inflammatory response’ and ‘inflammatory response’. Kyoto Encyclopedia of Genes and Genomes pathway analysis identified that the common downregulated DEGs were primarily enriched in the ‘complement and coagulation cascades’ signaling pathway; the common upregulated DEGs were mainly enriched in ‘cell cycle’, ‘DNA replication’, ‘oocyte meiosis’ and the ‘mismatch repair’ signaling pathways. …”
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“…Based on the transcriptomics data, the differential gene expression profiles of hHF-iPSCs, HLCs, and PHHs were analyzed by Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, FunRich, and network analysis methods. …”
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“…A heat map for the DEGs was constructed with the Morpheus online tool and the top 200 genes (100 upregulated and 100 downregulated) were selected for further bioinformatics analysis, including analysis of gene ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, protein-protein interaction networks and Spearman's correlation tests. …”
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“…Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to explore the potential biological functions of the lncRNAs in the signature. …”
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“…GO analysis demonstrated that the differentially upregulated lncRNAs are associated with cell differentiation, homeostasis, cell growth and angiogenesis. Kyoto Encyclopedia of Gene and Genomes pathway analysis demonstrated that the differentially downregulated lncRNAs are mainly associated with arrhythmogenic right ventricular cardiomyopathy, hypertrophic cardiomyopathy and dilated cardiomyopathy. …”
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“…Gene Ontology functional and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using DAVID software. …”
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“…Furthermore, potential miR-486-5p mRNA targets were identified using 12 prediction tools and enrichment analysis was performed on the encoding genes using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. The expression levels of miR-486-5p were consistently downregulated in PTC compared with in normal tissue across datasets from TCGA, GEO (GSE40807, GSE62054 and GSE73182) and ArrayExpress (E-MTAB-736). …”
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“…Further pathway analyses of the differential expression genes were carried out using the Kyoto Encyclopedia of Genes and Genomes (KEGG). And real-time quantitative RT-PCR (qRT-PCR) was used for verification of the key findings. …”
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“…Lastly, variants were grouped by UMLS Medical Subject Heading (MeSH) identifiers to determine pathway enrichment in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. RESULTS: By linking KEGG pathways through underlying variant associations, we elucidated connections between the human genetic variant-based disease phenome and metabolic pathways, finding novel disease connections not otherwise detected through gene-level analysis. …”
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“…Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS), ChEMBL, DrugBank, PubChem, and Kyoto Encyclopedia of Genes and Genomes (KEGG) were queried for computational and pharmacologic data. …”
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“…Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed, and the protein-protein interaction (PPI) network of the differentially expressed genes (DEGs) was constructed using Cytoscape software. …”
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“…Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs was conducted using Database for Annotation, Visualization and Integrated Discovery and KEGG Orthology-Based Annotation System (KOBAS) online tools, respectively. …”
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“…Gene Ontology enrichment analysis revealed that 2,107 differentially methylated genes were associated with ‘biological process’, 13,351 differentially methylated genes were associated with ‘molecular function’, and 18,041 differentially methylated genes were associated with ‘cellular component’. Kyoto Encyclopedia of Genes and Genomes pathway-based analysis revealed 43 signaling pathways that were associated with 5,195 differentially methylated genes. …”
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“…In addition, Kyoto Encyclopedia of Genes and Genomes analysis revealed that the prospective target genes of miR-224-5p were largely enriched in the amino sugar and nucleotide sugar metabolism signaling pathway, and three genes [UDP-N-acetylglucosamine pyrophosphorylase 1 (UAP1), hexokinase 2 (HK2) and chitinase 1 (CHIT1)] enriched in this pathway showed higher expression (P<0.05). …”
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“…Their functions mainly involved cell viability, proliferation, differentiation, regeneration, and myelination. (2) The gene with the most obvious increase of all DEmRNAs in adult rats was Thrsp (log(2) FC = 9.01, P < 0.05), and the gene with the most obvious reduction was Col2a1 (log(2)FC = –8.89, P < 0.05). (3) Gene Ontology analysis showed that DEmRNAs were mainly concentrated in oligosaccharide binding, nucleotide-binding oligomerization domain containing one signaling pathway, and peptide-transporting ATPase activity. (4) Analysis using the Kyoto Encyclopedia of Genes and Genomes showed that, with increased age, DEmRNAs were mainly enriched in steroid biosynthesis, Staphylococcus aureus infection, and graft-versus-host disease. (5) Spearman's correlation coefficient method for evaluating NGS accuracy showed that the NGS results and quantitative reverse transcription polymerase chain reaction results were positively correlated (r(s) = 0.74, P < 0.05). …”
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“…The differentially expressed lncRNAs were selected for bioinformatic analysis including gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG). Quantitative real time PCR (qRT-PCR) was used to confirm the differential expression of lncRNAs. …”
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“…The DEGs were picked using Sailfish software, followed by Gene Set Enrichment Analysis (GSEA) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis using KEGG. …”
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