Neoantigens and the tumor microenvironment play important roles in the prognosis of high-grade serous ovarian cancer by Hua Yang, Mei Yu, Sen Zhong, Yan You, Fengzhi Feng

“…Univariate Cox proportional hazard analysis revealed poorer progression-free survival (PFS) for those patients who carried a higher number of neoantigens (P =0.0069), higher TMB (P =0.0083), and higher ITH (P =0.0249). Further Kyoto Encyclopaedia of Genes and Genomes (KEGG) analysis indicated the Differentially expressed genes (DEGs) in platinum-resistant and platinum-sensitive patients were mainly enriched in the phosphatidylinositol 3-kinase-Akt (PI3K-Akt) signaling pathway and focal adhesion pathway, which are associated with platinum resistance. …”
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Computational annotation of genes differentially expressed along olive fruit development by Martinelli Federico, Cultrera Nicolò GM, Baldoni Luciana, Alagna Fiammetta, Collani Silvio, Ramina Angelo, Barcaccia Gianni, Galla Giulio, Sebastiani Luca, Tonutti Pietro

“…The olive fruit-specific transcriptome dataset was used to query all known KEGG (Kyoto Encyclopaedia of Genes and Genomes) metabolic pathways for characterizing and positioning retrieved EST records. …”
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La "Tavola Ritonda": le joug et le jeu de la chevalerie by Giulia Murgia

“…His anonymous compiler gives life to a project inspired by the desire to make the legend of Tristan and Yseut a sort of encyclopaedia, able to establish a dialogue with the Italian contemporaneity and to update the myth while rationalizing and moralizing its message. …”
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Mass spectrometry-based metabolic profiling for identification of biomarkers in serum related to the change of laying ducks in different physiological periods by Qian Tang, Hehe Liu, Jingjing Qi, Xiping Yan, Ahsan Mustafa, Yang Xi, Junpeng Li, Lili Bai, Li Liang, Chunchun Han, Jiwen Wang

“…In addition, the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis showed that sexual maturity was mainly involved in the biosynthesis of secondary plant metabolites, Tricarboxylic Acid Cycle, Mineral absorption, pentose phosphate pathway, and Oxocarboxylic acid metabolism. …”
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Exosomal miRNAs as Potential Biomarkers for Preeclampsia: miR-1283 Has the Highest Expression, while miR-152-3p Has the Lowest Expression by Herman Sumawan, Ifrinda Giantari, Sofia Mubarika, Diah Rumekti Hadiati, Heru Pradjatmo

“…Enrichment analysis of The Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways were performed to examine the pathophysiological pathways of preeclampsia, using the DIANA–miRPath v3.0. …”
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Effects of tea catechin extracts from BB35 and purple (TRFK 306) tea clones on the gene expression of Egfr, App, Bcl2, Dnmt, Casp3, Hif1a, Gadd45b and Psmb5 genes involved in tripl... by Joseph Ndacyayisenga, Festus M. Tolo, Fred Wamunyokoli, Esther N. Maina

“…In silico assessment including Absorption, Distribution, Metabolism and Excretion (ADME) study for drug-likeness evaluation, Drug target prediction, Protein-protein interaction (PPI) network analysis and construction, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment and analysis for targets and Molecular docking study was conducted. …”
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DPP6 and MFAP5 are associated with immune infiltration as diagnostic biomarkers in distinguishing uterine leiomyosarcoma from leiomyoma by Yumin Ke, LiuXia You, YanJuan Xu, Dandan Wu, Qiuya Lin, Zhuna Wu

“…The DEGs were used for Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Disease Ontology (DO) enrichment analyses as well as gene set enrichment analysis (GSEA). …”
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Associations between maternal lifetime stressors and negative events in pregnancy and breast milk-derived extracellular vesicle microRNAs in the programming of intergenerational st... by Anne K. Bozack, Elena Colicino, Rodosthenis Rodosthenous, Tessa R. Bloomquist, Andrea A. Baccarelli, Robert O. Wright, Rosalind J. Wright, Alison G. Lee

“…Abbreviations: EV: extracellular vesicle; PRISM: PRogramming of Intergenerational Stress Mechanisms pregnancy cohort; LSCR: Life Stressor Checklist-Revised survey; NLE: negative life event; CRISYS-R: Crisis in Family Systems-Revised survey; KEGG: Kyoto Encyclopaedia of Genes and Genomes; NYC: New York City; SD: standard deviation; IQR: interquartile range; Cq: relative cycle threshold values; PCA: principal component analysis…”
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A novel survival prediction signature outperforms PAM50 and artificial intelligence-based feature-selection methods by Foo, Reuben Jyong Kiat, Tian, Siqi, Tan, Ern Yu, Goh, Wilson Wen Bin

“…The robustness of a breast cancer gene signature, the super-proliferation set (SPS), is initially tested and investigated on breast cancer cell lines from the Cancer Cell Line Encyclopaedia (CCLE). Previously, SPS was derived via a meta-analysis of 47 independent breast cancer gene signatures, benchmarked on survival information from clinical data in the NKI dataset. …”
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ranscriptome profile and gene expression during different ovarian maturation stages of Macrobrachium rosenbergii (De Man, 1879) by Mardhiyyah, Mohd Pauzi, Zakaria, Muhammad Faiz, Amin-Safwan, Adnan, Nur-Syahirah, Mamat, Sung, Yeong Yik, Ma, Hongyu, Ikhwanuddin, Mhd

“…The BLASTX unigene search against National Centre for Biotechnology Information (NCBI), non-redundant (NR), nucleotide sequence (NT), Kyoto Encyclopaedia of Genes and Genomes Orthology (KO), Swiss-Prot, Protein Family (PFAM), Gene Ontology (GO), and euKaryotic Orthologous Groups (KOG) databases yielded 27,680 (28.24%), 7,449 (7.59%), 13,026 (13.29%), 22,606 (23.06%), 29,907 (30.51%), 30,025 (30.63%) and 14,368 (14.65%) significant matches, respectively, totalling to 37,338 annotated unigenes (38.09%). …”
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Genetic polymorphism in untranslated regions of PRKCZ influences mRNA structure, stability and binding sites by Aneela Mustafa, Maria Shabbir, Yasmin Badshah, Khushbukhat Khan, Fizzah Abid, Janeen H. Trembley, Tayyaba Afsar, Ali Almajwal, Suhail Razak

“…The analysis of the transcription binding sites (TFBS) was done through the Alibaba tool, and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) was employed to identify pathways associated with PRKCZ. …”
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MKRN1 promotes colorectal cancer metastasis by activating the TGF-β signalling pathway through SNIP1 protein degradation by Yi Zhang, Qin-shan Li, Hong-lin Liu, Hong-ting Tang, Han-lin Yang, Dao-qiu Wu, Yu-ying Huang, Li-cheng Li, Li-hong Liu, Meng-xing Li

“…Methods MKRN1 expression in CRC was analysed using the Cancer Cell Line Encyclopaedia and the Cancer Genome Atlas (TCGA) databases. …”
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Full-length transcriptome sequencing and comparative transcriptome analysis of Eriocheir sinensis in response to infection by the microsporidian Hepatospora eriocheir by Libo Hou, Mengdi Wang, Lei Zhu, Mingxiao Ning, Jingxiu Bi, Jie Du, Xianghui Kong, Wei Gu, Qingguo Meng

“…In addition, 74,732 unigenes were mapped to at least one of the following databases: Non-Redundant Protein Sequence Database (NR), Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), KEGG Orthology (KO) and Protein family (Pfam). …”
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A two-microRNA signature predicts the progression of male thyroid cancer by Liu Bingyang, Shi Haihong, Qiu Weigang, Wu Xinquan, Li Liqiong, Wu Wenyi

“…Gene Ontology (GO) and the Kyoto Encyclopaedia of Gene and Genome (KEGG) enrichment analyses were then used to explore the function of miRNA target genes. …”
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Identification of Key Genes for Pyroptosis-Induced Salivary Gland Inflammation in Sjogren’s Syndrome Based on Microarray Data and Immunohistochemistry Analysis by Zhang K, Luo Z, Zhu X, Yao X, Lu D, Chen L, Hong T, Ren Y, Wang X

“…Subsequently, ClueGO enrichment analysis, Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis, Protein-protein Interaction (PPI), and identification and co-expression analysis of hub genes were performed. …”
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The effect of high altitude on ephedrine content and metabolic variations in two species of Ephedra by Mengnan Lu, Wenjia He, Ziyan Xu, Yan Lu, M. James C. Crabbe, M. James C. Crabbe, M. James C. Crabbe, Ji De

“…We collected a total of 84 individuals representing five Ephedra gerardiana and nine Ephedra saxatilis populations respectively located from 3158 to 5200 meters altitude, and determined the relative content of 213 metabolites using UHPLC-MS/MS (Ultra-High-Performance Liquid Chromatography-tandem mass spectrometry). 37 Chemical compositions were annotated using the KEGG (Kyoto Encyclopaedia of Genes and Genomes) database. From the top five significant enrichments in metabolic KEGG pathway analysis, we found a total of 166 compounds belonging to phenylpropanoids, 123 flavonoids, 67 metabolites carried by ABC transporters, and 61 in purine metabolism. …”
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Network pharmacology and molecular docking analysis reveal insights into the molecular mechanism of shiliao decoction in the treatment of cancer-associated malnutrition by Sidan Long, Sidan Long, Shuangshuang Ji, Peng Xue, Hongting Xie, Yinjie Ma, Shijie Zhu

“…The network of target protein-protein interactions (PPI) was constructed using the STRING database, while gene ontology (GO) functional terms and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways associated with potential targets were analyzed using a program in R language (version 4.2.0). …”
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Overexpression of <i>DGAT2</i> Regulates the Differentiation of Bovine Preadipocytes by Pan-Pan Guo, Xin Jin, Jun-Fang Zhang, Qiang Li, Chang-Guo Yan, Xiang-Zi Li

“…The effects on the differentiation of Yanbian cattle preadipocytes were examined using molecular and transcriptomic techniques, including differentially expressed genes (DEGs) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. …”
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Integrated bioinformatics analysis for the screening of hub genes and therapeutic drugs in ovarian cancer by Dan Yang, Yang He, Bo Wu, Yan Deng, Nan Wang, Menglin Li, Yang Liu

“…Next, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses were performed for functional enrichment analysis of these DEGs. …”
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Epithelial to mesenchymal transition in mammary gland tissue fibrosis and insights into drug therapeutics by Mudasir Ahmad Syed, Basharat Bhat, Abiza Wali, Afnan Saleem, Lateef Ahmad Dar, Mudasir Bashir Gugjoo, Shakil Bhat, Sahar Saleem Bhat

“…In-silico analysis of protein-protein interactions suggest the possible role of MAPK1, actin alpha 2 (ACTA2), COL1A1, and NFκB1 in regulating TGFβ1, ubiquitin C (UBC), specificity protein 1 (SP1) and E1A binding protein P300 (EP300). Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment suggests advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signalling pathway, relaxin signalling pathway and extra cellular matrix (ECM) receptor interactions underlying fibrosis mechanism. …”
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