Transcriptomic, histological and biochemical analyses of Macrobrachium nipponense response to acute heat stress by Xiao Wu, Yaoran Fan, Jianbin Feng, Keyi Ma, Jiale Li

“…These DEGs were significantly involved in the regulation of transcription, proteolysis, nucleus, cytoplasm, metal ion binding, and ATP binding by Gene ontology (GO) enrichment analysis. Furthermore, the DEGs in the hepatopancreas were significantly enriched in KEGG pathways including neuroactive ligand-receptor interaction, thyroid hormone synthesis, and ECM-receptor interaction. …”
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Deciphering the Transcriptional Metabolic Profile of Adipose-Derived Stem Cells During Osteogenic Differentiation and Epigenetic Drug Treatment by Giulia Gerini, Alice Traversa, Fabrizio Cece, Matteo Cassandri, Paola Pontecorvi, Simona Camero, Giulia Nannini, Enrico Romano, Francesco Marampon, Mary Anna Venneri, Simona Ceccarelli, Antonio Angeloni, Amedeo Amedei, Cinzia Marchese, Francesca Megiorni

“…<i>In silico</i> annotation and gene ontology analysis highlighted the activation of ethanol oxidation, ROS regulation, retinoic acid metabolism, and steroid hormone metabolism, as well as in the metabolism of lipids, amino acids, and nucleotides, and pinpointed potential new osteogenic drivers like AOX1 and ADH1A. …”
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Microarray Analysis Reveals a Potential Role of lncRNA Expression in 3,4-Benzopyrene/Angiotensin II-Activated Macrophage in Abdominal Aortic Aneurysm by Yingying Zhou, Jiaoni Wang, Yangjing Xue, Aili Fang, Shaoze Wu, Kaiyu Huang, Luyuan Tao, Jie Wang, Yigen Shen, Jinsheng Wang, Lulu Pan, Lei Li, Kangting Ji

“…The function of differential mRNAs was determined by pathway and Gene Ontology analysis. Eight pathways associated with inflammation were upregulated, and seven pathways including cell apoptosis were downregulated. …”
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Mapping genomic regions for reproductive stage drought tolerance in rice from exotic landrace-derived population by Challa Venkateshwarlu, Challa Venkateshwarlu, Paresh Chandra Kole, Arun Kumar Singh, Pronob J. Paul, Pallavi Sinha, Vikas Kumar Singh, Arvind Kumar

“…Through candidate gene analysis, the identified QTL regions in chromosome 1 (qDTY1.1) and chromosome 8 (qDTY8.1) revealed seven and five candidate genes, respectively, based on gene ontology that were significantly associated with rice grain yield-related drought traits. …”
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Effect of Acetyl tributyl citrate on bone metabolism based on network toxicology and molecular docking technology by Xuan Lin, Kun Lin, Yue Lai, Qingping Peng, Miao Xu, Yiting Xu, Jialin Yang, Huan Liu, Jianlin Shen

“…Following rigorous refinement using the STRING platform and Cytoscape software, we pinpointed ten core targets, encompassing KDM1A, EP300, HDAC2, EHMT2, DNMT1, and several others. In-depth Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, conducted within the Metascape database, revealed that the core targets of ATBC’s influence on bone metabolism are predominantly concentrated within vital signaling cascades, including thyroid hormone signaling, FOXO signaling, glucagon signaling, AMPK signaling, insulin signaling, adipocytokine signaling, and Notch signaling pathways. …”
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Neuroinflammation mediates the progression of neonate hypoxia-ischemia brain damage to Alzheimer’s disease: a bioinformatics and experimental study by Shengjie Zhang, Ruqiu Zhang, Zhaoqin Chen, Zihan Shao, An Li, Fan Li, Fang Huang

“…After identifying the common differentially expressed genes (DEGs) of Alzheimer’s disease and neonate Hypoxia-Ischemia Brain Damage by limma package analysis, five kinds of analyses were performed on them, namely Gene Ontology (GO) and pathway enrichment analysis, protein–protein interaction network, DEG-transcription factor interactions and DEG-microRNA interactions, protein-drug interactions and protein-disease association analysis, and gene-inflammation association analysis and protein-inflammation association analysis.ResultsIn total, 12 common DEGs were identified including HSPB1, VIM, MVD, TUBB4A, AACS, ANXA6, DIRAS2, RPH3A, CEND1, KALM, THOP1, AREL1. …”
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In silico analysis of hub genes and regulatory networks implicates the putamen in non-motor Parkinson’s disease disorders by Stephen Tunmise Akanbi, Joshua Ayodele Yusuf, Thompson Oluwaferanmi Ayandele, Dayo Samson Oladipupo, Darasimi Racheal Olorunlowu, Blessing Dorcas Olawuyi, Joshua Oluwafisayo Adepoju, Dolapo Emmanuel Opasina, Elizabeth Kehinde Opoola, Uchenna Victor Ugwuanyi, Olufunto Omodele Adeleye

“…Enrichment analysis of target genes was conducted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). …”
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The dual anti-inflammatory and anticoagulant effects of Jianpi Huashi Tongluo prescription on Rheumatoid Arthritis through inhibiting the activation of the PI3K/AKT signaling pathw... by Fanfan Wang, Fanfan Wang, Jian Liu

“…Animal experimental data indicated that XFC effectively reduced the levels of inflammatory and coagulant markers (IL-6, D-D, FBG, PAF, VEGF, and TF) in adjuvant-induced arthritis (AA) rats while enhancing the expression of anti-inflammatory factors (IL-10) (p &lt; 0.05). Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) results suggested that the pharmacodynamic mechanism of XFC may be closely related to the regulation of the PI3K/AKT signaling pathway. …”
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Six MicroRNA Prognostic Models for Overall Survival of Lung Adenocarcinoma by Juan Li, Xuyu Gu, Chanchan Gao, Jun Zhang

“…Possible biological processes associated with the miRNAs target gene were analyzed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). …”
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Proteomic analysis of spinal dorsal horn in prior exercise protection against neuropathic pain by Binglin Chen, Jiabao Guo, Chan Gong, Chenchen Zhu, Yang Wu, Shengbo Wang, Yili Zheng, Haixia Lu

“…LC–MS/MS proteomic analysis based on the label-free approach was used to detect protein profiles, and volcano plots, Venn diagrams, and clustering heatmaps were used to identify differentially expressed proteins (DEPs). Gene Ontology (GO) annotations, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and protein–protein interaction networks were employed to explore the biological importance of DEPs. …”
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Developmental Proteomics Reveals the Dynamic Expression Profile of Global Proteins of <i>Haemaphysalis longicornis</i> (Parthenogenesis) by Min-Xuan Liu, Xiao-Pei Xu, Fan-Ming Meng, Bing Zhang, Wei-Gang Li, Yuan-Yuan Zhang, Qiao-Ying Zen, Wen-Ge Liu

“…Here, we used the isobaric tags for a relative and absolute quantification (iTRAQ) technique to systematically describe and analyze the dynamic expression of the protein and the molecular basis of the proteome of <i>H. longicornis</i> in seven differential developmental stages (eggs, unfed larvae, engorged larvae, unfed nymphs, engorged nymphs unfed adults, and engorged adults). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the differentially expressed proteins (DEPs) were used. …”
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Transcriptome analysis of jejunal mucosal tissue in breeder hens exposed to acute heat stress by Yongcai Zhu, Satoshi Kubota, Phocharapon Pasri, Sitthipong Rakngam, Supattra Okrathok, Chayanan Pukkung, Shenglin Yang, Sutisa Khempaka

“…Functional analysis through gene ontology classification, pathway mapping via the Kyoto encyclopedia of genes and genomes, and protein interaction networks identified several important regulatory genes in thermal response (HSPA8 and HSPA2), energy homeostasis and fat metabolism (PDK4, PPARA, and CD36), glucose transport (SLC2A5), and cholesterol synthesis pathway (SQLE, CYP51A1, and HSD17B7). …”
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CD14loCD301b+ macrophages gathering as a proangiogenic marker in adipose tissues by Yibing Lv, Yidan Zheng, Shanshan Su, Junyi Xiao, Jie Yang, Lingyun Xiong, Yanyan Guo, Xiaoqi Zhou, Nengqiang Guo, Ping Lei

“…To investigate the underlying mechanisms, adipose tissues (ATs) from Cd14−/− and WT mice were subjected to deep RNA sequencing. Gene Ontology enrichment analysis revealed a significant enhancement of angiogenesis-related function in the Cd14−/− epididymal adipose tissues compared to WT counterpart, which was accompanied by an upregulation of Cd301b. …”
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New Insights into the Role of Inflammatory Pathways and Immune Cell Infiltration in Sleep Deprivation-Induced Atrial Fibrillation: An Integrated Bioinformatics and Experimental Stu... by Liang J, Tang B, Shen J, Rejiepu M, Guo Y, Wang X, Shao S, Guo F, Wang Q, Zhang L

“…Analyses focusing on functional enrichment, such as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), were conducted to pinpoint crucial biological mechanisms and pathways. …”
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Arctiin Protects Chondrocytes from Interleukin-1β-Induced Inflammation and Apoptosis by RNA Sequence In vivo and In vitro by Yong-Jia Song, Jia-Min Bao, Zeng-Qiao Zhang, Yun-Xiang Hai, Hao-Nan Wen, Tian-Jun Zhai, Wei Feng, Min Song

“…The genes and signaling pathways that were identified underwent analysis through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment studies. …”
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Better understanding the phenotypic effects of drugs through shared targets in genetic disease networks by Elena Díaz-Santiago, Aurelio A. Moya-García, Jesús Pérez-García, Raquel Yahyaoui, Raquel Yahyaoui, Christine Orengo, Florencio Pazos, James R. Perkins, James R. Perkins, James R. Perkins, Juan A. G. Ranea, Juan A. G. Ranea, Juan A. G. Ranea, Juan A. G. Ranea

“…Gaining traction in this field is the use of disease data linking genes with pathological phenotypes and combining this with drugtarget interaction data.MethodsWe introduce methodology to associate drugs with effects, both intended and adverse, using a tripartite network approach that combines drug-target and target-phenotype data, in which targets can be represented as proteins and protein domains.ResultsWe were able to detect associations for over 140,000 ChEMBL drugs and 3,800 phenotypes, represented as Human Phenotype Ontology (HPO) terms. The overlap of these results with the SIDER databases of known drug side effects was up to 10 times higher than random, depending on the target type, disease database and score threshold used. …”
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Proteomics analysis reveals age-related proteins in the urine of chronic kidney disease patients by Lin Xiong, Changwei Wu, Sipei Chen, Yong Zhang, Li Wang, Yi Li, Guisen Li

“…The analyzes conducted using the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes revealed that DEPs were significantly enriched in several clusters related to aging. …”
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Inhibition of anti-tumour reactivity of immune cells in the salivary gland cancer: A proteomic approach by Rajdeep Chakraborty, Charbel Darido, Aidan Tay, Thiri Zaw, Shoba Ranganathan, Fei Liu, Giuseppe Palmisano

“…We performed SWATH, proteome profilers, gene ontology biological function, functional annotation clustering and protein interaction network analysis of all cancer samples in the co-culture models. …”
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Exosomes from LPS-Stimulated hDPSCs Activated the Angiogenic Potential of HUVECs In Vitro by Xiangyu Huang, Wei Qiu, Yuhua Pan, Jianjia Li, Zhao Chen, Kaiying Zhang, Yifei Luo, Buling Wu, Wenan Xu

“…To investigate the proangiogenic mechanism of LPS-EXO, microRNA sequencing was performed to explore the microRNA profile of N-EXO and LPS-EXO. Gene Ontology (GO) analysis was used to study the functions of the predicted target genes. …”
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Desmoglein-2 was a novel cancer-associated fibroblasts-related biomarker for oral squamous cell carcinoma by Jin Liu, Zhonghao Sun, Shihui Cao, Hao Dai, Ze Zhang, Jingtao Luo, Xudong Wang

“…Differentially expressed genes and Cox regression analyses were used to identify candidate genes, and their functions were evaluated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. …”
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