Article
Biochemistry & Molecular Biology
Stanislav Kotlyarov
Summary: Atherosclerosis is a serious medical condition that develops over many years and involves multiple cells and factors of clinical interest. This study investigated the gene ontology of differentially expressed genes in endothelial cells under the influence of atherogenic factors such as smoking, oscillatory shear, and oxidized low-density lipoproteins. The results showed that these genes were mainly involved in cytokine-mediated signaling pathway, innate immune response, lipid biosynthetic process, and nitric-oxide synthase activity.
Article
Medicine, General & Internal
Hailong Zhou, Jianmin Jiang, Xiaohua Chen, Zhiwei Zhang
Summary: This study investigated the genes, miRNAs, pathways, and miRNA-gene interaction pairs involved in female osteoporosis. The results revealed the important roles of miRNAs and genes in the pathogenesis of osteoporosis, and identified several pathways related to the disease.
Article
Biotechnology & Applied Microbiology
Jingwen Shi, Ying Huang
Summary: By using bioinformatics analysis, this study explored the potential genetic targets of adenomyosis. The results suggest that genes involved in tight junction may play a key role in the development of adenomyosis and could be a potential treatment strategy.
Article
Plant Sciences
Tao Yan, Meng Sun, Rui Su, Xiaozhong Wang, Xuedan Lu, Yunhua Xiao, Huabing Deng, Xiong Liu, Wenbang Tang, Guilian Zhang
Summary: Cold stress has a significant impact on the growth and development of rice, particularly the susceptible indica cultivar. This study identified genes and transcription factors associated with cold responsiveness in indica rice and revealed the molecular mechanisms underlying cold responses, providing important insights for enhancing cold tolerance in susceptible varieties.
Article
Plant Sciences
Maria Jurado, Ana Campa, Juan Jose Ferreira
Summary: This study identified differentially expressed genes (DEGs) related to response to anthracnose in common bean crops. The resistant genotype exhibited enriched GO terms associated with stimulus response, hormone signaling, cellular component organization, phosphorylation activities, and transcriptional regulation. The region containing the Co-2 cluster, a resistance gene, was identified and found to contain 23 DEGs, including 8 typical R genes. The structural changes observed in this region were used to design potential DNA markers for breeding purposes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Sarah Rashid, Scott G. Wilson, Kun Zhu, John P. Walsh, Jiake Xu, Benjamin H. Mullin
Summary: This study analyzed the transcriptome of human peripheral blood mononuclear cells and their differentiated osteoclast-like cells in culture, identifying differentially expressed genes and associated biological pathways in the progression of osteoporosis. Several well-established osteoclast genes were significantly upregulated in osteoporosis, and the upregulated genes were involved in cell division, migration, adhesion, as well as oxidative phosphorylation, glycolysis, lysosome, and focal adhesion pathways.
Article
Endocrinology & Metabolism
Luis Dias Ferreira Soares, Gerda Cristal Villalba Silva, Francyne Kubaski, Roberto Giugliani, Ursula Matte
Summary: This study developed a database containing differentially expressed genes from different public MPS data. Users can search for genes by species, MPS type, or tissue type, and view heatmaps and dot plots for top genes and ontologies.
MOLECULAR GENETICS AND METABOLISM
(2021)
Article
Multidisciplinary Sciences
Hai-Bo Zhang, Xiao-Bao Ding, Jie Jin, Wen-Ping Guo, Qiao-Lei Yang, Peng-Cheng Chen, Heng Yao, Li Ruan, Yu-Tian Tao, Xin Chen
Summary: The house mouse is a valuable mammalian model for genetic research, offering insights into human diseases. To facilitate molecular mechanism studies in mice, researchers have developed the Mouse Interactome Database and a gene set linkage analysis web tool.
Article
Biotechnology & Applied Microbiology
Yong Liu, Jing Huang, Rajan Pandey, Pengyuan Liu, Bhavika Therani, Qiongzi Qiu, Sridhar Rao, Aron M. Geurts, Allen W. Cowley Jr, Andrew S. Greene, Mingyu Liang
Summary: This study found that in order to accurately identify differentially expressed genes (DEGs) with various characteristics in single-cell clusters, there need to be at least 2000 cells. However, for the majority of DEGs with extremely small p values or transcript abundance greater than a few hundred transcripts per million in bulk RNA-seq analysis, clusters with as few as 50-100 cells may be sufficient.
Article
Biochemistry & Molecular Biology
Soraya Mousavi, Roberto Mariotti, Maria Cristina Valeri, Luca Regni, Emanuele Lilli, Emidio Albertini, Primo Proietti, Daniela Businelli, Luciana Baldoni
Summary: This study evaluated the salt tolerance of four olive cultivars and identified key genes involved in salt stress response. The results showed that Koroneiki was the most salt-tolerant cultivar, while Fadak86 and Picual were the most susceptible ones. The expression analysis of candidate genes suggested the important roles of OeNHX7, OeP5CS, OeRD19A, and OePetD in activating a salt tolerance mechanism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Leisheng Shi, Yan Wang, Chong Li, Kunlin Zhang, Quansheng Du, Mei Zhao
Summary: AddictGene is a resource that integrates multidimensional data related to commonly abused substances, including gene expression, gene-gene interaction, gene-drug interaction, and epigenetic regulatory information. This database provides detailed information about differentially expressed genes, offering a valuable resource for studying the molecular mechanisms underlying addiction.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Svetlana Shikhevich, Irina Chadaeva, Bato Khandaev, Rimma Kozhemyakina, Karina Zolotareva, Anna Kazachek, Dmitry Oshchepkov, Anton Bogomolov, Natalya V. Klimova, Vladimir A. Ivanisenko, Pavel Demenkov, Zakhar Mustafin, Arcady Markel, Ludmila Savinkova, Nikolay A. Kolchanov, Vladimir Kozlov, Mikhail Ponomarenko
Summary: Mainstream transcriptome profiling of susceptibility versus resistance to age-related diseases (ARDs) focuses on differentially expressed genes (DEGs) specific to gender, age, and pathogeneses. In this study, the periaqueductal gray (PAG) transcriptome of tame versus aggressive rats was sequenced and compared with known ARD-linked DEGs in animals. The analysis revealed significant correlations between behavior-related DEGs and ARD-susceptibility-related DEGs. With human ARD susceptibility and resistance DEGs as controls, a common molecular marker for ARDs was identified: excess expression of Fc gamma receptor IIb suppressing immune cell hyperactivation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Bokang Ko, Jeremy M. Van Raamsdonk
Summary: Gene expression studies provide valuable insights into biological processes, such as aging. This study shows that pooling individual RNA samples before sequencing can yield similar results as sequencing them individually, reducing the cost of experiments. Analysis of gene expression changes across the genome is a powerful and unbiased tool for understanding molecular mechanisms.
Article
Cell Biology
Xue-Min Cao, Sheng-Long Li, Yu-Qi Cao, Ye-Hua Lv, Ya-Xian Wang, Bin Yu, Chun Yao
Summary: The initial mechanical damage of a spinal cord injury triggers a complex secondary injury cascade involving multiple systems and cells. This study analyzed the differences in gene expression between rostral and caudal regions after injury and identified distinct biological process alterations in these two segments, providing new insights into the pathology of SCI.
NEURAL REGENERATION RESEARCH
(2022)
Article
Oncology
Jongchan Kim
Summary: Identification of specific biological functions and pathways in metastatic breast cancer can help predict clinical outcomes, and novel biomarkers such as CCNA2, CENPN, and ABAT may be associated with aggressive or metastatic breast cancer and patient prognosis.
WORLD JOURNAL OF SURGICAL ONCOLOGY
(2021)