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
Biology
Meiyu Duan, Yueying Wang, Ya Qiao, Yangyang Wang, Xingyuan Pan, Zhuyu Hu, Yanyue Ran, Xian Fu, Yusi Fan, Lan Huang, Fengfeng Zhou
Summary: The transcriptome is a comprehensive reflection of gene expression in a sample. This study proposes a novel approach to understanding the regulatory relationships between transcription factors (TFs) and their target genes (mRNAs) by quantitatively analyzing the differences in their expression levels. By using a multi-input multi-output regression model, this study explores the quantitative transcription regulation relationships of metabolism-related genes. The findings suggest that certain genes can exhibit differential regulation patterns even when their expression levels do not differ significantly, and these "dark biomarkers" may have important implications for disease detection and classification.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Medicine, Research & Experimental
Shengwei Liu, Jingdong Liu, Yuchun Wang, Ling Deng, Sha Chen, Xuan Wang, Tianrui Zuo, Qingwen Hu, Jiangyan Rao, Qian Wang, Zhi Dong
Summary: Through mRNA sequencing and analysis, this study found that BCP has multiple therapeutic targets on CIRI, significantly reducing neurological deficits and improving cerebral ischemia, including various genes and signaling pathways. Ten hub genes closely related to the treatment of BCP on CIRI were identified in the study.
Article
Multidisciplinary Sciences
Lulu Chen, Yingzhou Lu, Chiung-Ting Wu, Robert Clarke, Guoqiang Yu, Jennifer E. Van Eyk, David M. Herrington, Yue Wang
Summary: The study introduces a new method for detecting SDEGs, which was applied to gene expression datasets and demonstrated superior performance in improving deconvolution accuracy.
SCIENTIFIC REPORTS
(2021)
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
Biochemical Research Methods
Zimo Huang, Jun Wang, Zhongmin Yan, Maozu Guo
Summary: This paper proposes a Multiple Self-Attention (Epi-MSA) model for predicting differentially expressed genes (DEGs) from epigenetic data. The model uses convolutional neural networks for information embedding and multiple self-attention encoders to learn important gene locations. Experimental results show that Epi-MSA outperforms existing methods in performance and stability, and has good interpretability.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Xiaoying Lv, Xue Li, Shihong Chen, Gongyou Zhang, Kewei Li, Yueying Wang, Meiyu Duan, Fengfeng Zhou, Hongmei Liu
Summary: This study presents a complementary high-dimensional analysis procedure for transcriptome-based biomarker investigations, with a case study on metastatic colon cancer. By analyzing 805 samples, seven mRNA genes were identified as dark biomarkers that are non-differentially expressed in metastatic colon cancer but significantly associated with the disease.
Article
Biochemical Research Methods
Yixin Guo, Ziwei Xue, Ruihong Yuan, Jingyi Jessica Li, William A. Pastor, Wanlu Liu
Summary: With the introduction of RAD, a user-friendly web tool, researchers can identify both proximal and distal region associated differentially expressed genes (DEGs) and infer the regulatory function of these regions based on the distance to DEGs. RAD includes visualization of results and statistical inference for significance.
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
Multidisciplinary Sciences
Mohammed Dashti, Rasheeba Nizam, Prashantha Hebbar, Sindhu Jacob, Sumi Elsa John, Arshad Channanath, Hessa Al-Kandari, Thangavel Alphonse Thanaraj, Fahd Al-Mulla
Summary: This study identified differences in DNA methylation patterns between individuals with type 1 diabetes (T1D) and healthy individuals. Examining the genome-wide methylation of individuals from three Arab families, the study found that T1D-affected twins clustered together in terms of methylation patterns. The study also revealed 18 genes that were differentially methylated in T1D individuals compared to healthy individuals, and further validation confirmed the upregulation of ICA1 and DRAM1 genes in T1D samples.
SCIENTIFIC REPORTS
(2022)
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)
Review
Biochemistry & Molecular Biology
Alison K. Merikangas, Matthew Shelly, Alexys Knighton, Nicholas Kotler, Nicole Tanenbaum, Laura Almasy
Summary: Schizophrenia is a severe and complex mental disorder with a strong genetic component. Research on the genetic factors associated with schizophrenia is still in its early stages and further studies are needed to understand the influence of these genes on the etiology of the disorder.
MOLECULAR PSYCHIATRY
(2022)
Article
Multidisciplinary Sciences
Douglas Terra Machado, Otavio Jose Bernardes Brustolini, Yasmmin Cortes Martins, Marco Antonio Grivet Mattoso Maia, Ana Tereza Ribeiro de Vasconcelos
Summary: DEGRE is a user-friendly tool that considers fixed and random effects on individuals in the experimental design of RNA-Seq research to infer differentially expressed genes (DEGs). It preprocesses the data and applies generalized linear mixed models (GLMMs) to provide inference for DEGs. This tool efficiently removes genes that could impact the inference and offers improved assessment measures in cases with higher biological variability.
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
Biochemistry & Molecular Biology
Roubi Abuobeid, Luis V. Herrera-Marcos, Carmen Arnal, Seyed Hesamoddin Bidooki, Javier Sanchez-Marco, Roberto Lasheras, Joaquin C. Surra, Maria Jesus Rodriguez-Yoldi, Roberto Martinez-Beamonte, Jesus Osada
Summary: This study investigated the effect of squalene on the hepatic transcriptome by feeding pigs a high fat/cholesterol/fructose and methionine and choline-deficient steatotic diet with or without 0.5% squalene. The results showed that squalene accumulation in the liver correlated with the differential expression of 12 genes involved in the progression of non-alcoholic steatohepatitis. In vitro experiments also demonstrated a direct effect of squalene on the expression of these genes. These findings suggest that squalene may modulate gene expression changes that influence the progression of non-alcoholic steatohepatitis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)