Article
Genetics & Heredity
Mengmeng Pan, Pingping Yang, Fangce Wang, Xiu Luo, Bing Li, Yi Ding, Huina Lu, Yan Dong, Wenjun Zhang, Bing Xiu, Aibin Liang
Summary: A five-gene Cox model was developed for predicting the clinical outcome of DLBCL patients, which showed good predictive performance in training and validation datasets. Further analysis revealed the independent value and superiority of this prognostic model in risk prediction, as well as identifying vital pathways and potential therapeutic targets in DLBCL.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Shiyu Sun, Duoxiang Wang, Jingbin Li, Yaqi Lei, Gang Li, WenGuo Cai, Xiangxiang Zhao, Wanqi Liang, Dabing Zhang
Summary: This study used a transcriptomics approach to identify key genes and regulatory networks affecting pollen maturation in rice anthers in response to different day lengths. A total of 11,726 differentially expressed genes were revealed, with GO enrichment analysis showing enrichment in transport, carbohydrate, and lipid metabolic processes, as well as signaling pathways. Co-expression network analysis identified four modules strongly correlated with photoperiod, with 496 hub genes playing a key role in connecting photoperiod-sensitive genes affecting male fertility.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Medicine, General & Internal
Zhen-Chen Chu, Ting Cong, Jian-Yu Zhao, Jian Zhang, Zhi-Yuan Lou, Yang Gao, Xin Tang
Summary: This study identified three hub genes (HTRA1, P2RY6, and RCAN1) related to osteoarthritis through gene expression analysis and weighted gene co-expression network analysis. The expression levels of these genes were confirmed in osteoarthritis patients. The findings provide new insights for targeted treatment of osteoarthritis.
FRONTIERS IN MEDICINE
(2023)
Article
Microbiology
Li Zhang, Dan Song, Zufang Wu
Summary: The study demonstrates that Cyclocarya paliurus flavonoids can enhance the tolerance of E. faecalis to low pH environment by influencing the expression of genes related to cell wall and membrane, metabolism, etc. This finding deepens our understanding of the beneficial role of CPF on probiotics in the gastrointestinal environment.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Eleonora Porcu, Marie C. Sadler, Kaido Lepik, Chiara Auwerx, Andrew R. Wood, Antoine Weihs, Maroun S. Bou Sleiman, Diogo M. Ribeiro, Stefania Bandinelli, Toshiko Tanaka, Matthias Nauck, Uwe Volker, Olivier Delaneau, Andres Metspalu, Alexander Teumer, Timothy Frayling, Federico A. Santoni, Alexandre Reymond, Zoltan Kutalik
Summary: Identification of gene expression changes between healthy and diseased individuals can reveal mechanistic insights and biomarkers. The bi-directional transcriptome-wide Mendelian Randomization approach was proposed to assess causal effects between gene expression and complex traits. Comparing transcript levels between healthy and diseased individuals allows for the identification of differentially expressed genes that may be causes, consequences or mere correlates of the disease under scrutiny.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Shunuo Zhang, Yixin Zhang, Peiru Min
Summary: In this study, the biological characteristics during Hypertrophic scar (HS) formation were investigated through the integrative analysis of single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data. The study revealed that FB-1 fibroblasts were significantly expanded in HS, while the proportion of KC-2 keratinocytes was reduced. Cell-cell communication analysis showed changes in the autocrine signaling of HB-1 and the intercellular contacts between FB-1/FB-5 and KC-2 in HS. The transcriptionally regulatory network involved CREB3L1 and TWIST2 as critical transcription factors in myofibroblast formation in HS.
FRONTIERS IN GENETICS
(2022)
Article
Engineering, Biomedical
Zhenyu Tang, Hongda Cao, Yuyun Xu, Qing Yang, Jinda Wang, Han Zhang
Summary: In this study, a novel deep KNN-based OS time prediction method is proposed, which is more robust to data inconsistency and noise compared to end-to-end prediction methods. Moreover, a new inter-modality loss is introduced to extract complementary features from multiple imaging modalities. Experimental results on both an in-house dataset and a public dataset demonstrate that our method outperforms existing methods.
PHYSICS IN MEDICINE AND BIOLOGY
(2022)
Article
Genetics & Heredity
Hui Xie, Liushun Wang, Yihu Tang, Meng Zhao, Zihao Wang, Mingzhu Liu, Quangong Zhao, Jingxin Zhou, Yanhu Wu
Summary: This study investigates the potential pathogenesis of ferroptosis-related genes in mitral valve prolapse (MVP) and identifies CDKN2A, SLC1A4, and ATF3 as potential therapeutic targets.
FRONTIERS IN GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Wenqian Jia, Lei Wu, Zhong Zhuang, Minghong Xu, Yijia Lu, Zhixiu Wang, Hao Bai, Guohong Chen, Guobin Chang, Yong Jiang
Summary: This study investigated the molecular mechanism of threonine regulation on breast muscle development in Pekin ducks. The results showed that threonine intake level affected body weight and breast fiber size in Pekin ducks, and regulated the expression of many genes. This study provides new insights into the molecular mechanisms underlying breast muscle development in ducks.
Article
Obstetrics & Gynecology
Ashley W. Tiegs, Shiny Titus, Sameet Mehta, Rolando Garcia-Milian, Emre Seli, Richard T. Scott
Summary: The study found differential gene expression in cumulus cells from monosomy 21 and trisomy 21 embryos compared to euploid cumulus cells, with certain genes implicated in embryo developmental competence being differentially expressed in both conditions. Additionally, ingenuity pathway analysis showed that cell-cell contact function is affected in both monosomy and trisomy 21 cumulus cells, supporting the use of cumulus cell gene expression analysis as a potential tool for evaluating oocyte quality.
REPRODUCTIVE BIOMEDICINE ONLINE
(2021)
Article
Forestry
Kaikai Zhu, Lu Wei, Wenjuan Ma, Xiaoli Hu, Juan Zhao, Pengpeng Tan, Hui Liu, Gang Feng, Pinghua Fan, Fangren Peng
Summary: This study analyzed the transcriptome data of pecan trees under drought stress and identified thousands of differentially expressed genes (DEGs) involved in the response to drought. The study also provided insights into the functions of these drought-responsive genes and the molecular basis of pecan's drought stress response.
Article
Horticulture
Quan-Hui Li, Shi-Peng Yang, Ya-Nan Yu, Abid Khan, Peng-Long Feng, Muhammad Ali, Deng-kui Shao, Ya-Yi Wang, Rui-Xing Zhang, Wen-Xian Gai, Rui Han, Xiao Ma, Quan-Gang Hou, Zhen-Hui Gong
Summary: The color formation of red and orange pepper fruits is closely related to the composition and content of carotenoids, with significantly higher levels of zeaxanthin, beta-cryptoxanthin, beta-carotene, and capsanthin found in red peppers compared to orange peppers, and higher levels of lutein in orange peppers compared to red peppers. Differentially expressed genes (DEGs) were identified to be involved in the biosynthesis of carotenoids, phenylpropanoids, flavonoids, and phenylalanine metabolism. Key genes such as CHYB1 and CCS were found to play significant roles in carotenoid biosynthesis during fruit development. Additionally, transcription factors such as F-box protein SKIP23, GATA transcription factor 26, and others may be involved in the regulation of carotenoid metabolism pathway in pepper fruit color formation.
SCIENTIA HORTICULTURAE
(2021)
Article
Neurosciences
Chaoyou Fang, Houshi Xu, Yibo Liu, Chenkai Huang, Xiaoyu Wang, Zeyu Zhang, Yuanzhi Xu, Ling Yuan, Anke Zhang, Anwen Shao, Meiqing Lou
Summary: Through bioinformatic analysis, we found that aberrations of TRP family genes in glioma were correlated to prognosis, identified 10 hub genes that may play a crucial role in glioma, and demonstrated their significant association with patient prognosis.
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
Plant Sciences
Dong-ru Kang, Yi Zhu, Shuai-lei Li, Peng-hui Ai, Muhammad Ayoub Khan, Hong-xu Ding, Ying Wang, Zi-cheng Wang
Summary: This study investigates the effect of MET1 gene silencing on gene expression profile in Chrysanthemum x morifolium 'Zijingling', revealing significant changes in differentially expressed genes related to essential plant biological processes. While a sufficient number of candidate genes associated with flowering were identified, the overall number of genes with significant differences between transgenic and control lines was relatively low. This study sheds light on the transcriptional level interference of CmMET1 on chrysanthemum growth and development, providing a basis for further research on epigenetic regulation mechanisms in flower induction and development.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2021)