Article
Agronomy
Qin Lu, Yan Li, Jing Liao, Zhaohong Ni, Shunchao Xia, Maofa Yang, Haiyin Li, Jianjun Guo
Summary: This study investigated the role of histone H3 acetylation in diapause of the cotton bollworm and found that it is closely related to pupal diapause, suggesting its potential as a target for pest control.
PEST MANAGEMENT SCIENCE
(2023)
Article
Entomology
Yunxia Cheng, Min Hu, Aiguo Kang, Yonghong Xiao, Lizhi Luo, Xingfu Jiang
Summary: This study investigated the impact of sex ratio on the population size of beet webworms, and found that population outbreaks were associated with a sex ratio of two or more, while population collapse was associated with a sex ratio lower than one. The results suggest that sex ratio can serve as a definite indicator for predicting the occurrence cycle of beet webworms.
Article
Plant Sciences
Mengjie Cui, Suoyi Han, Du Wang, Muhammad Salman Haider, Junjia Guo, Qi Zhao, Pei Du, Ziqi Sun, Feiyan Qi, Zheng Zheng, Bingyan Huang, Wenzhao Dong, Peiwu Li, Xinyou Zhang
Summary: This study identifies hub genes positively associated with resistance to Aspergillus flavus in peanuts through comparative transcriptome and weighted gene co-expression network analysis. The resistant genotype shows a rapid response to A. flavus and quick preparation for the translation of resistance-related genes, possibly contributing to its high resistance. Several specific genes, including those encoding pathogenesis-related proteins, play major roles in peanut resistance to A. flavus.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Narges Rezaie, Farilie Reese, Ali Mortazavi
Summary: PyWGCNA is a Python package designed to identify co-expression modules from large RNA-seq datasets. It has a faster implementation than the R version and provides additional functionalities such as functional enrichment analysis, protein-protein interaction analysis, and comparison of multiple co-expression modules.
Article
Parasitology
Kennedy W. Mwangi, Rosaline W. Macharia, Joel L. Bargul
Summary: The study constructed a gene co-expression network of insect-stage trypanosomes using RNA-Seq data and identified enriched modules for genes that play key roles in the parasite's development in the tsetse fly. Additionally, potential 3' UTR regulatory elements for genes in the same module were predicted using the FIRE tool. This network provides a valuable resource for identifying candidate genes for functional studies and understanding the molecular mechanisms underlying important biological processes during the parasite's development in the tsetse fly, which could lead to the identification of potential molecular targets for disease control.
PARASITES & VECTORS
(2021)
Article
Biotechnology & Applied Microbiology
Yuxin Yang, Xueying Zhang, Lifen Wu, Lichao Zhang, Guoxiang Liu, Chuan Xia, Xu Liu, Xiuying Kong
Summary: Wheat heading date is crucial for environmental adaptability and yield component regulation. RNA-Seq analysis identified thousands of differentially expressed genes associated with flowering time. Co-expression networks of key flowering time genes were established, and a potential candidate gene was discovered for further study on the regulatory mechanism of wheat heading date.
Article
Genetics & Heredity
Ceyda Kasavi
Summary: In this study, a meta-analysis of transcriptome datasets of serous ovarian adenocarcinoma was performed to identify novel candidate biomarker signatures. A differential co-expression network was constructed, and 439 differentially expressed genes were identified. Module analysis revealed a co-expressed gene module consisting of 17 genes. Eleven biomarker candidates were determined through ROC curve analysis, and miRNAs targeting these genes were identified. Six genes and two miRNAs were suggested as novel candidate prognostic biomarkers for ovarian cancer.
FRONTIERS IN GENETICS
(2022)
Article
Horticulture
Caixia Wang, Jinjiao Yan, Bichun Hu, Ruifeng Wang, Bingjie Miao, Fanman Zeng, Fengwang Ma, Qingmei Guan, Jidi Xu
Summary: Histone acetylation is regulated by a pair of antagonistic enzymes, HATs and HDACs. This study identified and analyzed the HDACs genes in Apple, and found their dynamic expression during development and stress responses. Additionally, a candidate gene, MdHDA6, was found to play a significant role in drought and salt tolerance.
SCIENTIA HORTICULTURAE
(2023)
Article
Agronomy
Blaise Pascal Muvunyi, Xiang Lu, Junhui Zhan, Sang He, Guoyou Ye
Summary: This study conducted a meta-analysis of previous RNA-Seq studies to elucidate the genetic mechanisms regulating zinc deprivation response in rice. By using weighted gene co-expression network analysis (WGCNA), modules of co-expressed genes were identified, along with conserved differentially expressed genes (DEGs) and their molecular pathways. The findings provide a comprehensive insight into zinc deficiency response and may facilitate gene and pathway prioritization for improving zinc use efficiency and zinc biofortification in rice.
Article
Biotechnology & Applied Microbiology
Shan Zhang, Jian Liu, Lian Shi, Qianchao Wang, Ping Zhang, Hongxin Wang, Junna Liu, Hanxue Li, Li Li, Xinyi Li, Liubin Huang, Peng Qin
Summary: Through transcriptome analysis, we identified key genes associated with phosphorus level responses in quinoa seedlings. These genes encode proteins from various transcription factor families, such as MYB, WRKY, and ERF, which play crucial roles in abiotic stress resistance. This library of candidate genes associated with phosphorus level responses will aid in breeding phosphorus-tolerant quinoa varieties.
Article
Physiology
Mengyin Chen, Siliang Chen, Dan Yang, Jiawei Zhou, Bao Liu, Yuexin Chen, Wei Ye, Hui Zhang, Lei Ji, Yuehong Zheng
Summary: This study combined DEGs and WGCNA to establish a DEG co-expression network in carotid plaques, proposing potential therapeutic targets for carotid atherosclerosis.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sudhir Ghandikota, Mihika Sharma, Harshavardhana H. Ediga, Satish K. Madala, Anil G. Jegga
Summary: This study analyzed lung transcriptomic data to identify gene modules associated with idiopathic pulmonary fibrosis (IPF) and identified potential biomarkers. Validation studies confirmed the correlation of CRABP2 expression with decline in lung function.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Haiying Geng, Meng Wang, Jiazhen Gong, Yupu Xu, Shisong Ma
Summary: The study presents a computational approach named EXPLICIT to predict gene expression in Arabidopsis using transcription factors, demonstrating better accuracy in predicting transcriptomes compared to existing tools and offering new insights into transcriptional regulation in diverse plant pathways.
Article
Genetics & Heredity
James P. Blackmur, Peter G. Vaughan-Shaw, Kevin Donnelly, Bradley T. Harris, Victoria Svinti, Anna-Maria Ochocka-Fox, Paz Freile, Marion Walker, Toby Gurran, Stuart Reid, Colin A. Semple, Farhat V. N. Din, Maria Timofeeva, Malcolm G. Dunlop, Susan M. Farrington
Summary: This study used weighted gene co-expression network analysis to reveal the impact of vitamin D supplementation on gene modules in normal human rectal epithelial cells, and identified modules associated with immune system, hormone metabolism, cell growth, and RNA metabolism.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Tenghao Yang, Zepai Chi, Guoyuan Liu, Xuwei Hong, Sizhe Cao, Kequan Cheng, Yonghai Zhang
Summary: Bladder cancer (BLCA) is a common malignancy with a poor prognosis and high treatment costs. In this study, the genes ANLN and ASPM were identified as prognostic biomarkers for BLCA. High expression of ANLN and ASPM was associated with poor overall survival, and the ANLN gene showed a significant increase in high-grade BLCA. These findings suggest that ANLN and ASPM may be promising targets for improving BLCA occurrence and progression.
FRONTIERS IN GENETICS
(2023)