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Mapping of de novo mutations in primary biliary cholangitis to a disease-specific co-expression network underlying homeostasis and metabolism

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Journal of Genetics and Genomics 2022年第2期49卷 145-154页

作者： Lu Wang Jinchen Li Chan Wang Ruqi Tang Jialong Liang Yuhua Gong Yaping Dai Ningling Ding Jian Wu Na Dai Lei Liu Yi Zhao Youlin Shao Weifeng Zhao Peng Jiang Xingjuan Shi Weichang Chen Ye Tian Xiangdong Liu Xiong Ma Zhongsheng Sun Key Laboratory of Developmental Genes and Human Diseases Institute of Life SciencesSoutheast University2 Sipailou RoadNanjingJiangsu 210096China Beijing Institutes of Life Science Chinese Academy of SciencesNo.1 West Beichen RoadChaoyang DistrictBeijing 100101China Department of Gastroenterology and Hepatology Shanghai Institute of Digestive DiseasesShanghai Jiao Tong University School of Medicine Afﬁliated Renji Hospital145 Shandong Middle RoadShanghai 200001China Department of Laboratory Medicine The Third People’s Hospital of Zhenjiang300 DaijiamenZhenjiangJiangsu 212021China Department of Laboratory Medicine The Fifth People’s Hospital of Wuxi1215 Guangrui RoadWuxiJiangsu 214000China Department of Hepatology The Fifth People’s Hospital of SuzhouSoochow University10 Guangqian RoadSuzhouJiangsu 215131China Department of Rheumatology First Afﬁliated Hospital of Soochow University188 Shizi RoadSuzhouJiangsu 215006China Department of Gastroenterology Jiangsu University Afﬁliated Kunshan Hospital91 Qianjin West RoadKunshanJiangsu 215300China Department of Gastroenterology Yixing People’s Hospital75 Tongzhenguan RoadYixinJiangsu 214200China Department of Gastrointestinal Endoscopy Eastern Hepatobiliary Surgery Hospital700 Moyu North RoadShanghai 201800China Department of Hepatology The Third People’s Hospital of Changzhou300 Lanling North RoadChangzhouJiangsu 213001China Department of Infectious Diseases First Afﬁliated Hospital of Soochow University188 Shizi RoadSuzhouJiangsu 215006China Department of Gastroenterology First Afﬁliated Hospital of Soochow University188 Shizi RoadSuzhouJiangsu 215006China Department of Radiology Second Afﬁliated Hospital of Soochow University1055 Sanxiang RoadSuzhouJiangsu 215004China Institute of Genomic Medicine Wenzhou Medical UniversityUniversity TownChashanWenzhouZhejiang 325035China

Primary biliary cholangitis(PBC) is an autoimmune disease involving dysregulation of a broad array of homeostatic and metabolic processes. Although considerable single-nucleotide polymorphisms have been unveiled, a large fraction of risk factors remains enigmatic. Candidate genes with rare mutations that tend to confer more deleterious effects need to be identified. To help pinpoint cellular and developmental mechanisms beyond common noncoding variants, we integrate whole exome sequencing with integrative network analysis to investigate genes harboring de novo mutations. Prominent convergence has been revealed on a network of disease-specific co-expression comprised of 55 genes associated with homeostasis and metabolism. The transcription factor gene MEF2 D and the DNA repair gene PARP2 are highlighted as hub genes and identified to be up-and down-regulated, respectively, in peripheral blood data set. Enrichment analysis demonstrates that altered expression of MEF2 D and PARP2 may trigger a series of molecular and cellular processes with pivotal roles in PBC pathophysiology. Our study identifies genes with de novo mutations in PBC and suggests that a subset of genes in homeostasis and metabolism tend to act in synergy through converging on co-expression network, providing novel insights into the etiology of PBC and expanding the pool of molecular candidates for discovering clinically actionable biomarkers.

关键词： Primary biliary cholangitis de novo mutations Whole exome sequencing transcriptional networks Co-expression

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Phytochrome-regulated Gene Expression

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Journal of Integrative Plant Biology 2007年第1期49卷 11-20页

作者： Peter H. Quail Department of Plant and Microbial Biology University of Cafifomia Berkeley CA 94720 USA U.S. Department of Agriculture/Agriculture Research Service-Plant Gene Expression Center 800 Buchanan Street Albany CA 94710 LISA

Identification of all genes involved in the phytochrome （phy）-medieted responses of plants to their light environment is an important goal in providing an overall understanding of light-regulated growth end development. This article highlights end integrates the central findings of two recent comprehensive studies in Arabidopsis that have identified the genome-wide set of phy-reguleted genes that respond rapidly to red-light signals upon first exposure of dark-grown seedlings, and have tested the functional relevance to normal seedling photomorphogenesis of an Initial subset of these genes. The data：（a） reveal considerable complexity in the channeling of the light signals through the different phy-femily members （phyA to phyE） to responsive genes; （b） identify a diversity of transcription-factor-encoding genes as major early, if not primary, targets of phy signaling, end, therefore, as potentially important regulators in the transcriptional-network hierarchy; and （c） identify auxin-related genes as the dominant class among rapidly-regulated, hormone-related genes. However, reverse-genetic functional profiling of a selected subset of these genes reveals that only a limited fraction are necessary for optimal phy-induced seedling deetioletion.

关键词： expression profiling phytochrome signaling transcriptional networks microarrays reverse genetics functional profiling transcription factors auxin-related genes

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