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Deciphering Ascorbic Acid Regulatory Pathways in Ripening Tomato Fruit Using a Weighted Gene Correlation Network Analysis Approach 被引量:3
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作者 Chao Gao Zheng Ju +5 位作者 Shan Li Jinhua Zuo Daqi Fu Huiqin Tian Yunbo Luo Benzhong Zhu 《Journal of Integrative Plant Biology》 SCIE CAS CSCD 2013年第11期1080-1091,共12页
Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important informatio... Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important information about the gene function and regulatory mechanism. L-Ascorbic acid (AsA), which is an essential nutrient component for human health and plant metabolism, plays key roles in diverse biological processes such as cell cycle, cell expansion, stress resistance, hormone synthesis, and signaling. Here, we applied a weighted gene correlation network analysis approach based on gene expression values and AsA content data in ripening tomato (Solanum lycopersicum L.) fruit with different AsA content levels, which leads to identification of AsA relevant modules and vital genes in AsA regulatory pathways. Twenty- four modules were compartmentalized according to gene expression profiling. Among these modules, one negatively related module containing genes involved in redox processes and one positively related module enriched with genes involved in AsA biosynthetic and recycling pathways were further analyzed. The present work herein indicates that redox pathways as well as hormone-signal pathways are closely correlated with AsA accumulation in ripening tomato fruit, and allowed us to prioritize candidate genes for follow-up studies to dissect this interplay at the biochemical and molecular level. 展开更多
关键词 Gene co-expression L-ascorbic acid network system biology weighted gene correlation network analysis approach.
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Transcriptional activation of MdDEF30 by MdWRKY75 enhances apple resistance to Cytospora canker
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作者 Hongchen Jia Youwei Du +6 位作者 Yuanyuan Liu Shuanghong Wang Yan Wang Sadia Noorin Mark LGleason Rong Zhang Guangyu Sun 《Journal of Integrative Agriculture》 2025年第3期1108-1125,共18页
Defensin,an essential component of plant development,is indispensable in pathogen resistance.However,the molecular function of defensins under pathological conditions of Cytospora canker has not been characterized in ... Defensin,an essential component of plant development,is indispensable in pathogen resistance.However,the molecular function of defensins under pathological conditions of Cytospora canker has not been characterized in apple plants.The present study exhibits a detailed overview of the phylogeny and structure of 29 defensins(MdDEF)in apple.Expression analysis revealed that MdDEF genes were spatiotemporally diverse across apple tissues.Five MdDEF genes were found to be significantly up-regulated following a challenge with Cytospora mali.The transgenic overexpression of five defensin genes in apple calli enhanced resistance to C.mali.Among them,MdDEF30 was strongly induced and conferred the highest resistance level in vivo.Meanwhile,antifungal activity assays in vitro demonstrated that a recombinant protein produced from MdDEF30could inhibit the growth of C.mali.Notably,MdDEF30 promoted the accumulation of reactive oxygen species(ROS)and activated defense-related genes such as PR4,PR10,CML13,and MPK3.Co-expression regulatory network analysis showed that MdWRKY75 may regulate the expression of MdDEF30.Further yeast onehybrid(Y1H),luciferase,and chromatin Immunoprecipitation quantitative polymerase chain reaction(ChIPqPCR)assays verified that MdWRKY75 could directly bind to the promoter of MdDEF30.Importantly,pathogen inoculation assays confirmed that MdWRKY75 positively regulates resistance by transcriptionally activating MdDEF30.Overall,these results demonstrated that MdDEF30 promotes resistance to C.mali in apple plants and that MdWRKY75 regulates MdDEF30 expression during the induction of resistance,thereby clarifying biochemical mechanisms of resistance to C.mali in apple trees. 展开更多
关键词 apple calli DEFENSIN gene family Cytospora mali induced resistance antifungal activity weighted correlation network analysis(WGCNA) transcription factors
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Nav1.6 drives colorectal cancer proliferation and invasion through MAPK signaling pathway
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作者 Li-Ming Zhao Wan-Ying Hong +6 位作者 Jian-Guang Xu Shui-Quan Lin Ming-Sheng Liu Li-Hui Wang Xu-Li Jiang Ming Sang Yang-Bo Lv 《World Journal of Gastrointestinal Oncology》 2025年第7期281-296,共16页
BACKGROUND Voltage-gated sodium channels(VGSCs,or Navs)are highly expressed in various tumors and play a critical role in tumor metastasis and invasion.AIM To identify Nav1.6-associated cancer genes through bioinforma... BACKGROUND Voltage-gated sodium channels(VGSCs,or Navs)are highly expressed in various tumors and play a critical role in tumor metastasis and invasion.AIM To identify Nav1.6-associated cancer genes through bioinformatics analysis and experimental validation,with the goal of determining the role of Nav1.6 in colorectal cancer(CRC)metastasis.METHODS The Cancer Genome Atlas(TCGA)and Gene Expression Omnibus(GEO)data were analyzed using weighted correlation network analysis(WGCNA)and Venn analysis to identify Nav1.6-associated genes in CRC.siRNA,real-time PCR,and western blotting were employed to validate the Nav1.6-associated cancer genes and signaling pathways identified in CRC.Cell counting kit-8 and Transwell migration assays were used to assess the proliferation and migration of CRC cells.RESULTS The analysis of TCGA and GEO datasets,along with WGCNA,identified 575 differentially expressed genes associated with SCN8A(Nav1.6)in CRC,which were particularly enriched in MAPK signaling pathways.Tissue microarray analysis of surgical samples revealed elevated Nav1.6 levels in CRC tissues,which were predominantly in the cytoplasm and nucleus rather than in the membrane.Cytoplasmic Nav1.6 expression increased with T stage increases,consistent with the TCGA findings.SCN8A knockdown in colon tumor cells significantly reduced cell proliferation and invasion and downregulated key proteins in the RAF-MAPK pathway.CONCLUSION These findings suggest that Nav1.6 promotes CRC cell proliferation and invasion which is related to the MAPK signaling pathway. 展开更多
关键词 Nav1.6 Colorectal cancer Weighted correlation network analysis MAPK signaling Cancer proliferation
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Bioinformatics Analysis Revealed Potential Tumor Suppressors (KLF4/CGN), Oncogenes (SHH/LIF) and Biomarkers of Asian Stomach Adenocarcinoma
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作者 Yang Zhou Yingying Wang +7 位作者 Junting Cheng Ying Zhang Wenqi Cai Ziwen Han Moyu Wang Qi Huang Xiaochun Peng Hongwu Xin 《Yangtze Medicine》 2021年第2期141-156,共16页
Stomach adenocarcinoma (STAD) is the fifth most prevalent cancer and the third leading cause of cancer-related death in the world and is more common in Asia than in most Western countries. There is an urgent need to i... Stomach adenocarcinoma (STAD) is the fifth most prevalent cancer and the third leading cause of cancer-related death in the world and is more common in Asia than in most Western countries. There is an urgent need to identify potential novel oncogenes and tumor suppressor genes, and biomarkers for STAD. 6652 differentially expressed genes were identified between STAD and normal samples based on the transcriptome data analysis of the TCGA and GEO databases. 13 key modules were identified in STAD by WGCNA analysis. 293 potential STAD associated genes were identified from intersection by Venn Diagram. The 293 intersected genes were enriched in cell cortex and infection by GO and KEGG analysis. 10 hub genes were identified from PPI and Cytoscape analyses of the intersected genes. KLF4/CGN low and SHH/LIF high expression were associated with short overall survival of Asian STAD patients. Bioinformatics analysis revealed potential novel tumor suppressors (KLF4/CGN), oncogenes (SHH/LIF) and biomarkers for diagnosis, therapy and prognosis of STAD, specifically for Asian patients. 展开更多
关键词 WGCNA (Weighted correlation network analysis) Tumor Suppressors ONCOGENES Stomach Adenocarcinoma (STAD) Hub Gene
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Transcriptome and co-expression network analyses reveal the mechanisms of early response to drought stress in oat leaves
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作者 Nan Fei Jinghui Liu +4 位作者 Junzhen Mi Xiquan Wang Xingyan Li Baoping Zhao Zhongshan Xu 《Food Quality and Safety》 2025年第3期590-604,共15页
Drought,as major abiotic stress,primarily restricts the production of oat(Avena sativa)around the world.With the aim of elucidating oat leaves’early response to drought stress,this study focused on examining the cont... Drought,as major abiotic stress,primarily restricts the production of oat(Avena sativa)around the world.With the aim of elucidating oat leaves’early response to drought stress,this study focused on examining the contents of malondialdehyde(MDA),soluble sugar(SS),and proline(Pro)and the transcriptome of oat leaves under 0,12,24,36,and 48 h of drought treatment,revealing that the content of MDA increased with drought duration,whereas the contents of SS and Pro reached their maximum at 24 h of treatment,with a total between 0 h of treatment and the other groups.Differentially expressed genes(DEGs)presented significant enrichment in the phenylpropanoid biosynthetic pathway,flavonoid biosynthetic pathway,galactose metabolism,and glutathione metabolism.The biological changes caused by drought stress resulted in the obvious activation of antioxidase genes.The sugar and flavonoid biosynthetic genes were studied based on the detailed temporal patterns of expression of four major metabolic pathways.Additionally,14 candidate hub genes,such as the genes that encoded galactinol synthase,serine/threonineprotein kinase,and 1-aminocyclopropane-1-carboxylate oxidase,were identified by virtue of weighted gene co-expression network analysis.Differential transcription factor(TF)analysis showed that NAM,ATAF1/2,CUC2(NAC),Heat Shock(HS),Trihelix,TEOSINTE BRANCHED1/CYCLOIDEA/PCF(TCP),and other 11 TF families were closely related to drought stress.These findings help us understand the early responses of oat to drought stress from new perspectives and can guide further research. 展开更多
关键词 Drought stress oat RNA-seq transcription factor(TF) weighted gene correlation network analysis(WGCNA)
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Combinatorial analysis of transcription and metabolism reveals the regulatory network associated with antioxidant substances in waxy corn 被引量:1
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作者 Jianhong Ke Rui Wang +10 位作者 Bangqian Song Jinglun Du Xiaojiao Li Ningning Song Zhirong Cai Rongli Chen Honghua Yi Xiangyin Lu Chen Jiang Zhengguo Li Baowen Huang 《Food Quality and Safety》 SCIE CSCD 2022年第4期638-650,共13页
Maize is an essential source of nutrition for humans and animals and is rich in various metabolites that determine its quality.Different maize varieties show significant differences in metabolite content.Two kinds of ... Maize is an essential source of nutrition for humans and animals and is rich in various metabolites that determine its quality.Different maize varieties show significant differences in metabolite content.Two kinds of waxy maize parental materials,S181 and 49B,created by the Chongqing Academy of Agricultural Sciences,are widely grown in China.S181 shows higher starch and sugar contents than 49B.This study generated metabolic profiles to assess the differences between the two varieties.A total of 674 metabolites that were significantly differentially expressed between the two varieties were identified by gas chromatography and untargeted metabolomics technology.These metabolites were associated with 21 categories,including antioxidant metabolites.Moreover,6415 differentially expressed genes(DEGs)were identified by RNA-seq.Interestingly,these DEGs comprised starch and sugar synthesis pathway genes and 72 different transcription factor families.Among these,six families that were reported to play an essential role in plant antioxidant action accounted for 39.2%of the transcription factor families.Using the Kyoto Encyclopedia of Genes and Genomes(KEGG)classification,the DEGs were mainly involved in amino acid biosynthesis,glycolysis/glucose metabolism,and the synthetic and metabolic pathways of antioxidant active substances.Furthermore,the correlation analysis of transcriptome and metabolomics identified five key transcription factors(ZmbHLH172,ZmNAC44,ZmNAC-like18,ZmS1FA2,ZmERF172),one ubiquitin ligase gene(ZmE25A)and one sucrose synthase gene(ZmSS1).They likely contribute to the quality traits of waxy corn through involvement in the metabolic regulatory network of antioxidant substances.Thus,our results provide new insights into maize quality-related antioxidant metabolite networks and have potential applications for waxy corn breeding. 展开更多
关键词 Maize quality ANTIOXIDANTS widely targeted metabolomics TRANSCRIPTOMICS weighted correlation network analysis
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Characteristics of Atmospheric Fine Particulate Matter(PM2.5)Induced Differentially Expressed Proteins Determined by Proteomics and Bioinformatics Analyses
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作者 ZHENG Kai CAI Ying +7 位作者 WANG Bing Yu QIN Shuang Jian LI Bo Ru HUANG Hai Yan QIN Xiao Yun LONG Ding Xin ZHANG Zhao Hui XU Xin Yun 《Biomedical and Environmental Sciences》 SCIE CAS CSCD 2020年第8期583-592,共10页
Objective To screen the differentially expressed proteins(DEPs)in human bronchial epithelial cells(HBE)treated with atmospheric fine particulate matter(PM2.5).Methods HBE cells were treated with PM2.5 samples from She... Objective To screen the differentially expressed proteins(DEPs)in human bronchial epithelial cells(HBE)treated with atmospheric fine particulate matter(PM2.5).Methods HBE cells were treated with PM2.5 samples from Shenzhen and Taiyuan for 24 h.To detect overall protein expression,the Q Exactive mass spectrometer was used.Gene ontology(GO),Kyoto encyclopedia of genes and genomes(KEGG),and Perseus software were used to screen DEPs.Results Overall,67 DEPs were screened in the Shenzhen sample-treated group,of which 46 were upregulated and 21 were downregulated.In total,252 DEPs were screened in the Taiyuan sampletreated group,of which 134 were upregulated and 118 were downregulated.KEGG analysis demonstrated that DEPs were mainly enriched in ubiquitin-mediated proteolysis and HIF-1 signal pathways in Shenzhen PM2.5 samples-treated group.The GO analysis demonstrated that Shenzhen sample-induced DEPs were mainly involved in the biological process for absorption of various metal ions and cell components.The Taiyuan PM2.5-induced DEPs were mainly involved in biological processes of protein aggregation regulation and molecular function of oxidase activity.Additionally,three important DEPs,including ANXA2,DIABLO,and AIMP1,were screened.Conclusion Our findings provide a valuable basis for further evaluation of PM2.5-associated carcinogenesis. 展开更多
关键词 PM2.5 PROTEOMICS BIOINFORMATICS Differentially expressed proteins Weighted correlation network analysis
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Multi-omics association analysis reveals the pathogenesis of Parkinson's disease and the treatment mechanisms of a medicinal and food plant:Cistanches Herba
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作者 Guoxue Zhu Wang Wang +7 位作者 Yuwen Wang Wei Li Shilin Yi Kai Wang Lu Fan Xinyu Lu Juanjuan Tang Ruini Chen 《Journal of Future Foods》 2026年第1期143-159,共17页
Parkinson' s disease(PD) is a progressive neurodegenerative disorder affecting movement,with no treatments currently available to halt or slow its progression.Therefore,the development of new anti-PD drugs is urge... Parkinson' s disease(PD) is a progressive neurodegenerative disorder affecting movement,with no treatments currently available to halt or slow its progression.Therefore,the development of new anti-PD drugs is urgently needed.As a kind of medicine and food homologous plant,Cistanches Herba has a promising future for the treatment of PD.In this study,a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine(MPTP)-induced PD mouse model was used to detect Cistanches Herba' s anti-PD effects via histopathology and molecular biology.Simultaneously,the effect of Cistanches Herba on the "gut microbiota-barrier axis" was assessed through gut microbiota and intestinal barrier function in mice.Finally,transcriptomics analysis was conducted to further verify the results.As a result,37 differential metabolites and 16 microbial genera were screened and tentatively identified.Thirty-two metabolites and sixteen microbial genera were simultaneously altered with opposing trends in variation after MPTP and Cistanches Herba treatments.We built a framework for predicting targets and hostmicrobe interaction mechanisms,as well as identifying alternative treatment for PD,which should be validated further for clinical application.In conclusion,Cistanches Herba exerts a protective effect against the development of PD by manipulating the structural feature of intestinal flora to influence the host metabolites. 展开更多
关键词 Parkinson's disease Cistanches Herba Multi-omics association analysis Chemometrics correlation network analysis
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