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De Novo Transcriptome Analysis in Hevea brasiliensis to Unveil genes Involved in Low Temperature Stress Response

Phyton-International Journal of Experimental Botany 2023年第2期92卷 559-575页

作者： Bingsong Yang Xiaomeng Shi Tingting Guo Meixia Liang College of Agriculture Ludong UniversityYantai264025China The Engineering Research Institute of Agriculture and Forestry Ludong UniversityYantai264025China

Low temperature is one of the adversities threatening the growth and development and reduces the yield of rubber ***,molecular mechanisms toward rubber trees in response to low temperature are largely *** this study,7,159 and 7,600 differentially expressed genes(DEGs)were identified in‘Reyan 73397’rubber *** GO analysis,the catalytic activity was the representative of the GO term in the only DEGs at the two studied temperatures(room temperature and 4°C,respectively),while KEGG analysis showed that carbon metabolism was the most important grouping under the comparison of these two *** addition,expression of 9 members of transcription factor MYB family genes were further verified by qRT-PCR,and MYB family genes may play important roles in the regulation of rubber trees under low temperature *** study provided a theoretical foundation for(1)revealing the molecular mechanisms of rubber trees in response to low temperature and(2)breeding of tolerant varieties of rubber trees.

关键词： Hevea brasiliensis low temperature stress transcriptome differential expressed genes

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Microarray analysis of gene expression profile of multidrug resistance in pancreatic cancer

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Chinese Medical Journal 2007年第20期120卷 1743-1752页

作者： ZHAO Yu-pei CHEN Ge FENG Bin ZHANG Tai-ping MA En-ling WU Yuan-de Department of General Surgery Chinese Academy of Medical Sciences and Peking Union Medical College Hospital Beijing 100730 China

Background Chemotherapy is the most frequently adopted adjuvant therapy of pancreatic ductal adenocarcinoma （PDAC）, but the development of drug resistance reduces its effectiveness. Clarification of the mechanism of multidrug resistance （MDR） development in PDAC is needed to improve the therapeutic effect of chemotherapy. This study was aimed to investigate the molecular mechanism of MDR of PDAC and to identify genes associated with MDR development.Methods The gene expression profiles of cell line SW1990 and three drug-selected pancreatic chemoresistant sub-lines, SW1990/5-Fu, SW1990/ADM and SW1990/GEM, were obtained using an oligonucleotide microarray （Affymetrix HG U133 2.0 plus） that contained approximately 38 000 human genes. The microarray results were validated by real-time quantitative polymerase chain reaction and Western blot analysis.Results There were 165 genes and expressed sequence tags, some of which have never been linked to drug resistance, that were up- or down-regulated at least 2-fold in all resistant sub-lines when compared with SW1990. According to Gene Ontology annotation, differentially expressed genes related to MDR in pancreatic cancer belong to many functional families and with diverse biological processes. genes related to antioxidant activity, apoptosis, the cell cycle, signal transduction and intracellular adhesion may undergo epigenetic changes preceding MDR development. A hierarchical clustering was conducted and several interesting clusters were discovered that may be primarily related to cell cycle and developmental regulation. A prediction rule was built from the expression profiles of 117 genes after support vector machine （SVM） analysis, and the prediction result was examined by cytotoxic testing. As a result, a differential gene expression pattern was constructed in multidrug resistant pancreatic cancer cells. Conclusions The findings of this study prove that construction of a chemoresistance prediction rule, based on gene

关键词： pancreatic cancer multidrug resistance microarray differential expressed genes chemoresistance prediction

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Screening and bioinformatics analysis of thyroid cancer-related hub genes

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TMR Clinical Research 2020年第3期3卷 109-116页

作者： Shu-Fei Wu Shuang Yang Jiu Pu Zheng-Hai Ling Zheng-Wei Leng Ling-Mi Hou Department of Anesthesiology North Sichuan Medical CollegeNanchong 637000China Department of Clinical Medical North Sichuan Medical CollegeNanchong 637000China Department of Hepatobiliary SurgeryⅡ North Sichuan Medical CollegeNanchong 637000China Department of Thyroid and Mammary Surgery Affiliated Hospital of North Sichuan Medical CollegeNanchong 637000China

Objective:To identify the thyroid cancer-related hub genes and pathways by bioinformatics initially in order to lay the foundation for further ***:The expression profile chips and data of thyroid cancer were screened and downloaded from the gene expression omnibus(GEO).The GEO2R was applied to identify the differential expressed genes between thyroid cancer tissues and normal thyroid *** the Metascape online website was used for pathway and function *** the usage of STRING and Cytoscape,the protein-protein interaction network was constructed,and the plug-in app cytoHubba in Cytoscape was applied to screen hub ***-Meier Plotter was implemented to conduct survival analysis of hub genes for further screening and ***:A total of 304 differential expressed genes were screened,and were mainly enriched in the biological processes of extracellular matrix,cell-substrate adhesion,response to wounding,muscle structure development and hormone metabolic process *** ***-protein interaction network visualized 284 nodes;the top ten scores of Maximal Clique Centrality algorithm were taken as the criteria to screen out the hub genes with high connectivity in the gene expression *** KM plotter analysis confirmed that 5 of 9 hub genes were correlated with the prognosis of thyroid cancer ***:FN1,SPP1,TIMP1,VCAN,COL1A1,COL1A2,MMP1,DCN,COMP and FMOD may play a significant role in the development of thyroid *** which have prognostic significance in survival analyses were found to be relevant to the composition and regulation of extracellular matrix.

关键词： Bioinformatics Thyroid cancer Hub genes differential expressed genes

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