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Altered Expression of Differential Genes in Thoracic Spinal Cord Involved in Experimental Cholestatic Itch Mouse Model 认领 引用 被引量：1
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作者 Ming CHEN Zhi-xiao LI +1 位作者 Qian WANG Hong-bing XIANG 《Current Medical Science》 SCIE CAS 2018年第4期679-683,共5页
The spinal origin of cholestatic itch in experimental obstructive jaundice mouse model remains poorly understood.In this study,the jaundice model was established by bile duct ligation(BDL)in mice,and differential gene... The spinal origin of cholestatic itch in experimental obstructive jaundice mouse model remains poorly understood.In this study,the jaundice model was established by bile duct ligation(BDL)in mice,and differential gene expression patterns were analyzed in the lower thoracic spinal cord involved in cholestatic pruritus after BDL operation using high-throughput RNA sequencing.At 21st day after BDL,the expression levels of ENSRNOG00000060523,ENSRNOG00000058405 and ENSRNOG00000055193 mRNA were significantly up-regulated,and those of ENSRNOG00000042197,ENSRNOG00000008478,ENSRNOG00000019607,ENSRNOG00000020647,ENSRNOG00000046289,Gemin8,Serpina3n and Trim63 mRNA were significantly down-regulated in BDL group.The RNAseq data of selected mRNAs were validated by RT-qPCR.The expression levels of ENSRNOG00000042197,ENSRNOG00000008478,ENSRNOG00000019607,ENSRNOG00000020647,ENSRNOG00000046289 and Serpina3n mRNA were significantly down-regulated in BDL group.This study suggested that cholestatic pruritus in experimental obstructive jaundice mouse model is related with in the changes of gene expression profiles in spinal cord. 展开更多
关键词 cholestatic itch differential genes spinal cord high-throughput RNA sequencing
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IDENTIFICATION OF DIFFERENTIAL GENES IN OVARIAN CANCER USING REPRESENTATIONAL DIFFERENCE ANALYSIS OF cDNA 认领 引用
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作者 Hong Chen Min Wang +3 位作者 Xin-yan Wang Shan Gao Jun Wang Xiao-ming Guan 《Chinese Medical Sciences Journal》 CAS 2005年第3期185-189,共5页
Objoctive To identify differential genes between normal ovarian epithelium tissue and ovarian epithelial cancer using representational difference analysis of cDNA （cDNA-RDA）. Methods cDNA-RDA was performed to identi... Objoctive To identify differential genes between normal ovarian epithelium tissue and ovarian epithelial cancer using representational difference analysis of cDNA （cDNA-RDA）. Methods cDNA-RDA was performed to identify the differentially expressed sequences between cDNAs from cancer tissue and cDNAs from normal ovarian tissue in the same patient who was in the early stage of ovarian serous cystadenocarcinoma. These differentially expressed fragments were cloned and analyzed, then sequenced and compared with known genes. Results Three differentially cxpressed cDNA fragments were isolated using cDNA from normal ovarian tissue as tester and cDNA from cancer tissue as driver amplicon by cDNA-RDA. DP Ⅲ- 1 and DP Ⅲ-2 cDNA clone showed significant homology to the cDNA of alpha actin gene; DPⅢ-3 cDNA clone showed significant homology to the cDNA oftransgelin gene. Conclusion cDNA-RDA can bc used to sensitively identify the differentially expressed genes in ovarian serous cystadenocarcinoma. Ovarian serous cystadenocarcinoma involves alteration of multiple genes. 展开更多
关键词 representational difference analysis of cDNA ovarian cancer differential expressed gene tumor suppressive gene
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Differentially expressed genes in rabbits with traumatic proliferative vitreoretinopathy based on high-throughput sequencing 认领 引用
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作者 Yu-Jie Tang Jiang-Ying Liu +3 位作者 Sheng-Xiang Zhang Bo-Yu Liu Liao Quan Qi-Hua Xu 《International Journal of Ophthalmology(English edition)》 SCIE CAS 2026年第4期665-672,共8页
AIM:To identify differentially expressed genes(DEGs)in rabbits with traumatic proliferative vitreoretinopathy(PVR)using high-throughput sequencing(HTS).METHODS:Thirty-six rabbits were randomly allocated to the control... AIM:To identify differentially expressed genes(DEGs)in rabbits with traumatic proliferative vitreoretinopathy(PVR)using high-throughput sequencing(HTS).METHODS:Thirty-six rabbits were randomly allocated to the control group and the PVR group induced by scleral puncture.On the 28th day following modeling,fundus B-ultrasound and fundus photography were performed on all rabbits,and hematoxylin-eosin(HE)staining was conducted on retinal tissues.RNA sequencing(RNA-Seq)combined with bioinformatics analysis was used to screen PVRassociated DEGs.Gene Ontology(GO)functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis were carried out for the identified DEGs.S100A6,EDNRB and CEBPD were randomly selected for quantitative reverse transcription polymerase chain reaction(RT-qPCR)validation to verify the reliability of the RNA-Seq results.RESULTS:Fundus B-ultrasound,fundus photography and retinal HE staining confirmed the successful establishment of the traumatic PVR rabbit model.A total of 1587 DEGs were screened,of which 1094 were significantly up-regulated and 493 were significantly down-regulated.GO function enrichment analysis showed that these DEGs were mainly enriched in immune response,extracellular region and inflammatory response.KEGG pathway enrichment analysis showed that DEGs were mainly involved in the cytokine-cytokine receptor interaction and hematopoietic cell lineage pathway.RT-qPCR results showed that S100A6,CEBPD and EDNRB were significantly increased in PVR group.CONCLUSION:A large number of genes exhibit significant differential expression in rabbits with traumatic PVR,among which S100A6,CEBPD and EDNRB may play an important role in traumatic PVR. 展开更多
关键词 proliferative vitreoretinopathy highthroughput sequencing differentially expressed genes rabbits
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Anti-inflammatory mechanisms of Hedysarum polybotrys polysaccharide in endotoxin-induced uveitis:insights into candidate genes and pathways 认领 引用
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作者 Shuo Yu Jin-Yi Yu +3 位作者 Xin-Li Liu Jing Wang Shi-Lan Feng Hong Lu 《International Journal of Ophthalmology(English edition)》 SCIE CAS 2026年第2期230-238,共9页
AIM:To identify key genes and inflammatory signaling pathways involved in the anti-inflammatory effects of Hedysarum polybotrys polysaccharide(HPS)in a rat model of endotoxin-induced uveitis(EIU).METHODS:EIU was induc... AIM:To identify key genes and inflammatory signaling pathways involved in the anti-inflammatory effects of Hedysarum polybotrys polysaccharide(HPS)in a rat model of endotoxin-induced uveitis(EIU).METHODS:EIU was induced in Wistar rats through subcutaneous injection of lipopolysaccharide(LPS,200μg)and the rats were then randomly assigned to EIU group(n=5)and the HPS intervention group(n=5).HPS(400 mg/kg,intraperitoneally)or its carrier was administered 24h and 1h prior to EIU induction.Eyes were examined and enucleated 24h post-induction,and total RNA was extracted from the iris-ciliary body.Gene expression microarrays were used to identify differentially expressed genes(DEGs),followed by bioinformatics analyses,including gene ontology(GO)and pathway analysis.Key findings were not experimentally validated at the mRNA or protein level.RESULTS:A total of 322 DEGs were identified,comprising 254 mRNA and 68 lncRNA genes.GO analysis revealed significant functional categories,including response to LPS.Pathway analysis identified key signaling pathways involved in uveitis,such as cytokine-cytokine receptor interactions.Notably,16 mRNA and 7 lncRNA DEGs emerged as central nodes in the gene correlation network.CONCLUSION:HPS exerts its anti-inflammatory effects through coordinated signaling pathways,offering insights into potential therapeutic targets for managing uveitis. 展开更多
关键词 differentially expressed genes Hedysarum polybotrys polysaccharide endotoxin-induced uveitis lncRNA gene expression microarray
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Differential metabolites facilitate metabolic dysfunction-associated fatty liver disease malignancy via immune evasion and M2-polarized macrophages 认领 引用
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作者 Jie Yang Wen-Li Sai +5 位作者 Xiao-Xiao Xia Hao Tang Min Xu Qun Xie Deng-Fu Yao Min Yao 《World Journal of Gastroenterology》 SCIE CAS 2026年第24期97-116,共20页
BACKGROUND Differential metabolites(DMs)are associated with metabolic dysfunction-associated fatty liver disease(MAFLD)malignant transformation.However,their underlying mechanisms remain to be identified.AIM To invest... BACKGROUND Differential metabolites(DMs)are associated with metabolic dysfunction-associated fatty liver disease(MAFLD)malignant transformation.However,their underlying mechanisms remain to be identified.AIM To investigate the dynamic alterations of DMs,carnitine palmitoyl transferase-II(CPT-II)and immune cells during MAFLD malignancy.METHODS A rat model was constructed with high fat diet plus 2-fluorenylacetamide to induce hepatocyte malignancy.Livers were divided into MAFLD,metabolic dysfunction-associated steatohepatitis,liver cirrhosis(LC)and hepatocellular carcinoma(HCC)groups based on hematoxylin and eosin staining,with normal rats as control.DMs were identified via RNA transcriptomics or metabolomics.Proteins were detected by western blotting,and immune cells were analyzed by single-cell sequencing.RESULTS Model livers with obvious lipid accumulation and cells were examined during MAFLD malignancy from inflammation or necrosis to LC or HCC and exhibited a pathological alteration of nuclear pleomorphism,disordered arrangement and a progressive decrease in CPT-II activity.The number of DMs was 131 in MAFLD,134 in metabolic dysfunction-associated steatohepatitis,27 in liver fibrosis/LC,and 130 in HCC,respectively.Cyclin B1 and cyclin-dependent kinase 1 were involved in the P53 pathway and cell cycle,and they held key positions in the protein interaction network,which involved metabolic regulation of cell response to stimuli.DMs,such as phosphatidylcholine or sphingomyelin in steroid biosynthesis,were significantly related to MAFLD malignancy.Mechanistically,liver immune cells undergo dynamic changes in a fat-rich microenvironment,with decreased T cell abundance and increased programmed death ligand 1 expression and M2-polarized macrophages.CONCLUSION Downregulated CPT-II aggravates the accumulation of metabolites associated with MAFLD malignancy via immune evasion and M2-polarized macrophages. 展开更多
关键词 Differential metabolites Carnitine palmitoyl transferase-II Immune escape Differentially expressed genes M2-polarized macrophages Hepatocarcinogenesis
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DyNDG:Identifying Leukemia-related Genes Based on Time-series Dynamic Network by Integrating Differential Genes 认领 引用 被引量：1
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作者 Jin A Ju Xiang +3 位作者 Xiangmao Meng Yue Sheng Hongling Peng Min Li 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2025年第2期179-195,共17页
Leukemia is a malignant disease characterized by progressive accumulation with high morbidity and mortality rates,and investigating its disease genes is crucial for understanding its etiology and pathogenesis.Network ... Leukemia is a malignant disease characterized by progressive accumulation with high morbidity and mortality rates,and investigating its disease genes is crucial for understanding its etiology and pathogenesis.Network propagation methods have emerged and been widely employed in disease gene prediction,but most of them focus on static biological networks,which hinders their applicability and effectiveness in the study of progressive diseases.Moreover,there is currently a lack of special algorithms for the identification of leukemia disease genes.Here,we proposed a novel Dynamic Network-based model integrating Differentially expressed Genes(DyNDG)to identify leukemia-related genes.Initially,we constructed a time-series dynamic network to model the development trajectory of leukemia.Then,we built a background-temporal multilayer network by integrating both the dynamic network and the static background network,which was initialized with differentially expressed genes at each stage.To quantify the associations between genes and leukemia,we extended a random walk process to the background-temporal multilayer network.The results demonstrate that DyNDG achieves superior accuracy compared to several state-of-the-art methods.Moreover,after excluding housekeeping genes,DyNDG yields a set of promising candidate genes associated with leukemia progression or potential biomarkers,indicating the value of dynamic network information in identifying leukemia-related genes.The implementation of DyNDG is available at both https:/gdc.cncb.ac.cn/biocodeool/BT7617 and http://gffzz188fe103f8f1460asb6fvpw69vwwb6wvu.ffgz.tsg.suse.edu.cn/CSUBioGroup/DyNDG. 展开更多
关键词 Leukemia Dynamic network Random walk Differentially expressed gene Disease gene prediction
Prognosis and Immunotherapy Effect of Triple-Negative Breast Cancer by Lactylation-Related Genes and Experimental Validation 认领 引用
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作者 Yang Wang Ying Xie +7 位作者 Yiyi Ye Youyang Shi Feifei Li Mengdie Zhu Ciyi Hua Yuan Xu Rui Yang Sheng Liu 《Oncology Research》 SCIE 2026年第7期688-712,共25页
Background Triple-negative breast cancer(TNBC)is an aggressive subtype of breast malignancy characterized by poor clinical outcomes and limited therapeutic options.The identification of reliable biomarkers for predict... Background Triple-negative breast cancer(TNBC)is an aggressive subtype of breast malignancy characterized by poor clinical outcomes and limited therapeutic options.The identification of reliable biomarkers for predicting prognosis and immunotherapeutic response remains an urgent clinical need.This study aimed to develop an integrative lactylation-related gene signature to simultaneously evaluate prognostic trajectories and immunotherapeutic sensitivity in TNBC.Methods Transcriptomic and clinical data from public TNBC cohorts were systematically analyzed.Lactylation-related gene signatures were used to stratify patients via consensus clustering.A scoring model was constructed based on differentially expressed genes between clusters,and its associations with immune infiltration,pathway enrichment,drug sensitivity,and clinical outcomes were evaluated.Finally,quantitative real-time polymerase chain reaction,Western blot and Confocal immunofluorescence Microscopy were used to validate the hub genes.Results Significant gene expression differences stratified TNBC patients into high-and low-score groups,with the high-score group demonstrating superior clinical outcomes.These patients also showed better responses to immunotherapy,as indicated by immune checkpoint profiles and chemotherapy sensitivity.Experimental validation confirmed Programmed Cell Death 1 Ligand 2,Immunoglobulin J Chain,and Colony Stimulating Factor 2 Receptor Beta as key molecular nodes.Our scoring model predicts immunotherapy efficacy,and these three genes may represent potential candidates for further therapeutic exploration in TNBC.Conclusions This study establishes a novel lactylation-related gene signature that effectively predicts both prognosis and immunotherapeutic sensitivity in TNBC.The identified hub genes represent promising biomarkers and potential therapeutic targets warranting further investigation. 展开更多
关键词 Triple-negative breast cancer(TNBC) lactylation immune infiltration prognosis differentially expressed genes
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Effects of Mycobacterium vaccae vaccine in a mouse model of tuberculosis: protective action and differentially expressed genes 认领 引用 被引量：12
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作者 Wen-Ping Gong Yan Liang +6 位作者 Yan-Bo Ling Jun-Xian Zhang You-Rong Yang Lan Wang Jie Wang Ying-Chang Shi Xue-Qiong Wu 《Military Medical Research》 SCIE CAS CSCD 2020年第2期125-139,共15页
Background:Tuberculosis is a leading cause of death worldwide.BCG is an effective vaccine,but not widely used in many parts of the world due to a variety of issues.Mycobacterium vaccae(M.vaccae)is another vaccine used... Background:Tuberculosis is a leading cause of death worldwide.BCG is an effective vaccine,but not widely used in many parts of the world due to a variety of issues.Mycobacterium vaccae(M.vaccae)is another vaccine used in human subjects to prevent tuberculosis.In the current study,we investigated the potential mechanisms of M.vaccae vaccination by determining differentially expressed genes in mice infected with M.tuberculosis before and after M.vaccae vaccination.Methods:Three days after exposure to M.tuberculosis H37 Rv strain(5×10~5 CFU),adult BALB/c mice randomly received either M.vaccae vaccine(22.5μg)or vehicle via intramuscular injection(n=8).Booster immunization was conducted 14 and 28 days after the primary immunization.Differentially expressed genes were identified by microarray followed by standard bioinformatics analysis.Results:M.vaccae vaccination provided protection against M.tuberculosis infection(most prominent in the lungs).We identified 2,326 upregulated and 2,221 downregulated genes in vaccinated mice.These changes could be mapped to a total of 123 signaling pathways(68 upregulated and 55 downregulated).Further analysis pinpointed to the MyD88-dependent TLR signaling pathway and PI3 K-Akt signaling pathway as most likely to be functional.Conclusions:M.vaccae vaccine provided good protection in mice against M.tuberculosis infection,via a highly complex set of molecular changes.Our findings may provide clue to guide development of more effective vaccine against tuberculosis. 展开更多
关键词 Mycobacterium tuberculosis Immunotherapeutic effect Immunotherapy Vaccae vaccine Differentially expressed genes Signaling pathway
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ExerGeneDB:A physical exercise-regulated differential gene expression database 认领 引用 被引量：2
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作者 Ling Pan Songwei Ai +7 位作者 Xiaohui Shi Xiaolan Tong Michail Spanos Guoping Li Dragos Cretoiu Juan Gao Qiulian Zhou Junjie Xiao 《Journal of Sport and Health Science》 SCIE CSCD 2025年第4期113-126,共14页
Background:Exercise induces molecular changes that involve multiple organs and tissues.Moreover,these changes are modulated by various exercise parameters—such as intensity,frequency,mode,and duration—as well as by ... Background:Exercise induces molecular changes that involve multiple organs and tissues.Moreover,these changes are modulated by various exercise parameters—such as intensity,frequency,mode,and duration—as well as by clinical features like gender,age,and body mass index(BMI),each eliciting distinct biological effects.To assist exercise researchers in understanding these changes from a comprehensive perspective that includes multiple organs,diverse exercise regimens,and a range of clinical features,we developed Exercise Regulated Genes Database(ExerGeneDB),a database of exercise-regulated differential genes.Methods:ExerGeneDB aggregated publicly available exercise-related sequencing datasets and subjected them to uniform quality control and preprocessing.The data,encompassing a variety of types,were organized into a specialized database of exercise-regulated genes.Notably,Exer-GeneDB conducted differential analyses on this collected data,leveraging curated clinical information and accounting for important factors such as gender,age,and BMI.Results:ExerGeneDB has assembled 1692 samples from rats and mice as well as 4492 human samples.It contains data from various tissues and organs,such as skeletal muscle,blood,adipose tissue,intestine,heart,liver,spleen,lungs,kidneys,brain,spinal cord,bone marrow,and bones.ExerGeneDB features bulk ribonucleic acid sequencing(RNA-seq)(including non-coding RNA(ncRNA)and protein-coding RNA),microarray(including ncRNA and protein-coding RNA),and single cell RNA-seq data.Conclusion:ExerGeneDB compiles and re-analyzes exercise-related data with a focus on clinical information.This has culminated in the crea-tion of an interactive database for exercise regulation genes.The website for ExerGeneDB can be found at:http://gffzz4d9827957b154551sb6fvpw69vwwb6wvu.ffgz.tsg.suse.edu.cn. 展开更多
关键词 Exercise database Physical exercise Exercise-regulated differential genes
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RNA-seq profiling reveals differentially expressed genes as potential markers for vital reaction in skin contusion:a pilot study 认领 引用 被引量：4
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作者 Jingtao Xu Rui Zhao +7 位作者 Ye Xue Huanqin Xiao Yanliang Sheng Dong Zhao Jietao He Hongyan Huang Qi Wang Huijun Wang 《Forensic Sciences Research》 2018年第2期153-160,共8页
Detection of the vitality of wounds is essential in forensic practice.The present study used Illumina RNA-seq technology to determine gene expression profiles in contused mouse skin.In obtained high quality sequencing... Detection of the vitality of wounds is essential in forensic practice.The present study used Illumina RNA-seq technology to determine gene expression profiles in contused mouse skin.In obtained high quality sequencing reads,the reads were mapped onto a reference transcriptome(Mus_musculus.GRCm38.83).The results revealed that there were 659 upregulated and 996 down-regulated differentially expressed genes(DEGs)in contused mouse skin.The DEGs were further analyzed using the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases.Genes from different functional categories and signalling pathways were enriched,including the immune system process,immune response,defense response,cytokine-cytokine receptor interaction,complement and coagulation cascades and chemokine signalling pathway.Expression patterns of 11 DEGs were verified by RT-qPCR in mice skins.In addition,alterations of five DEGs were also analyzed in postmortem human wound samples.The results were in concordance with the results of RNA-seq.These findings suggest that RNA-seq is a powerful tool to reveal DEGs as potential markers for vital reaction in terms of forensic practices. 展开更多
关键词 Forensic pathology skin contusion vital reaction RNA-seq differentially expressed genes
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A comparative analysis of differentially expressed genes in rostral and caudal regions after spinal cord injury in rats 认领 引用 被引量：1
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作者 Xue-Min Cao Sheng-Long Li +4 位作者 Yu-Qi Cao Ye-Hua Lv Ya-Xian Wang Bin Yu Chun Yao 《Neural Regeneration Research》 SCIE CAS CSCD 2022年第10期2267-2271,共5页
The initial mechanical damage of a spinal cord injury(SCI)triggers a progressive secondary injury cascade,which is a complicated process integrating multiple systems and cells.It is crucial to explore the molecular an... The initial mechanical damage of a spinal cord injury(SCI)triggers a progressive secondary injury cascade,which is a complicated process integrating multiple systems and cells.It is crucial to explore the molecular and biological process alterations that occur after SCI for therapy development.The differences between the rostral and caudal regions around an SCI lesion have received little attention.Here,we analyzed the differentially expressed genes between rostral and caudal sites after injury to determine the biological processes in these two segments after SCI.We identified a set of differentially expressed genes,including Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1,between rostral and caudal regions at different time points following SCI.Functional enrichment analysis indicated that these genes were involved in response to mechanical stimulus,blood vessel development,and brain development.We then chose Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1 for quantitative real-time PCR and Fn1 for immunostaining validation.Our results indicate alterations in different biological events enriched in the rostral and caudal lesion areas,providing new insights into the pathology of SCI. 展开更多
关键词 biological process caudal differentially expressed genes Gene Ontology hemisection immunostaining Rattus norvegicus RNA-sequencing rostral spinal cord injury
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Effects of β-catenin on Differentially Expressed Genes in Multiple Myeloma 认领 引用 被引量：3
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作者 陈辉 柴伟 +7 位作者 李斌 倪明 张国强 刘华玮 张卓 陈继营 周勇刚 王岩 《Journal of Huazhong University of Science and Technology(Medical Sciences)》 2015年第4期546-552,共7页
Summary： This study aimed to identify the differentially expressed genes after silencing of β-catenin in multiple myeloma transduced with β-catenin shRNA. The DNA microarray dataset GSE17385 was downloaded from Gen... Summary： This study aimed to identify the differentially expressed genes after silencing of β-catenin in multiple myeloma transduced with β-catenin shRNA. The DNA microarray dataset GSE17385 was downloaded from Gene Expression Omnibus, including 3 samples of MM1.S （human multiple mye- loma cell lines） cells transduced with control shRNA and 3 samples of MM1.S cells transduced with β-catenin shRNA. Then the differentially expressed genes （DEGs） were screened by using Limma. Their underlying functions were analyzed by employing Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. Moreover, DEGs annotation was conducted based on the databases of tumor associated genes, tumor suppressed genes and the transcriptional regulation from patterns to profiles. Furthermore, the protein-protein interaction （PPI） relationship was obtained from STRING and the protein-protein interaction network and the functional modules were visual- ized by Cytoscape. Then, the pathway enrichment for the DEGs in the functional module was per- formed. A total of 301 DEGs, including 124 up-regulated and 117 down-regulated DEGs, were screened. Functional enrichment showed that CCNB1 and CDK1 were significantly related to the function of cell proliferation. FOS and JUN were related to innate immune response-activating signal transduction. Pathway enrichment analysis indicated that CCNB 1 and CDK1 were most significantly enriched in the pathway of cell cycle. Besides, FOS and JUN were significantly enriched in the Toll-like receptor signaling pathway. FOXM1 was identified as a transcription factor. Moreover, there existed interactions among CCNB1, FOXM1 and CDK1 in PPI network. The expression of FOS, JUN, CCNB1, FOXM1 and CDK1 may be affected by β-catenin in multiple myeloma. 展开更多
关键词 multiple myeloma β-catenin differentially gene expression fimctional enrichment
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Identifi cation of the differential expressive tumor associated genes in rectal cancers by cDNA microarray 认领 引用 被引量：1
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作者 Xue-Qin Gao Jin-Xiang Han +3 位作者 Zhong-Fa Xu Wei-Dong Zhang Hua-Ning Zhang Hai-Yan Huang 《World Journal of Gastroenterology》 SCIE CAS 2007年第3期341-348,共8页
AIM： To identify tumor associated genes of rectal cancer and to probe the application possibility of gene expression profiles for the classification of tumors.METHODS： Rectal cancer tissues and their paired normal m... AIM： To identify tumor associated genes of rectal cancer and to probe the application possibility of gene expression profiles for the classification of tumors.METHODS： Rectal cancer tissues and their paired normal mucosa were obtained from patients undergoing surgical resection of rectal cancer. Total RNA was extracted using Trizol reagents. First strand cDNA synthesis was indirectly labeled with aminoallyl-dUTP and coupled with Cy3 or Cy5 dye NHS mono-functional ester. After normalization to total spots, the genes which background subtracted intensity did not exceed 2 SD above the mean blank were excluded. The data were then sorted to obtain genes differentially expressed by ≥ 2 fold up or down in at least 5 of the 21 patients.RESULTS： In the 21 rectal cancer patients, 23 genes were up-regulated in at least 5 samples and 15 genes were down-regulated in at least 5 patients. Hierachical cluster analysis classified the patients into two groups according to the clinicopathological stage, with one group being all above stage Ⅱ and one group all below stage Ⅱ.CONCLUSION： The up-regulated genes and downregulated genes may be molecular markers of rectal cancer. The expression profiles can be used for classification of rectal cancer. 展开更多
关键词 Rectal cancer Tumor associated genes cDNA microarray Differential expression genes
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Differential expression of salt tolerance related genes in Brassica campestris L.ssp.chinensis(L.)Makino var.communis Tsen et Lee 认领 引用 被引量：1
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作者 Yang QIU Xi-xiang LI +2 位作者 Hai-ying ZHI Di SHEN Peng LU 《Journal of Zhejiang University-SCIENCE B》 SCIE CAS 2009年第11期847-851,共5页
We examined salt tolerance responsive genes in Pak-choi under salt stress and analyze their potential function.The LRNA differential display was used to screen the transcript derived fragments(TDFs)related to salinity... We examined salt tolerance responsive genes in Pak-choi under salt stress and analyze their potential function.The LRNA differential display was used to screen the transcript derived fragments(TDFs)related to salinity tolerance in tolerant and Loderately tolerant Pak-choi germplasm.Seventy-eight primer combinations generated 101 differential eDNA fragments,which ere divided into 10 expression types.Seven cDNA sequences(GenBank accession Nos.DQ006915-DQ006921)obtained and,~quenced were highly homologous to some known expression genes or the genes related to the signaling pathways in plants under ifferent abiotic stress. 展开更多
关键词 Brassica campestris L.ssp.chinensis(L.)Makino var.communis Tsen et Lee Salinity tolerance Gene differential expression cDNA fragments Basic local alignment search tool(BLAST)analysis
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cDNA-SCoT Analysis of Differential Expressed Genes in Allium tuberosum Induced by Botrytis cinerea 认领 引用
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作者 Minghui CHEN Zhilu ZHANG +3 位作者 Yanjiao LI Pengqiang YAO Shiping CHENG Ganqing ZHAO 《Asian Agricultural Research》 2020年第10期38-41,共4页
[Objectives]To investigate the molecular mechanism of gene differential expression in A.tuberosum under Botrytis cinerea stress.[Methods]The leaf of A.tuberosum was inoculated with B.cinerea to induce resistance,then ... [Objectives]To investigate the molecular mechanism of gene differential expression in A.tuberosum under Botrytis cinerea stress.[Methods]The leaf of A.tuberosum was inoculated with B.cinerea to induce resistance,then leaf samples were taken at 2,4,8,12 and 24 h,respectively,after inoculation,and used for cDNA-SCoT analysis to detect the gene differential expressions.[Results]More than 800 bands with length of 100-1800 bp were obtained using 60 SCoT primers.A total of 40 differentially expressed EST sequences were screened out,and 18 non-redundant ESTs with high quality were obtained by cluster analyses of the ESTs sequencing.The results of BlastN showed that the differential genes of A.tuberosum mainly related to disease defense,signal transduction,and protein metabolism.[Conclusions]Further analysis of gene function indicated that brassinosteroid biosynthesis-like proteins,NBS-LRR type disease resistance protein,jasmonic acid induced protein,abscisic stress ripening protein may be involved in the process of the incompatible interaction between the A.tuberosum and B.cinerea. 展开更多
关键词 Allium tuberosum Grey mould cDNA-SCoT Differential genes
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Analysis of differentially expressed genes in Verruca vulgaris vs.adjacent normal skin by RNA-sequencing 认领 引用
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作者 QINGQING GUO JIAYUE QI +4 位作者 XIAOQIANG LIANG ZIGANG ZHAO JIA BAI FANG XIE CHENGXIN LI 《BIOCELL》 SCIE 2023年第11期2435-2443,共9页
Introduction:Verruca vulgaris is one of the most common low-risk HPV infections and is characterized by excessive proliferation of keratinocytes.Currently,very little genetic information is available regarding verruca... Introduction:Verruca vulgaris is one of the most common low-risk HPV infections and is characterized by excessive proliferation of keratinocytes.Currently,very little genetic information is available regarding verruca vulgaris in the Chinese population.This study aimed to obtain comprehensive transcript information of verruca vulgaris by RNA sequencing.Methods:High-throughput sequencing was performed on three fresh verruca vulgaris samples and adjacent normal skin on the Illumina sequencing platform.The transcriptomes were analyzed using bioinformatics and the differentially expressed genes(DEGs)were verified by immunohistochemistry.Verruca vulgaris exhibited a unique molecular signature.Results:In total,1,643 DEGs were identified in verruca vulgaris compared to normal skin.The functions of the DEGs were studies by Gene Ontology(GO)enrichment,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis,DEGs Reactome analysis,disease annotation function,and STRING protein-protein interaction(PPI)network analysis.The results revealed 595 GO terms associated with the cell cycle,signal transduction,immune system,signaling molecules,and interaction.The Reactome analysis revealed enrichment in reversible hydration of carbon dioxide and BMP signaling,while the disease annotation function revealed that the enriched DEGs are involved in keratosis disorders.The STRING PPI network showed that the edges with the highest density mainly included the 2′-5′oligoadenylate synthase(OAS)family-related proteins.Furthermore,the M-code analysis found ISG15,IRF7,and OASL were scored as significant modules and their high expression compared to the control was verified by immunohistochemistry.Conclusion:These findings contribute to the genetic information of verruca vulgaris in the Chinese population,revealing that interferon-stimulated genes may play essential roles in verruca vulgaris. 展开更多
关键词 Differentially expressed genes RNA-seq Transcriptome Verruca vulgaris Interferon-stimulated genes
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Analysis on differentially expressed genes in watermelon rind color based on RNA–Seq 认领 引用
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作者 杨侃侃 梁志怀 吴才君 《Journal of Central South University》 SCIE EI CAS CSCD 2016年第11期2818-2826,共9页
In order to screen the genes controlling watermelon rind color and luster, the experiment was carried out with yellow watermelon skin mutants as tester and green wild type watermelon as control, and transcriptome sequ... In order to screen the genes controlling watermelon rind color and luster, the experiment was carried out with yellow watermelon skin mutants as tester and green wild type watermelon as control, and transcriptome sequencing and bioinformatics analysis were done. The results show that 34.27 Gb clean data were got by transcriptome sequencing. There are 261 differentially expressed genes among Y_1_vs_G_1, Y_2_vs_G_2 and Y_3_vs_G_3. The pathways contenting most differentially expressed genes are plant hormone signal transduction pathway, phenylpropanoid biosynthesis pathway, photosynthesis pathway, starch and sucrose metabolism pathway. 9-cis-epoxycarotenoid dioxygenase(Cla002942), alcohol dehydrogenase(Cla004992), photosystem Ⅰ reaction center subunit Ⅲ, chloroplastic(precursor)(Cla009181), long-chain acyl coenzyme A synthetase(Cla017341), threonine dehydratase biosynthetic(Cla018352) candidates genes were screened out. 展开更多
关键词 watermelon rind color transcriptome sequencing differentially expressed genes
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Analysis of differentially expressed genes related to cerebral ischaemia in young rats based on the Gene Expression Omnibus database 认领 引用
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作者 Yu Xia Han Liu Rui Zhu 《World Journal of Clinical Cases》 SCIE 2023年第7期1467-1476,共10页
BACKGROUND The incidence rate of cerebral infarction in young people is increasing day by day,the age of onset tends to be younger,and its internal pathogenesis and mechanism are very complicated,which leads to greate... BACKGROUND The incidence rate of cerebral infarction in young people is increasing day by day,the age of onset tends to be younger,and its internal pathogenesis and mechanism are very complicated,which leads to greater difficulties in treatment.Therefore,it is essential to analyze the key pathway that affects the onset of cerebral infarction in young people from the perspective of genetics.AIM To compare the differentially expressed genes in the brain tissue of young and aged rats with middle cerebral artery occlusion and to analyse their effect on the key signalling pathway involved in the development of cerebral ischaemia in young rats.METHODS The Gene Expression Omnibus 2R online analysis tool was used to analyse the differentially expressed genes in the GSE166162 dataset regarding the development of cerebral ischaemia in young and aged groups of rats.DAVID 6.8 software was further used to filter the differentially expressed genes.These genes were subjected to Gene Ontology(GO)function analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis to determine the key gene pathway that affects the occurrence of cerebral ischaemia in young rats.RESULTS Thirty-five differentially expressed genes(such as Igf2,Col1a2,and Sfrp1)were obtained;73 GO enrichment analysis pathways are mainly involved in biological processes such as drug response,amino acid stimulation response,blood vessel development,various signalling pathways,and enzyme regulation.They are involved in molecular functions such as drug binding,protein binding,dopamine binding,metal ion binding,and dopamine neurotransmitter receptor activity.KEGG pathway enrichment analysis showed a significantly enriched pathway:The cyclic adenosine monophosphate(c-AMP)signalling pathway.CONCLUSION The c-AMP signalling pathway might be the key pathway in the intervention of cerebral infarction in young people. 展开更多
关键词 Gene Expression Omnibus database Cerebral infarction in young people Rats Differential gene enrichment analysis Pathway
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Decoding exercise-induced atomic components and prognostic shifts in endometrial carcinoma through differentially expressed genes 认领 引用
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作者 Yan Li Zhuo Wang +11 位作者 Hai-Ning Li Yuan-Yuan Yong Min Kong Ngenzi Richard Djurist Xin Yang Sana Mushtaq Yan Ma Zhi-Fang Wang Ayang Mba Teresa Yue-Yue Shi Yao He Suo-Fei Li 《Traditional Medicine Research》 2024年第11期51-64,共14页
Background:This study aimed to portray the atomic intelligence and prognostic implications of differentially expressed genes and their involvement in biological pathways in endometrial carcinoma,with a specific focus ... Background:This study aimed to portray the atomic intelligence and prognostic implications of differentially expressed genes and their involvement in biological pathways in endometrial carcinoma,with a specific focus on the impacts of exercise on cancer.Methods:We utilized a multi-faceted approach,including volcano plots,Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses,Venn diagrams,protein-protein interaction networks,Kaplan-Meier survival analysis,Gene Set Variety Analysis,and single-cell transcriptomic analysis.Furthermore,we profiled tumor mutational scenes,assessed the prognostic value of immune-related features,and conducted a comprehensive examination of genetic variations and their impact on tumor mutational burden across different cancer types.Multidimensional genomic interactions and methylation elements were also investigated.Using real-time quantitative PCR and immunofluorescence staining,the effects of B-cell lymphoma 2(BCL2)silencing on TNF-αand caspase-3 gene expression were evaluated.Results:Our study identified a noteworthy number of differentially expressed genes in endometrial carcinoma with potential links to athletic performance traits.BCL2 expression levels were found to be associated with survival outcomes,and its changeability across cancers was related to immune cell infiltration and immune checkpoint gene expression.Single-cell investigations uncovered cellular complexity within tumor microenvironments and critical biological pathways in BCL2-overexpressing cells.The expression flow and mutational effect of BCL2 in endometrial carcinoma were characterized,and the prognostic implications of immune-related features were assessed.Hereditary variations,including copy number variations and their relationship with gene expression and tumor mutational burden,were investigated.Multidimensional genomic transaction highlighted the essential role of regulatory genes in cancer pathogenesis.Silencing of the BCL2 gene significantly inhibited the proliferation of HEC-108 cells and promoted apoptosis,as evidenced by decreased TNF-αgene expression and increased caspase-3 gene expression.Immunofluorescence staining further confirmed these results.Conclusion:This study gives a point-by-point understanding of the atomic intelligence and prognostic implications in endometrial carcinoma and across various other cancers.BCL2’s role as a modulatory factor within the tumor-resistant environment and its potential impact on disease prognosis and response to immunotherapy were underscored.The multidimensional genomic analysis provides insights into the complex interaction between genetic and epigenetic variables in cancer,which may shed light on future therapeutic strategies.This study indicates that silencing the BCL2 gene can significantly inhibit tumor cell proliferation and promote apoptosis through the regulation of the TNF-αand caspase-3 pathways. 展开更多
关键词 endometrial carcinoma differentially expressed genes pathway enrichment immune pathways prognostic implications exercise and cancer
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ANALYSES ON DIFFERENTIALLY EXPRESSED GENES ASSOCIATED WITH HUMAN BREAST CANCER 认领 引用
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作者 孟旭莉 丁小文 徐笑红 《Chinese Journal of Cancer Research》 CAS 2006年第3期193-197,共5页
Objective： To investigate the molecular etiology of breast cancer by way of studying the differential expression and initial function of the related genes in the occurrence and development of breast cancer. Methods：... Objective： To investigate the molecular etiology of breast cancer by way of studying the differential expression and initial function of the related genes in the occurrence and development of breast cancer. Methods： Two hundred and eighty-eight human tumor related genes were chosen for preparation of the oligochips probe, mRNA was extracted from 16 breast cancer tissues and the corresponding normal breast tissues, and cDNA probe was prepared through reverse-transcription and hybridized with the gene chip. A laser focused fluorescent scanner was used to scan the chip.The different gene expressions were thereafter automatically compared and analyzed between the two sample groups. Cy3/Cy5〉3.5 meant significant up-regulation. Cy3/Cy5〈0.25 meant significant down-regulation. Results： The comparison between the breast cancer tissues and their corresponding normal tissues showed that 84 genes had differential expression in the Chip. Among the differently expressed genes, there were 4 genes with significant down-regulation and 6 with significant up-regulation. Compared with normal breast tissues, differentially expressed genes did partially exist in the breast cancer tissues. Conclusion： Changes in multi-gene expression regulations take place during the occurrence and development of breast cancer; and the research on related genes can help understanding the mechanism of tumor occurrence. 展开更多
关键词 Breast cancer Differentially expressed genes Gene chip
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