Cluster analysis of gene expression and glioblastoma-associated gene by using cDNA microarray
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Objective To study function and screen differentially expressed genes in development of human glioblastoma by using cDNA microarray.Methods BioStarH140S microarray (including 8 347 old genes and 5 592 novel genes) was adopted and hybridized with probes which were prepared for total RNA. These probes were isolated from 2 cases of normal adult brain tissues and 18 cases of glioma tissues. Differentially expressed genes between normal tissues and glioma tissues were analyzed after scanning microarray with ScanArray4 000. These genes were studied with Hierarchical method and Northern hybridization was used for the function of genes. Results Among the 13 939 target genes, there were multiple differentially expressed genes and 5 genes were significantly up-regulated in glioblastoma. Two of them were testified by Northern-blot.Conclusion cDNA microarray technology is a powerful technique in screening differentially expressed genes; 5 up-regulated genes would be helpful to understand the molecular mechanism of glioblastoma. These genes were tightly related to invasion of glioblastoma and might become molecular index of prognosis of glioblastoma.Keywords:
Gene chip analysis
Northern blot
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Objective To study the gene expression profiles of ovarian cancer by cDNA microarray,and preliminarily analyze the function of part of differential expression genes.Methods BiostarH-40s gene microarray containing 4 097 genes was used to analyze gene expression patterns in tissue samples from 5 cases of human ovarian serous cystadenocarinoma(cy5-dUTP present ) and 5 cases of normal ovarian tissues(cy3-dUTP present).Results 163 genes of differential expression were found in more than 4 cases of ovarian cancer,the expression of 66 genes increased(up-regulated),the expression of 97 genes decreased(down-regulated). 37 differential genes with difinite gene function classification were found including three protocogene and tumor suppressor genes,one cyclin protein gene,three cytoskeletal and movement protein genes,one DNA binding,transcription and transcription factors gene,two cell receptor genes,five immune-related protein genes,seven metabolism genes,two protein translation and synthesis genes,three growth-related genes and seven other types of genes.Conclusion Gene expression profiles of ovarian cancer can be detected by cDNA microarray,and differential expression genes and their gene function classification of ovarian cancer are found.
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Objective To screen the human pancreatic cancer-associated genes by cDNA microarray.Methods The PCR products of 14 000 genes were spotted onto a chemical-material-coated-glass plates in array.DNAs were fixed onto the glass plate after series of treatments.The total RNAs were isolated from 4 specimens of the pancreatic cancer and the normal tumor-surrounding pancreatic tissues.Both equal quantity RNAs were reversely transcribed to cDNAs and labeled with the fluorescent Cy5-dCTP and Cy3-dCTP to prepare the hybridization probes.The mixed probes were hybridized to the cDNA microarray.After high-stringent washing,the fluorescent signals were scanned by ScanArray 4000 scanner.The values of Cy5-dCTP and Cy3-dCTP on each spot were analyzed and calculated by GenePix Pro 3.0 software.Results By applying this cDNA microarray,189 differentially expressed genes in pancreatic cancer,whose ratios of Cy5/Cy3 were higher than 2.0 or lower than 0.5,were screened out among the 14 000 target genes,comprising 101 known genes and 88 novel gene.Among the known genes,upregulated and downregulated genes were 50 and 51 respectively,including oncogenes and tumor suppression genes,cell cycle related genes,cell skeleton and cinetc-protein related genes,cell apoptosis related genes,DNA synthesis related genes,DNA damage and repair-related genes,transcription factors,receptor related genes,immune related genes,signal transduction related genes,protein translation and synthesis related genes,metabolism related genes.Conclusion The analysis of gene expression profile of tumor based on cDNA microarray can realize high-throughput screening of the genes associated with the pancreatic cancer,and it can help to rapidly explore the genes function.Further analysis of the obtained genes will help to understand the molecular mechanism of the pancreatic cancer.
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Objective To study the expression of astrocytoma genes and characterization classification genes by using cDNA microarray. Methods BioStarH140S microarray (including 5 592 novel genes) were used and hybridized with probes, which were prepared for total RNA. It was extracted from 2 cases of normal adult brain tissues and 18 cases of glioma tissues. Differentially expre-ssed genes between normal tissues and glioma tissues were assayed after scanning cDNA microarray with ScanArray 4 000. The gene's characterizations were studied with Hierarchical method. Results Among the 13 939 target genes, there were 438 (3.14%) differentially expressed genes between astrocytoma and normal brain tissue. By bioinformal analysis, those genes were associated with cell signal, cytoskeleton, oncogenes and suppressor genes, etc. MAP7, DBCCR1, PCDHA5, KCNAB1, NAP1L2 genes were relevant to classification by Hierarchical method. Molecular classification was in accordance with pathology and revealed internal essence in tumorigenesis. Conclusion cDNA microarray is an available technique in screening marker genes of glioma and understanding its molecular mechanism and is helpful to diagnosis and therapy of the glioma.
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Objective:To investigate the differentially expressed genes in hepatic cellular carcinoma(HCC)using cDNA microarray and screen for HCC-related genes.Methods:Total RNA was extracted from normal human liver tissues and hepatic cellular carcinoma tissues.The mRNA was used to prepare probes. The mixed probes were hybridized to the cDNA microarray. After washing, the DNA chips were scanned by laser scanner, The acquired was analyzed.Results:Among the 9182 target genes, 102 genes were identified in HCC tissues that were either over or under-expressed as compared to controls.Forty two genes were up-regulated and 60 down-regulated.Twelve new genes were found in the study. Conclusion: The cDNA microarray for analysis of gene expression profile is a powerful method for screening hepatic cellular carcinoma-related genes.
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Objective To screen the differentially expressed genes between esophageal carcer and carcer adjacent tissue using cDNA microarray.Methods The total RNAs were isolated from the tissues,reversely transcribed to cDNAs to prepare the hybridizaion probes.The mixed probes were hybridized to the cDNA microarray(14?114 target genes).After washing,the cDNA microarray was scanned for the fluorescent signals and showed differences between 2 tissues.Results 31 genes whose expression level differe in 3 cases between the tissues,10 genes up regulation,21 genes down regulation.Conclusion the differentially expressed genes between 2 different kinds of tissue.
Gene chip analysis
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Objective To study the expression and function of genes correlating with invasion in glioblastoma by using cDNA microarray. Methods BioStarH140S microarray containing 8 347 old genes and 5 592 novel genes were adopted and hybridized with probes which were prepared for total RNA. These probes were isolated from 6 cases of glioblastoma tissues and normal adult brain tissues. Differentially expressed genes between normal brain tissues and glioblastoma tissues were analyzed after scanning microarray with ScanArray4 000. These related genes were studied with bioinformatical analysis. Results Among the 13 939 target genes, 198 genes (1.42 %) were differentially expressed. Bioinformatical analysis revealed that these genes were closely associated with cell signal transduction, cell metabolize, cytoskeleton, motility, immunity, oncogene and tumor suppressor, cell cycle and cell apoptosis. There were 8 cytoskeleton and matrix motility genes which expressed similarly, such as a-Catenin, CDH1, LAMA4, FN1, MMP2, COL3A1, TIMP1 and PDGFRA.Conclusion cDNA microarray technology is effective in screening differentially expressed genes. Invasive genes would supply molecular target which can estimate prognosis of glioblastoma and be helpful to clinical therapy.
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Gene chip analysis
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Radiosensitivity
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To screen differentially expressed genes in the development of human glioma and establish molecular classification of glioma preliminary based on gene expression using cDNA microarray.Brain specimens were obtained from 18 patients with glioma, 10 males and 8 females, aged 14 approximately 62 with an average age of 44.4. The total RNAs of these glioma specimens and 2 specimens of donated brain of normal adults were extracted. BioStarH140S microarray (including 8347 old genes and 5592 novel genes) were adopted and hybridized with probes which were prepared from the total RNAs. Differentially expressed genes between the normal tissues and glioma tissues were assayed after scanning cDNA microarray with ScanArray 4000. Northern hybridization, and in situ hybridization (ISH) were used to identify the functions of novel genes. Those differentially expressed genes were studied with Hierarchical method and molecular classification of glioma was preliminarily carried out.Among the 13 939 target genes, there were 1200 (8.61%) differentially expressed genes and 395 (2.83%) novel genes. 348 genes were up-regulated and 852 genes were down-regulated in glioma. The results of bioinformatical analysis, Northern hybridization and ISH revealed that those novel genes were highly associated with glioma. There were multiple genes which were relevance to classification by Hierarchical method, such as MAP gene, cytoskeleton and matrix motility genes, etc. Molecular classification of glioma with Hierarchical cluster was in accordance with pathology and revealed internal essence in tumorigenesis and development.Multiple genes play important roles in development of glioma. cDNA microarray technology is a powerful technique in screening for differentially expressed genes between two different kinds of tissues.
Gene chip analysis
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