Dataset Information

Analysis of gene expression profile of pancreatic carcinoma using cDNA microarray.

ABSTRACT: AIM:To identify new diagnostic markers and drug targets, the gene expression profiles of pancreatic cancer were compared with that of adjacent normal tissues utilizing cDNA microarray analysis. METHODS:cDNA probes were prepared by labeling mRNA from samples of six pancreatic carcinoma tissues with Cy5-dUTP and mRNA from adjacent normal tissues with Cy3-dUTP respectively through reverse transcription. The mixed probes of each sample were then hybridized with 12 800 cDNA arrays (12 648 unique human cDNA sequences), and the fluorescent signals were scanned by ScanArray 3 000 scanner (General Scanning, Inc.). The values of Cy5-dUTP and Cy3-dUTP on each spot were analyzed and calculated by ImaGene 3.0 software (BioDiscovery, Inc.). Differentially expressed genes were screened according to the criterion that the absolute value of natural logarithm of the ratio of Cy5-dUTP to Cy3-dUTP was greater-than 0.69. RESULTS:Among 6 samples investigated, 301 genes, which accounted for 2.38 % of genes on the microarry slides, exhibited differentially expression at least in 5. There were 166 over-expressed genes including 136 having been registered in Genebank, and 135 under-expressed genes including 79 in Genebank in cancerous tissues. CONCLUSION:Microarray analysis may provide invaluable information on disease pathology, progression, resistance to treatment, and response to cellular microenvironments of pancreatic carcinoma and ultimately may lead to improving early diagnosis and discovering innovative therapeutic approaches for cancer.

SUBMITTER: Tan ZJ

PROVIDER: S-EPMC4611457 | biostudies-literature | 2003 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Analysis of gene expression profile of pancreatic carcinoma using cDNA microarray.

Tan Zhi-Jun ZJ Hu Xian-Gui XG Cao Gui-Song GS Tang Yan Y

World journal of gastroenterology 20030401 4

<h4>Aim</h4>To identify new diagnostic markers and drug targets, the gene expression profiles of pancreatic cancer were compared with that of adjacent normal tissues utilizing cDNA microarray analysis.<h4>Methods</h4>cDNA probes were prepared by labeling mRNA from samples of six pancreatic carcinoma tissues with Cy5-dUTP and mRNA from adjacent normal tissues with Cy3-dUTP respectively through reverse transcription. The mixed probes of each sample were then hybridized with 12 800 cDNA arrays (12 ...[more]

PMID: 12679940

Similar Datasets

Project description:ObjectiveTo analyze the expression profile variation of lncRNAs in normal urinary bladder tissue and urothelial carcinoma of the urinary bladder through microarray technology. The differentially expressed lncRNAs were identified and classified, and their biological information was analyzed. The data obtained in the study will prove helpful for the diagnosis, treatment, and prevention of urothelial carcinoma of the bladder.Materials and methodsThree specimens of urothelial carcinoma of the bladder and three specimens of normal bladder tissue were identified by histology. The total RNA was isolated from the bladder urothelial carcinomas and normal tissue and purified. The targets were mixed and hybridized with the genes on the microarray, which contained thirty thousand lncRNAs. The bladder urothelial carcinomas were then compared with the normal bladder tissue. The lncRNAs that were differentially expressed between the two groups were identified based on the signal-to-noise ratios using the Agilent Feature Extraction software and were analyzed with the Agilent Genespring GX software (Agilent). The outcome was obtained, and the biological information of these genes was deposited in GenBank.ResultsThe expression profile of lncRNAs was significantly different between normal bladder tissue and urothelial carcinoma of the bladder. Compared with normal bladder tissue, 1,122 lncRNAs exhibited at least a twofold, significant difference (P < 0.05) and are thus regarded as differentially expressed lncRNAs. Of these, 734 and 388 lncRNAs were upregulated and down regulated. The differentially expressed lncRNAs in the urothelial carcinoma of the bladder are distributed on every chromosome, and most of these lncRNAs are distributed on chromosomes 1, 2, 3, 4, 6, and X.ConclusionsUrothelial carcinoma of the bladder is a complicated disease that involves the regulation of multiple genes and the participation of multiple chromosomes. Some of the differentially expressed lncRNAs that were upregulated, such as AK124776, lincRNA-RAB12-1, KRT8P25, RP11-474J18.4, AC000110.1, KRT8P13, KRT8P10, BC072678, and downregulated, such as nc-HOXB9-206, RP11-160A10.2, nc-HOXA11-86, nc-HOXD10-7, nc-HOXB9-205, CES4, nc-HOXD12-3, systematic research on these lncRNAs will help clarify the mechanisms of urothelial carcinoma of the bladder and guide the early diagnosis and treatment of this cancer in the future.

Project description:BACKGROUND: After fertilization, embryo development involves differentiation, as well as development of the fetal body and extra-embryonic tissues until the moment of implantation. During this period various cellular and molecular changes take place with a genetic origin, e.g. the elongation of embryonic tissues, cell-cell contact between the mother and the embryo and placentation. To identify genetic profiles and search for new candidate molecules involved during this period, embryonic gene expression was analyzed with a custom designed utero-placental complementary DNA (cDNA) microarray. METHODS: Bovine embryos on days 7, 14 and 21, extra-embryonic membranes on day 28 and fetuses on days 28 were collected to represent early embryo, elongating embryo, pre-implantation embryo, post-implantation extra-embryonic membrane and fetus, respectively. Gene expression at these different time points was analyzed using our cDNA microarray. Two clustering algorithms such as k-means and hierarchical clustering methods identified the expression patterns of differentially expressed genes across pre-implantation period. Novel candidate genes were confirmed by real-time RT-PCR. RESULTS: In total, 1,773 individual genes were analyzed by complete k-means clustering. Comparison of day 7 and day 14 revealed most genes increased during this period, and a small number of genes exhibiting altered expression decreased as gestation progressed. Clustering analysis demonstrated that trophoblast-cell-specific molecules such as placental lactogens (PLs), prolactin-related proteins (PRPs), interferon-tau, and adhesion molecules apparently all play pivotal roles in the preparation needed for implantation, since their expression was remarkably enhanced during the pre-implantation period. The hierarchical clustering analysis and RT-PCR data revealed new functional roles for certain known genes (dickkopf-1, NPM, etc) as well as novel candidate genes (AW464053, AW465434, AW462349, AW485575) related to already established trophoblast-specific genes such as PLs and PRPs. CONCLUSIONS: A large number of genes in extra-embryonic membrane increased up to implantation and these profiles provide information fundamental to an understanding of extra-embryonic membrane differentiation and development. Genes in significant expression suggest novel molecules in trophoblast differentiation.

Dataset Information

Analysis of gene expression profile of pancreatic carcinoma using cDNA microarray.

Publications

Analysis of gene expression profile of pancreatic carcinoma using cDNA microarray.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets