Please use this identifier to cite or link to this item: http://hdl.handle.net/10603/4994
Title: Identification and validation of differentially expressed genes in gastric Adenocarcinoma
Researcher: Marimuthu, Arivusudar
Guide(s): Chaerkady, Raghothama
Keywords: Health Sciences
Gastric cancer
Cancer disease
Upload Date: 26-Oct-2012
University: Manipal University
Completed Date: 15/11/2011
Abstract: Gastric cancer is the second leading cause of cancer death worldwide, both in men and women. In India, it is one of the leading cancers in males. Tumorigenesis is asymptomatic and patients with gastric cancer are diagnosed at an advanced stage. There is a dire need to identify molecular newlinemarkers for early detection of gastric cancer. Discovery of genes that are aberrantly expressed in cancer as compared to normal would lead to the development of biomarkers for clinical diagnosis and prognosis. In order to achieve this, two different approaches were used. In the first newlineapproach, a genome wide gene expression analysis was carried out to identify differentially expressed genes in gastric adenocarcinoma tissues as compared to adjacent normal tissues. Agilent?s whole human genome oligonucleotide microarray platform representing ~41,000 newlinetranscripts was used to carry out gene expression analysis. Through this approach, several previously known candidate genes along with a number of novel candidate genes were identified in gastric cancer. Testican-1 (SPOCK1) was one among the novel candidates that was found to be 10-fold upregulated in tumors. Using tissue microarrays, the expression of testican-1 was validated by immunohistochemical staining. It was overexpressed in 56% (160/282) of the cases newlinetested. Secondly, mass spectrometry-based quantitative proteomic analysis was carried out to identify genes that were differentially expressed at protein level. In particular, the proteins that were specifically secreted from gastric cancer were studied using gastric cancer cell lines. Stable isotope labeling with amino acids in cell culture (SILAC) was employed to identify differentially secreted proteins. This study led to the identification of several markers. PCSK9, LMAN2, LGALS4 and PDAP1 were four novel candidates chosen for validation by immunohistochemical analysis. Through this study, a robust pipeline to discover biomarkers has been established.
Pagination: 112p.
URI: http://hdl.handle.net/10603/4994
Appears in Departments:Institute of Bioinformatics, Bangalore

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01_title.pdfAttached File70.84 kBAdobe PDFView/Open
02_certificate.pdf75.08 kBAdobe PDFView/Open
03_abstract.pdf58.47 kBAdobe PDFView/Open
04_declaration.pdf56.62 kBAdobe PDFView/Open
05_acknowledgments.pdf55.13 kBAdobe PDFView/Open
06_contents.pdf54.87 kBAdobe PDFView/Open
07_list_of_tables.pdf54.47 kBAdobe PDFView/Open
08_list_of_figures.pdf55.12 kBAdobe PDFView/Open
09_abbreviations.pdf55.56 kBAdobe PDFView/Open
10_chapter1.pdf428.05 kBAdobe PDFView/Open
11_chapter2.pdf58.29 kBAdobe PDFView/Open
12_chapter3.pdf228.72 kBAdobe PDFView/Open
13_chapter4.pdf928.21 kBAdobe PDFView/Open
14_chapter5.pdf886.56 kBAdobe PDFView/Open
15_conclusion.pdf59.11 kBAdobe PDFView/Open
16_bibliography.pdf95.11 kBAdobe PDFView/Open
17_appendix_1.pdf114.87 kBAdobe PDFView/Open
18_appendix_ii.pdf102.28 kBAdobe PDFView/Open
19_appendix_iii.pdf55.27 kBAdobe PDFView/Open


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