title: Gene Expression Profiling of Gastric Cancer.
abstract: Gastric cancer is the second leading cause of cancer death worldwide, both in men and women. A genomewide gene expression analysis was carried out to identify differentially expressed genes in gastric adenocarcinoma tissues as compared to adjacent normal tissues. We used Agilent's whole human genome oligonucleotide microarray platform representing ~41,000 genes to carry out gene expression analysis. Two-color microarray analysis was employed to directly compare the expression of genes between tumor and normal tissues. Through this approach, we identified several previously known candidate genes along with a number of novel candidate genes in gastric cancer. Testican-1 (SPOCK1) was one of the novel molecules that was 10-fold upregulated in tumors. Using tissue microarrays, we validated the expression of testican-1 by immunohistochemical staining. It was overexpressed in 56% (160/282) of the cases tested. Pathway analysis led to the identification of several networks in whichSPOCK1was among the topmost networks of interacting genes. By gene enrichment analysis, we identified several genes involved in cell adhesion and cell proliferation to be significantly upregulated while those corresponding to metabolic pathways were significantly downregulated. The differentially expressed genes identified in this study are candidate biomarkers for gastric adenoacarcinoma.
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India.
authors.forename: Arivusudar
authors.initials: A
authors.lastname: Marimuthu
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA.
authors.forename: Harrys K C
authors.initials: HK
authors.lastname: Jacob
authors.affiliation: Department of Zoology, Gauhati University, Guwahati 781014, Assam, India; Imgenex India, Bhubaneswar 751024, Orissa, India.
authors.forename: Aniruddha
authors.initials: A
authors.lastname: Jakharia
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; Rajiv Gandhi University of Health Sciences, Bangalore, 560041, Karnataka, India.
authors.forename: Yashwanth
authors.initials: Y
authors.lastname: Subbannayya
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
authors.forename: Shivakumar
authors.initials: S
authors.lastname: Keerthikumar
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India.
authors.forename: Manoj Kumar
authors.initials: MK
authors.lastname: Kashyap
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India.
authors.forename: Renu
authors.initials: R
authors.lastname: Goel
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India.
authors.forename: Lavanya
authors.initials: L
authors.lastname: Balakrishnan
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; School of Biotechnology, Amrita Vishwa Vidyapeetham University, Kollam 690525, Kerala, India.
authors.forename: Sutopa
authors.initials: S
authors.lastname: Dwivedi
authors.affiliation: Strand Life Sciences, Bangalore 560024, Karnataka, India.
authors.forename: Swapnali
authors.initials: S
authors.lastname: Pathare
authors.affiliation: Strand Life Sciences, Bangalore 560024, Karnataka, India.
authors.forename: Jyoti Bajpai
authors.initials: JB
authors.lastname: Dikshit
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; RajaRajeswari Medical college, Bangalore, 560074, India.
authors.forename: Jagadeesha
authors.initials: J
authors.lastname: Maharudraiah
authors.affiliation: Imgenex India, Bhubaneswar 751024, Orissa, India; Imgenex Corporation, San Diego 92121, California, USA.
authors.forename: Sujay
authors.initials: S
authors.lastname: Singh
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India.
authors.forename: Ghantasala S
authors.initials: GS
authors.lastname: Sameer Kumar
authors.affiliation: Departments of Surgical Oncology, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka; India.
authors.forename: M
authors.initials: M
authors.lastname: Vijayakumar
authors.affiliation: Departments of Surgical Oncology, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka; India.
authors.forename: Kariyanakatte Veeraiah
authors.initials: KV
authors.lastname: Veerendra Kumar
authors.affiliation: Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka; India.
authors.forename: Chennagiri Shrinivasamurthy
authors.initials: CS
authors.lastname: Premalatha
authors.affiliation: Strand Life Sciences, Bangalore 560024, Karnataka, India.
authors.forename: Pramila
authors.initials: P
authors.lastname: Tata
authors.affiliation: Strand Life Sciences, Bangalore 560024, Karnataka, India.
authors.forename: Ramesh
authors.initials: R
authors.lastname: Hariharan
authors.affiliation: Department of Pathology, Universidad de La Frontera, Temuco, Chile.
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Roa
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India.
authors.forename: T S K
authors.initials: TS
authors.lastname: Prasad
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA.
authors.forename: Raghothama
authors.initials: R
authors.lastname: Chaerkady
authors.affiliation: Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka; India.
authors.forename: Rekha Vijay
authors.initials: RV
authors.lastname: Kumar
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA.
authors.forename: Akhilesh
authors.initials: A
authors.lastname: Pandey
keywords: DNA microarray; Gastric cancer; GeneSpring GX; Immunohistochemistry