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Series GSE15459 Query DataSets for GSE15459
Status Public on Oct 06, 2009
Title Gastric Cancer Project '08 (Singapore Patient Cohort)
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Genome-wide mRNA expression profiles of 200 primary gastric tumors from the Singapore patient cohort. Gastric cancer (GC) is the second leading cause of global cancer mortality, with individual gastric tumors displaying significant heterogeneity in their deregulation of various oncogenic pathways. We aim to identify major oncogenic pathways in GC that robustly impact patient survival and treatment response. We used an in silico strategy based on gene expression signatures and connectivity analytics to map patterns of oncogenic pathway activation in 25 unique GC cell lines, and in 301 primary gastric cancers from three independent patient cohorts. Of 11 oncogenic pathways previously implicated in GC, we identified three predominant pathways (proliferation/stem cell, NF-kB, and Wnt/b-catenin) deregulated in the majority (>70%) of gastric tumors. Using a variety of proliferative, Wnt, and NF-kB-related assays, we experimentally validated the pathway predictions in multiple GC cell lines showing similar pathway activation patterns in vitro. Patients stratified at the level of individual pathways did not exhibit consistent differences in clinical outcome. However, patients grouped by oncogenic pathway combinations demonstrated robust and significant survival differences (e.g., high proliferation/high NF-kB vs. low proliferation/low NF-kB), suggesting that tumor behavior in GC is likely influenced by the combined effects of multiple oncogenic pathways. Our results demonstrate that GCs can be successfully taxonomized by oncogenic pathway activity into biologically and clinically relevant subgroups.
Keywords: gastric cancer, primary tumor
 
Overall design Profiling of 200 primary gastric tumors on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. All tumors were collected with approvals from the National Cancer Centre, Singapore; the Research Ethics Review Committee; and signed patient informed consent.

FINAL PUBLICATION ANALYSIS INCLUDED 192 GASTRIC ADENOCARCINOMA SAMPLES [LIU ET AL. (2013) GASTROENTEROLOGY]

FAILED QUALITY CONTROL:
GC-011LGE-T, GC-021LAH-T, GC-035PCC-T, GC-038LYC-T

NOT GASTRIC ADENOCARCINOMA:
GC-026-GJK-T, GC-039-TSC-T, GC-2000619T, GC-980327T
 
Contributor(s) Ooi C, Tan P
Citation(s) 19798449, 21471434, 25008978, 25053715, 23684942
Submission date Mar 30, 2009
Last update date Jan 08, 2019
Contact name Chia-Huey Ooi
E-mail chia-huey.ooi@roche.com
Phone +41 61 688 96 95
Organization name F. Hoffmann-La Roche Ltd.
Department Bioinformatics and Exploratory Data Analysis
Street address Grenzacherstrasse 124
City Basel
ZIP/Postal code 4070
Country Switzerland
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (200)
GSM387788 GC-011LGE-T [EXCLUDED]
GSM387789 GC-017TPC-T
GSM387790 GC-021LAH-T [EXCLUDED]
This SubSeries is part of SuperSeries:
GSE15460 Oncogenic Pathway Combinations Predict Clinical Prognosis in Gastric Cancer
Relations
BioProject PRJNA122965

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE15459_RAW.tar 960.5 Mb (http)(custom) TAR (of CEL)
GSE15459_outcome.xls 155.5 Kb (ftp)(http) XLS
Raw data provided as supplementary file
Processed data included within Sample table

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