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Series GSE9074 Query DataSets for GSE9074
Status Public on Apr 01, 2022
Title High grade neuroendocrine lung cancer expression profile
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Genomic gains and losses, particularly amplification of oncogenes and deletion of tumor suppressor genes, are critical molecular events involved in tumorigenesis and cancer progression. These genomic structural abnormalities trigger pathway alterations which activate/inactivate transcription factors along protein network, and then affect gene transcription profiles. Therefore, trace-back analysis of the pathway alteration by integrating genomic copy number, transcription profile, and known protein network data is expected to provide key information to interpret tumorigenesis and cancer progression processes. However, there are a number of pathway alteration candidates, so that it is difficult to understand overall picture. Primitive approaches such as filtering by arbitrary selection of thresholds involve a risk of overlooking important pathway alterations and their triggers. We proposed a visualization method for the trace-back analysis of pathway alterations, called a Cluster Overlap Distribution Map (CODM). We applied the CODM to trace-back analysis of pathway alterations related to subtype classifications of high grade neuroendocrine carcinoma samples; 1) small cell lung carcinoma (SCLC) vs. large cell neuroendocrine carcinoma (LCNEC), and 2) group1 vs. group2 (this is the classification based on transcription profiles and group2 has a higher survival rate than group1). By effective use of 3D and color spaces, the CODM allowed us to understand the overall picture of pathway alteration without arbitrary selection of thresholds and to extract 6 pathway alterations related to only group1 vs. groups2, 2 pathway alterations related to only SCLC vs. LCNEC, and 2 pathway alterations related to both group1 vs. group2 and SCLC vs. LCNEC.
Keywords: lung cancer profile
 
Overall design High-grade neuroendocrine tumors of the lung were obtained from 29 patients undergoing pneumoresection at the Cancer Institute Hospital of Japanese Foundation of Cancer Research. All subjects gave their informed consent to participation in the study. Among the 29 patients, 20 were small cell lung carcinoma (SCLC) and 9 were large cell neuroendocrine carcinoma (LCNEC). About three-fourths of samples are common to the previous report (Jones MH, 2004). In the previous report, the samples were classified into group1 and group2 based on transcription profiles and statistical analysis indicated that group2 has a higher survival rate than group1. We also classified 29 samples into group1 and group2 based on transcription profiles and confirmed that group2 has a higher survival rate than group1.
Web link http://www.genome.rcast.u-tokyo.ac.jp/CODM_PathwayAlteration/
 
Contributor(s) Kano M, Ishikawa S, Yamamoto S, Tanaka Y, Ishikawa Y, Aburatani H
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Sep 18, 2007
Last update date Apr 01, 2022
Contact name Shogo Yamamoto
E-mail(s) yamamoto@genome.rcast.u-tokyo.ac.jp
Organization name The University of Tokyo
Department Research Center for Advanced Science and Technology
Lab Genomescience
Street address 4-6-1 Komaba, Megro-ku
City Tokyo
ZIP/Postal code 1538904
Country Japan
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (29)
GSM230093 LungCa_205
GSM230094 LungCa_207
GSM230095 LungCa_209
Relations
BioProject PRJNA102589

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
GSE9074_RAW.tar 224.8 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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