During the period 2000-2004, we constructed a comprehensive collection of gene expression and clinical data from a large number of patients with the major cancers. It is followed by a number of informatics studies for knowledge extraction. The expression data have been obtained by adaptor-tagged competitive PCR (ATAC-PCR), a high-throughput RT-PCR technique. RT-PCR has a wider dynamic range of detection, compared to hybridization-based techniques. In addition, tumor specimens are obtained from a limited number of hospitals, and uniform clinical backgrounds are expected. The main focus of the following researches was exploration of correlation between gene expression and clinical data for future diagnostic application.
The main part of the project was carried out
in Taisho Laboratory of Functional Genomics, Nara Institute of
Science and Technology. The tumor samples were mainly supplied
from Osaka University Medical School. Glioblastoma and lung cancer
is from Kyoto University Medical School and from Osaka Medical
Center for Cancer and Cardiovascular Diseases, respectively.
For gene expression profiling, we at first surveyed expressed
genes in each cancer tissue by EST sequencing. Genes for the ATAC-PCR
assay were selected by the order of the abundance. Genes selected
by specialists were also added for the assay. The number of genes
for the ATAC-PCR assay was ranged from 1536 to 3072. Gene expression
data were obtained as relative expression levels against control
samples. We usually used mixtures of tumor tissues from several
patients to detect the slight differences among tumor tissues
from different patients.
Currently, acquisition of data for breast, colorectal, hepatocellular,
esophageal, thyroid,gastric and lung cancers, and glioblastoma
has been finished.
Factual details of each cancer project
Breast cancer (molecular classification)
Specimen: 301 samples (Nov 1996 to Sep 2000, Osaka University
Medical School Hospital). 98 samples were used for gene expression
profiling. Others were for validation.
Number of assayed genes: 2412 genes
Reference: 3
Breast cancer (docetaxel resistance)
Specimen: 70 samples (Feb 1999 to June 2002, Osaka University
Medical School Hospital) subjected for neoadjuvant therapy by
docetaxel. All samples were obtained by biopsy before the therapy.
44 samples for the learning set are included in CGED.
Number of assayed genes: 2453 genes
Reference: 11
Colorectal cancer
Specimen: 100 samples (April 1994 to September 2000, Osaka University
Medical School Hospital).
Number of assayed genes: 1536 genes
Reference: 4
Hepatocellular cancer
Specimen: tumor 120, non-tumor 86, normal 32 (January 1997 to
April 2003, Osaka University Medical School Hospital)
Number of assayed genes: 3072 genes
References: 5, 7, 8, 9, 10
Gastric cancer
Specimen: 123 samples (Feburary 1994 to April 2003, Osaka University
Medical School Hospital).
Number of assayed genes: 2304 genes
Reference: 4, 18
Thyroid cancer
Specinen: papillary
carcinoma 42, follicular carcinoma 28, follicular adenoma 58,
normal thyroid tissue 40 (Feb 1997 to Nov 2002, Osaka University
Medical School Hospital, Kuma Hospital)
Number
of assayed genes: 2516 genes
Reference: 15
Esophageal cancer (squamaous cell carcinoma)
Specimen: cancer tissues 160 (April 1997 to Feb 1999,
Osaka Medical Center for Cancer and Cardiovascular Diseases)
Number of assayed genes: 1904 genes
Glioma
Specimen: 152 gliomas
(100 glioblastomas, 21 anaplastic astrocytomas, 19 diffuse astrocytomas,
and 12 anaplastic oligodendrogliomas) (Department of Neurosurgery,
Kyoto University Graduate School of Medicine)
Number
of assayed genes: 3456 genes
Reference: 12
CGED (http://lifesciencedb.jp/cged/) is an integrated database of gene expression data and clinical information. The current update (March, 2007) includes data of the CGIP first phase for breast, breast (docetaxel response), colorectal, hepatocellular, esophageal, gastric and thyroid cancers.
The data are logarithmically converted relative expression levels against controls, normalized by median of samples and then by genes. Upper and lower cut-off values are set at 20 and 0.05 folds of the control, respectively. This normalization procedure is chosen for better presentation in mosaic plots. Although the procedure is popular, we have been used data nomalized only by median of samples for statistical studies. Such data sets are found in http://genome.mc.pref.osaka.jp/data_download.html. Due to space limitation, all of the data are not deposited for hepatocellular and thyroid cancers. In esophageal cancer, samples without clinical data are not depoisted.
Breast cancer (molecular classfication)
[Zip]
Breast cancer (docetaxel response)
[Zip]
Colorectal cancer [Zip]
Hepatocellular cancer
[Zip]
Esophageal cancer [Zip]
Gastric
cancer [Zip]
Thyroid cancer
[Zip]
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