Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 35
Release date: Sep 1 2007
Last update date: Jan 18 2013
Access: Public
Diseases: Breast Neoplasms, Carcinoma, Neoplasms, Neoplasms, Glandular and Epithelial
Dataset link Integrated SV40 T/t-antigen Cancer Signature in Aggressive Breast, Prostate and Lung Carcinomas with Poor Prognosis 1

Experimental Protocol


Gene expression profiles from the SV40 T/t-antigen mouse models were compared with respect to specimen type (normal vs. tumor tissue), location of tumor (mammary, lung, prostate, seminal vesicle), and background strain of mice (FVB vs. C57BL/6). A three-way ANOVA model with one interaction effect (type X location) was fitted. Cancer genes that differ among all four tumor locations were identified, as those that had a significant interaction effect at the 0.001 level and showed at least a 2-fold change between the maximal and minimal mean tumor/normal ratio over the different locations (2638 cDNA probes). Based on the ANOVA model, differentially expressed genes between normal and tumor specimens within each tumor location were also identified, as those genes whose expression were significant at the 0.001 level and were at least 2-fold different compared to the mean expression ratio. Overall 3004 unique array features were selected using ANOVA. Further selection was applied based upon identification of differentially expressed genes between normal and tumor tissue for the three epithelial tumors (mammary, lung and prostate). The SV40 T/t-antigen oncogene-specific signature included genes similarly differentially expressed in each epithelial tumor (153 cDNA clones). In contrast, genes were included in a tissue-specific SV40 T/t-antigen tumor signature if they were found to be differentially expressed between the tumor and normal samples exclusively for one location. Two-hundred and eighty three, 220 and 999 cDNA clones were identified as specifically dysregulated in mammary, lung and prostate tumors, respectively).

Repositories


GEO

GSE8662

ArrayExpress

E-GEOD-8662

BioProject

PRJNA101865

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Contact


Jeffrey Green
Jeffrey E Green