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Assessment of tumor characteristic gene expression in cell lines using a tissue similarity index (TSI).


ABSTRACT: The gene expression profiles of 60 cell lines, derived from nine different tissues, were compared with their corresponding in vivo tumors and tissues. Cell lines expressed few tissue-specific (2%) or tumor-specific (5%) genes when analyzed group-wise. A tissue similarity index (TSI) was designed based upon singular value decomposition that measured in vivo tumor characteristic gene expression in each cell line independently. Only 34 of the 60 cell lines received the highest TSI toward its tumor of origin. In addition, we identified the most appropriate cell lines to be used as model systems for different in vivo tumors. Seven cell lines were identified as being of another origin than the originally presumed one. The proposed TSI will likely become an important tool for the selection of the most appropriate cell lines in pharmaceutical screening programs and experimental and biomedical research.

SUBMITTER: Sandberg R 

PROVIDER: S-EPMC548538 | biostudies-literature | 2005 Feb

REPOSITORIES: biostudies-literature

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Assessment of tumor characteristic gene expression in cell lines using a tissue similarity index (TSI).

Sandberg Rickard R   Ernberg Ingemar I  

Proceedings of the National Academy of Sciences of the United States of America 20050125 6


The gene expression profiles of 60 cell lines, derived from nine different tissues, were compared with their corresponding in vivo tumors and tissues. Cell lines expressed few tissue-specific (2%) or tumor-specific (5%) genes when analyzed group-wise. A tissue similarity index (TSI) was designed based upon singular value decomposition that measured in vivo tumor characteristic gene expression in each cell line independently. Only 34 of the 60 cell lines received the highest TSI toward its tumor  ...[more]

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