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Gene expression patterns within cell lines are predictive of chemosensitivity


ABSTRACT: We generated RNA's and measured expression of 40000 genes using spotted cDNA microarrays from the fifty nine publicly available cell lines of the NCI Developmental Therapeutics Program's NCI60 studies and an additional set of seven cell lines for which GI50 compound sensitivity data were available. All cell lines were grown to 80% confluence in RPMI 1640 supplemented with phenol red, glutamine (2 mM) and 5% fetal calf serum. This expression data, in conjunction with the compound sensitivity data sets available from the DTP, were used to empirically determine whether gene-compound correlates of a sufficiently high correlation coefficient would have a suitable low false discovery rate to support the use of a correlative approach and these datasets for early discovery approaches for new targeted therapies. A cell type comparison design experiment design type compares cells of different type for example different cell lines. Sixty six cell lines were analysed, with no repetitions. Twelve cell lines were pooled for a common reference.

ORGANISM(S): Homo sapiens

SUBMITTER: Brian Ring 

PROVIDER: E-GEOD-7947 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression patterns within cell lines are predictive of chemosensitivity.

Ring Brian Z BZ   Chang Stella S   Ring L Winston LW   Seitz Robert S RS   Ross Douglas T DT  

BMC genomics 20080208


<h4>Background</h4>The NCI has undertaken a twenty-year project to characterize compound sensitivity patterns in a selected set of sixty tumor derived cell lines. Previous studies have explored the relationship between compound sensitivity patterns to gene expression, protein expression, and DNA copy number for these same cell lines. A strong correlation between the pattern of expression of a biomarker and sensitivity to a compound could suggest a clinically interesting biological relationship b  ...[more]

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