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Transcription profiling of human head and neck paired diseased squamous cell carcinoma samples vs normal

ABSTRACT: Forty-four paired (from the same patient) samples of head and neck squamous cell carcinoma (HNSCC) and normal tissue were studied with Affymetrix U95A chips. A stringent multi-test approach, combining 7 traditional and microarray-specific statistical tests, was used to analyze the resultant data. Candidate genes were assigned to tiers of significance based on the number of statistical tests that each gene satisfied. Representative genes (both up-regulated and down-regulated) from each of the 3 tiers would be quantified with RT-PCR on both microarray-tested and new samples of HNSCC. The goal of this study is to identify reliable differentially-expressed genes on HNSCC and to testify our hypothesis whether or not a combinatorial approach (multi-tests) to analyzing microarray data can really identify differentially-expressed genes with fewer false-positives. Experiment Overall Design: Paired HNSCC tumor and normal samples from 22 patients were evaluated for differential gene expression on Affymetrix U95A chips.

ORGANISM(S): Homo sapiens

SUBMITTER: Fang-An Chen 

PROVIDER: E-GEOD-6631 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Selection and validation of differentially expressed genes in head and neck cancer.

Kuriakose M A MA   Chen W T WT   He Z M ZM   Sikora A G AG   Zhang P P   Zhang Z Y ZY   Qiu W L WL   Hsu D F DF   McMunn-Coffran C C   Brown S M SM   Elango E M EM   Delacure M D MD   Chen F A FA  

Cellular and molecular life sciences : CMLS 20040601 11

We applied a robust combinatorial (multi-test) approach to microarray data to identify genes consistently up- or down-regulated in head and neck squamous cell carcinoma (HNSCC). RNA was extracted from 22 paired samples of HNSCC and normal tissue from the same donors and hybridized to the Affymetrix U95A chip. Forty-two differentially expressed probe sets (representing 38 genes and one expressed sequence tag) satisfied all statistical tests of significance and were selected for further validation  ...[more]

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