E-GEOD-6631 - Transcription profiling of human head and neck paired diseased squamous cell carcinoma samples vs normal

Status
Submitted on 3 January 2007, released on 6 February 2009, last updated on 2 May 2014
Organism
Homo sapiens
Samples (44)
Array (1)
Protocols (4)
Description
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.
Experiment types
transcription profiling by array, individual comparison,disease state
Contact
Citation
Selection and validation of differentially expressed genes in head and neck cancer. Kuriakose MA, Chen WT, He ZM, Sikora AG, Zhang P, Zhang ZY, Qiu WL, Hsu DF, McMunn-Coffran C, Brown SM, Elango EM, Delacure MD, Chen FA. Cell Mol Life Sci 61(11):1372-83 (2004)
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-6631.idf.txt
Sample and data relationshipE-GEOD-6631.sdrf.txt
Raw data (1)E-GEOD-6631.raw.1.zip
Processed data (1)E-GEOD-6631.processed.1.zip
Array designA-AFFY-1.adf.txt
R ExpressionSetE-GEOD-6631.eSet.r
Links