Oral Squamous Cell Carcinoma Microarray Analysis

The data were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) and were selected based on the following criteria to ensure the reliability of the data analyses: (1) availability of raw microarray data; (2) inclusion of both oral squamous cell carcinoma and normal control (either adjacent normal or oral mucosa from healthy individuals); and (3) more than 10 tumor samples. Consequently, there were 6 datasets [11 (link),12 (link),13 (link),14 (link),15 ,16 (link)] using Affymetrix microarray that met our requirements (S1 Table). A total of 481 samples (326 OSCC and 165 normal controls) were included in this analysis. To ensure abundant availability of information for subsequent analyses, GSE9844/GSE30784/GSE31056 were labeled as “group I” (which was from Affymetrix Human Genome U133A Plus 2.0 array) and the remaining datasets were labeled as “group II” (which consisted of the former version of Affymetrix such as Human Genome U133A, Human Genome U95Av2 and Human Genome U133A2.0) according to their microarray platform.

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He Y., Shao F., Pi W., Shi C., Chen Y., Gong D., Wang B., Cao Z, & Tang K. (2016). Largescale Transcriptomics Analysis Suggests Over-Expression of BGH3, MMP9 and PDIA3 in Oral Squamous Cell Carcinoma. PLoS ONE, 11(1), e0146530.

Publication 2016

Human Genome U133A Plus 2.0 array Human Genome U133A Human Genome U95Av2 Human Genome U133A2.0

Carcinoma Human genome Inclusion cell Microarray Oral mucosa Tumor

Corresponding Organization : Tongji University

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Variable analysis

independent variables

Oral squamous cell carcinoma (OSCC) samples
Normal control samples (either adjacent normal or oral mucosa from healthy individuals)

dependent variables

Gene expression from microarray data

control variables

Availability of raw microarray data
Inclusion of both OSCC and normal control samples
More than 10 tumor samples
Microarray platform (Affymetrix Human Genome U133A Plus 2.0 array for Group I, and former versions of Affymetrix array for Group II)

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

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