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ALT conceived of the experiment, conducted GC and microarray studies, analyzed the data, and wrote the paper.
JBS carried out the microarray studies, analyzed the data and drafted the manuscript; YS contributed to the data analysis and the preparation of the manuscript; EB contributed to the experimental design, data analysis and the final preparation of the manuscript.
JRA (Jagannadha R Avasarala) designed, conceptualized the study format and wrote the manuscript; SVC (Sridar V Chittur) did the microarray studies, analyzed the data and authored the materials and methods section; JAT (John A Tine) did quantitative RT-PCR while ADG (Ajish D George) performed the transcription factor network analysis.
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For microarray studies analyzing the differentially expressed hepatic genes between A/J and C57BL/6J mice, analysis was performed using a minimum of three samples of hepatic mRNA, with each sample pooled from two mice (San Diego, CA).
Previous microarray studies have analyzed gene expression patterns [12], [18], [19] yielding evidence of substantial differences among sarcoma subtypes.
Gene expression from 15 of the 90 axon growth promoting proteins identified in the microarray studies were analyzed using qPCR methods.
Seven cancer microarray studies are analyzed.
Through microarray studies, we analyzed the gene expression profile of renal tubular epithelial cells, stimulated with interferon-alpha.
To determine the OCIAD2 expression, different available microarray studies were analyzed by the Oncomine database and GEO gene microarray data analysis tools.
In order to validate the results from microarray analysis, transcripts of 13 selected genes, which were significantly expressed in the microarray studies, were analyzed by Real-Time-qPCR (see Additional file 4).
A set of 199 adjuvant-naïve, node-negative (N0), estrogen receptor-negative breast cancers annotated for distant metastasis-free survival (DMFS) was identified as HRneg training cases from three published microarray studies similarly analyzed on the Affymetrix (Santa Clara, CA, USA) U133A platform ([GEO GSE2034] [ 17], [GEO GSE5327] [ 28], and [GEO GSE7390] [ 29]).
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