Intergrated analysis of array-miRNAs and matched Affymetrix gene

MicroRNAs are considered to be essential regulators during post-transcription in gene expression that mainly through repression mechanism to regulate target mRNAs. We generate expression data from profiling of 664 miRNA in 113 paired tumors and non-tumors of esophageal squamous carcinoma (ESCC), along with matched genome-wide mRNA gene expression data and extensive analysis association study with clinical viable. We identified an expanded list of miRNA dysregulated with Bonferroni correction at 0.05 and genes expression over 2 fold changes in esophageal squamous cell carcinoma. We also found of sixteen miRNAs significant associated with 195 genes. Further analysis show a group of miRNAs correlated with clinical variables including tumor metastasis, tumor stage, grade, and location, family history of UGI cancer, tobacco or alcohol use and pickled vegetable consumption. Survival correlation with either miRNAs or mRNAs was done. Finally, intersect genes correlated with survival and regulated by miRNAs are pulled out. This study provides a comprehensive dataset that can be used as groundwork for further studies of the involvement of miRNA and targeted mRNAs in ESCC and a group of genes may potential serve as biomarkers for prognosis. miRNA profiling from 113 paired tumor and non-tumor frozen tissues of esophageal squamous carcinoma was performed. TaqMan® Low Density Array was used for MicroRNA expression study that containing a two-card set of TaqMan® Array MicroRNA Cards (Cards A and B) for a total of 754 assays specific to unique 664 human miRNAs. It was using 9700HT fast real-time PCR system from ABI. Expression level (fold changes) was calculated when both tumor and normal sample giving signals in the assays using DataAssist software v2.0 (Life Technologies, http://www.lifetechnologies.com/about-life-technologies.html). In the present study, the data are presented as the fold change. mRNA profiling from 113 paired ESCC samples same as above was performed. Affymetrix Human Genome U133 Chip were used, and of the 113 paired ESCC samples, 34 pairs were using Human U133A chips, 73 pairs using U133A_2 chips, and 6 pairs using U133Plus_2 chips. All the Affymetrix array data (CEL files on all samples) were normalized by the RMA method using the software Affymetrix Expression Console, version 1.2.1.