Expression of mRNAs and lncRNAs in cancer revealed by microarray

Long noncoding RNAs (lncRNAs), which are noncoding RNAs (ncRNAs) with length more than 200 nucleotides (nt), have been demonstrated to be involved in various types of cancer. In this study, a custom designed microarray platform covering both mRNAs and lncRNAs was applied to tumor tissues of gastric, colon, liver and lung. 316 and 157 differential expressed (DE-) protein coding genes and lncRNAs common to these four types of cancer were identified respectively. The expression profiles of cancer and adjacent normal tissues form 76 patients (20 with gastric cancer, 20 with colon cancer, 16 with liver cancer and 20 with lung cancer) were studied by microarray and a set of lncRNAs as well as PCGs were identified as potential biomarkers general to different types of cancer. Please note that experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but the results were processed though they are single channel (total 152 sample records for 76 raw data files; Cy3 and Cy5 signals are calculated). Therefore, raw data file for each sample was duplicated and linked to each paired sample records. For example, the raw data files for the 'Normal_tissue_Colon_cancer_patient_01'(Cy5) sample and 'Cancer_tissue_Colon_cancer_patient_01'(Cy3) sample are identical.