PMC:4996403 / 5421-10330 JSONTXT

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Microarray Types\n\n3.1. Expression Array\nThe major application of DNA microarrays has been for the measurement of gene expression levels. RNA is extracted from cells, directly fluorescently labeled, and converted to labeled cDNA. The labeled cDNA is hybridized to the microarray, the array is washed, and the signal is detected by measuring fluorescence at each spot. The intensity of the signal on each spot is taken as a measure of the expression level of the corresponding gene [9,15].\nMultiple studies have successfully used these techniques to evaluate gene expression levels in human diseases, including cancers. Shim et al. [16] performed an expression profile of genes associated with human cervical cancer using cDNA expression arrays. Rhee et al. [17] showed molecular evidence of the qualitative and quantitative high heterogeneity in gene expression among three human glioblastoma cell lines using cDNA expression arrays.\n\n3.2. Methylation Array\nCancers often exhibit aberrant methylation status of gene promoter regions associated with loss of gene function [18,19]. This epigenetic process acts as an alternative strategy to mutations to disrupt tumor suppressor gene function. CpG island hypermethylation has been shown to be a common event in cancers [20,21]. To detect hypermethylation status, the demethylating agent 5-Aza-2′-deoxycytidine is used [22] and gene expression changes are subsequently measured by microarrays [23]. Methylation arrays can also aid in the identification of three tumor suppressor genes including CRIP-1, Apolipoprotein D, and Neuromedin U by comparing the methylation of CpG islands of promoter regions in cancer tissue and corresponding normal tissue [24]. Notably, the demethylation status of particular genes is also related to carcinogenesis. Genes upregulated by demethylation can play a clinically significant role in cancer tissues [25].\n\n3.3. Comparative Genomic Hybridization (CGH) Array\nThe CGH method measures genomic changes such as deletions of chromosome copy number and amplification [26]. The CGH array was developed as a method to detect genome abnormalities such as the minute gene amplification, deletion, and DNA copy number alterations [27,28,29,30,31,32,33].\n\n3.4. Single Nucleotide Polymorphism (SNP) Array\nA SNP, a variation at a single site in DNA, is the most frequent type of variation in the genome [34,35], with an estimated 10 million SNPs in the human genome [36]. SNPs have been associated with disease and drug metabolism. The SNP array is a type of DNA microarray used to detect polymorphisms within a population [37,38,39,40] and this array can detect SNPs associated with diseases [41,42], genotyping [40,43,44,45], copy number variation [46], and loss of heterozygosity (LOH) [38,39].\n\n3.5. MicroRNA(miRNA) Array\nIn 1993, Lee et al. [47] discovered that lin-4, a gene known to control the timing of Caenorhabditis elegans larval development, does not code for a protein but instead produces a pair of small RNAs approximately 22 and 61 nt in length. The shorter lin-4RNA is now recognized as the founding member of an abundant class of short regulatory RNAs called microRNAs or miRNAs [48,49,50]. The importance and the role of miRNA-directed gene regulation are coming into focus as their regulatory targets and functions [51]. Liu et al. [52] described the using of the first miRNA microarray. After that, the miRNA microarrays revealed their functions in control of cell proliferation, cell death associated with carcinogenesis [53,54], fat metabolism in flies [55,56], and modulation of hematopoietic lineage differentiation in mammals [57]. For example, miR-21 was detected by miRNA array in various cancers [58], and high miR-21 expression is associated with the poor survival and poor therapeutic outcome in colon cancer [59].\n\n3.6. Long-Noncoding RNA (LncRNA) Array\nMore recently, lncRNAs, generally defined as short RNAs greater than 200 nt in length, have risen to prominence with important roles in a broad range of biological processes [60]. LncRNAs regulate gene expression at the level of post-transcriptional processing such as protein synthesis, RNA maturation, transport, cell differentiation, immune responses, and activity and localization of protein coding genes [61,62]. They also exert their effects in transcriptional gene silencing through the regulation of chromatin structure [60,63]. Dysregulation of lncRNAs is associated with many human diseases, including various types of cancers [64]. Many studies have used lncRNA microarrays to demonstrate lncRNA gene expression profiles and the prognostic potential of lncRNA profiles in various cancers [65,66].\n\n3.7. Platform Description\nThe presently available and most used platforms show Table 3. These platforms are used widely in many laboratories.\nmicroarrays-04-00454-t003_Table 3 Table 3 List of the main platforms ion the each microarrays.\n\n4."}