Tiling array

The combination of chromatin immunoprecipitation with DNA microarrays allows the genome-wide analysis of the distribution of an antigen. The immunoprecipitated DNA is quantitatively amplified, labeled and used to probe DNA microarrays. In principle ChIP-on-chip methods can be divided into two basic groups, depending on the content of the microarrays which are used (i) microarrays/promoter tiling arrays and (ii) genome tiling arrays. 

In microarrays the probes are designed with a focus on specific genomic elements such as promoters. These promoter tiling arrays have the advantage that costs are reduced, but they are biased since array design relies on known aimotation. Thus, relevant regions may not be covered [20]. 

Methyl-DNA immunoprecipitation (MeDip) can be used to identify methylated CpG islands in the genome. MeDip utilizes either antibodies against methylated CpG or the MBD (GpG methylation binding) proteins for immunoprecipitation of methylated DNA. Analysis of the DNA by tiling arrays or sequencing makes DNA methylation mapping across the genome possible [25]. 

Fig. 38 Transmission electron micrographs of gold nanoparticles organized in 2D arrays through binding of two types of three-branched DNA motifs, (a) Array where only one tile contains 5 nm particles. The resulting arrangement has two different characteristic length scales, (b) Array where both tiles contain 5-nm particles, yielding an equally spaced pattern, (c) Array where one tile contains a 5-nm particle and the other tile contains a 10-nm particle. The pattern of alternating smaller and bigger spheres mimics the rhombic pattern of the tile array. Adapted with permission from [164]...

Kapranov P, Drenkow J, Cheng J, et al. (2005). Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 15 987-997. 

Taskesen, E., R. Beekman, J. de Ridder, B. J. Wouters, J. K. Peeters, I. P. Touw, M. J. Reinders, and R. Delwel. 2010. HAT Hypergeometric analysis of tiling-arrays with application to promoter-GeneChip data. BMC Bioinformatics 11 275. 

Key words Alternative polyadenylation, Posttranscriptional processing, RADPRE, Tiling array... 

RADPRE was designed to use the transcriptome data from tilling arrays [5]. The underlining principle of how the tiling data might be employed to identify the differential APA events was illustrated in Fig. 1 and detailed previously [5]. The RADPRE pipeline constituted three major steps. In the first step, RADPRE took a set of tiling array data as input and calculated the ratios of normalized probe intensities between two conditions (Fig. 2a). 

By doing so, one of the major problems intrinsic to tiling array data—the variation of probe affinities—was significantly alleviated. In the second step, RADPRE took the probe ratios as inputs and performed a hierarchy of statistical tests to identify differentially processed genes (DPG) and differentially expressed genes (DEG) (Fig. 2b-d). In the final step, the false discovery rate (FDR) of the DEG and DPG was estimated by using the balanced random combinations of the replicates between two conditions. The output of RADPRE was a few tabular text files with one of them containing the DPG, one the DEG and the others as intermediate files. 

When analyzing your own tiling array data, make sure that your CEL files were downloaded to the CEL files folder within RADPRE package. 

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