NTAP is originally developed for the analysis of NimbleGen tiling array data. Tiling array is widely adopted to do genome wide profiling studies such as novel transcription region identification, transcription binding sites determination and DNA methylation or histone modifications detection. Many of the applications of tiling array have specific request for downstream analysis after identified the significantly enriched/depleted oligos. For example, people are interested with following questions:
1. Is there difference on the chromosome scale histone modification level between different organs or different treatments;
2. Where the DNA methylation occurs in terms of gene structure? The promoter region or the coding region? Is there difference between protein coding genes and transposons?
3. For transcription factors binding, are the genes activated by the transcription factor have more binding in their promoter region then those repressed genes?
NTAP can answer the questions as well as generate good quality figures for publish purose. Further more, it enables the users to conveniently process the tiling array data and generate various statistical reporting results including the correlation coefficient between replicates. All functions are modulized so that you can use whatever you are interested to use in NTAP and do the rest by other your favorite tools.
Example Figure: The modification levels throughout the gene coding region of three group genes whose expression levels are in High, Medium and Low levels.
User may choose any interested gene groups to compare, just prepare the gene lists and put them into the NTAP geneslist/ sub-directory. NTAP will determine the relative position of a specific oligo to its nearby gene models, align the genes and then generate the plot for the user to compare either "Averaged Ratio" or "Significantly Oligos Percentage" between lists.