PinkThing is a service on the web to compare peak positions from ChIP-on-chip with the positions of genes. This is an important first analysis of ChIP-on-chip results for two reasons :Firstly, if the peak positions are significantly different from a random distribution they are likely to indicate functional elements. Secondly, by inspecting the positions relative to genes it may be possible to infer their function.
The peaks are uniquely classified as upstream, intronic, exonic, downstream or distant regions. Due to the unique classification a statistical comparison with the chipdesign or other experiments is possible. Overrepresented GO terms can be found with a built-in version of the Ontoligizer. This can be done without any knowledge about programming and statistics. Also other epigenetic features like methylation and histone modifications can be compared with genes, EST's, miRNA's and CpG islands. Everything is easily accessible here here.