Accompanying this warehouse is a graphical visualization tool to enable the display of these data for a user-selected set of genes, and statistical analysis tools to facilitate the identification of significant trends or biases present in the histone modification patterns associated with a user-selected set of genes.

• Visualization: The first main tool we provide is visualization of histone modification patterns and other chromatin features of selected genes. Shown in these images are the average relative enrichment of each histone modification type (e.g. lysine acetylation) for the user selected subset of genes. Data is available for 22 different histone modifications (e.g. acetylation or methylation) or histone occupancy levels. These data can be visualized for promoter regions or open reading frames (ORFs).
  
  Two distinct types of data are available to visualize:
  
  
  • Standard ChIP-microarray data, which gives the relative enrichment of each histone modification at the selected promoter regions or ORFs.
  
  
  • Nucleosome-normalized ChIP-microarray data, which gives the enrichment of each histone modification after it has been normalized for the relative amount of nuclesomal histones present in the promoter or ORF region.


• Statistical Analysis: The statistical analysis tool allows the user to search for statistically significant patterns of enrichment in the histone modifications present in the genes that they have selected. This tool uses the non-parametric Wilcoxon Rank Sum Test to determine whether there is bias in each of the histone modification data sets for the genes that the user has selected. The advantage of this method is that it avoids arbitrary cutoffs commonly used to identify enriched gene patterns. The statistical tool is embedded as a part of the output for the visualization tool. The selection page allows the user to set the p-value cutoff used to determine whether a histone modification is significantly enriched. The user can also select whether or not to correct for multiple hypothesis testing using the Bonferroni correction.


• Data download: The data download tool provides the user with easy access to the histone modification ChIP-microarray data sets that are stored in ChromatinDB.