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Gerstein Lab

About the Aggregate Tool

This website presents a tool designed to analyze genomic data in the form of signal maps. One component of the tool aims to provide an easy way to calculate the average signal of probes on a device such as a microarray versus their position relative to a set of annotation coordinates. These coordinates can correspond to any start and end pairs, such as annotations. The hope is that by taking the aggregate signal across many locations that noise will cancel out, and it can be determined whether or not there really is a correlation between, say, binding signal of a transcription factor and its location on a gene. Further information on this component can be found here.

A second component of the tool takes Zhengdong's correlation tool used in Genome Res 17: 787-97 and expands it. It takes a set of bed files as input, each bed file representing significant hit regions for a factor, or any element within a group for which you want to perform correlation. The bed files are simple text files with the columns, in this order, chromosome name, start, stop, and value. It takes some time to run, depending on how many factors are involved and the number of bootstrap cycles requested, and then it produces in the end graphical and text representations of the correlation among the factors. It calls Zhengdong's program to do the matrix generation, and then it takes the results and feeds it to phylip and R's heatmap function.

The source code for the tool can be found here.