Rank Rank Hypergeometric Overlap

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Looking for the simple version?

Looking for the batch version?


NEWS:
A <batch submit RRHO interface> is now available.
Please contact RRHO development if you are interested in an executable version of RRHO

Manuscript

The RRHO algorithm allows for the comparison of two gene expression signatures. Each signature is processed as a ranked list based on expression differences between two classes of samples. The signatures can be input either as raw expression data and sample and class labels, or as a preranked gene list.

Getting started

File formats

Species

This version of Rank Rank Hypergeometric Overlap (RRHO) currently recognizes only Mus musculus and Homo sapiens.

Rank rank options

The step size is used to bin the ranked items to improve the run time of calculating the hypergeometric distribution. An optimal step size is small enough to match the image resolution to the overlap patterns in the data, but large enough to reduce computational time. For gene expression data on the scale of 10,000-50,000 probes, we recommend a step size of 100-500.

Reverse rank lists will reverse the ranks of the items in one or both of the datasets.

In addition to the hypergeometric heat map, you may select two additional graphs:

Benjamini-Yekutieli multiple hypothesis correction can be applied.

The output can include a list(s) of the overlapping genes within the region(s) of maximal statistical overlap.

Example

The following parameters are used as an example analysis of Rank Rank Hypergeometric Overlap (RRHO). Feel free to download the sample files and try it yourself.

Show sample files and parameters [+]

Simple version

A simple version of Rank Rank Hypergeometric Overlap (RRHO) is available if you already have a list of ranked items that you want analyzed.

Parameters

Dataset 1
GCT
CLS
Class 1
vs.
Class 2
Annotation
Species
Description

Dataset 2
GCT
CLS
Class 1
vs.
Class 2
Annotation
Species
Description

Rank rank options
Step size
[recommended: 100 (see above)]
Reverse rank list 1
Reverse rank list 2

Rank scatter plot
Metric scatter plot
Perform Benjamini-Yekutieli p-value correction

Overlapping gene list - Statistics Summary

Depending on the speed of your connection and the size of your datasets, it may take a few minutes to complete the analysis.

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Related algorithms: Gene Set Enrichment Analysis (GSEA)