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Castillo-Davis, C.I. and D.L. Hartl 2003. Bioinformatics 19(7):891-892 | Supp. Material.

What is GeneMerge?

GeneMerge tests for statistical over-representation of gene attributes in a given set of genes compared to the genome background.

It answers the question, Is there functional or categorical 'enrichment' of some kind among this set of genes?

It is useful for the analysis of gene expression data like RNA-seq and other genome-scale data, for example, those generated by evolutionary and population genomic studies.

What can it tell me?

GeneMerge returns functional/categorical information for a given set of genes and provides statistical rank scores for over-representation of particular functions or categories in the dataset.

Given a set of genes, GeneMerge can tell you, for example, whether these genes are statistically over-represented for a particular biological functional, clustered on a particular chromosome, are associated with a particular RNAi phenotype, or any categorical gene attribute for which you have data.

GeneMerge uses the statistically exact hypergeometric probability distribution to calculate over-representation of gene attributes and provides both Bonferroni and False Discovery Rate (FDR) correction for multiple tests.

Why Use GeneMerge?

The big advantage of GeneMerge over other similar programs is that it is very easy to use (even by non-specialists) and it is very flexible with respect to the data it can analyze.

A simple input file format means GM can be used with non-model species and custom gene-association data. You can create your own gene-association files to test for enrichment of discrete gene attributes of any kind.

GM's straightforward design also makes it ideal for use in bioinformatics pipelines or for integration into larger software projects.



GeneMerge is available as a stand-alone package under the GNU GPL and as a web application.


The rationale and statistical methods behind GeneMerge can be found in Castillo-Davis, C.I. and D.L. Hartl 2003. Bioinformatics 19(7):891-892 and Castillo-Davis, C.I. and D.L. Hartl 2003. unpublished (long version with worked out examples).

Details on installing and running GeneMerge can be found in the documentation.

What's New in Version 1.4?

GeneMerge v1.4 has:

Download GeneMerge v1.4

Download | Online | Documentation | Usage | Gene-Association Files