Castillo-Davis, C.I. and D.L. Hartl 2003. Bioinformatics 19(7):891-892
Supplementary Information
Over 22,000 web-based analyses, 2068 downloads, 25 publications and counting.
Thank you for your continued support of GeneMerge.
Updated GO Gene-Association Files
for all model organisms.
Gene-association files for Bos taurus (Cow) and Gallus gallus (Chicken) are now available!
The Gene Name Converter has been updated to reflect new gene naming conventions.
Updated GeneMerge Usage Statistics and Publications List.
What is GeneMerge?
GeneMerge is a versatile genomics program that can be used to
analyze a wide range of functional genomic data.
In particular GeneMerge is useful for the analysis of microarray data and
other large biological datasets.
What can GeneMerge tell me?
GeneMerge returns functional and categorical genomic data for a given set of genes
and provides statistical rank scores for over-representation of particular functions or
categories in the dataset.
Regulatory and metabolic pathway analysis, tests of population genetic hypotheses,
cross-experiment comparisons, and tests of chromosomal clustering, among others, are possible
with GeneMerge.
Given a set of genes, GeneMerge can tell you, for example, whether
these genes are statistically over-represented in a particular functional or biochemical class,
clustered in a region of the genome, or are associated with a particular RNAi or deletion phenotype.
Why Use GeneMerge?
The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing
your data from the perspective of a pre-packaged set of gene-association data. You can download or create
gene-association files to analyze your data from an unlimited number of perspectives.
See the
documentation
to see how easy is it to make your own gene-association data.
Additionally:
- GeneMerge runs on any platform and has a cool interface for Mac OS X.
- GeneMerge is free.
- You don't have to sign-up to get it.
- You can use it over the web.
- It's published in a peer-reviewed journal.
- It's widely used.
Availability
GeneMerge is available free of charge for use online over the web as well as a
stand-alone package under the
GNU GPL.
Documentation
Details on how GeneMerge works are provided 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 unpublished (long version with worked out examples).
Analysis of sample data sets and further information is available in the documentation.
What's New
Updated GO Gene-Association Files
(April, 2007) for all model organisms, including:
- Arabidopsis thaliana
- Bos taurus
- C. elegans
- D. melanogaster
- Danio rerio
- Gallus gallus
- H. sapiens
- M. musculus
- O. sativa
- P. falciparum
- R. norvegicus
- S. cerevisiae
Gene-association files for Bos taurus (Cow) and Gallus gallus (Chicken) are now available.
The Gene Name Converter has been updated to reflect new gene naming conventions (April 2007).
Updated GeneMerge Usage Statistics and publications that cite GeneMerge are now available (April 2007).
Other News
If you like GeneMerge and work with time-course microarray data, be sure to check out the
powerful and accurate data-driven clustering algorithm: Smoothing Spline Clustering.
Ma, Castillo-Davis et al. 2006. Nucleic Acids Res. 2006
GeneMerge - Post-genomic analysis, data mining, and hypothesis testing
Cristian I. Castillo-Davis
Department of Biology
University of Maryland
castill0@umd.edu