HOMECAT

HOMECAT (HOmology Mapper for Enrichment and Comparative Analysis with Translation) is a Cytoscape plugin allowing cross-species data comparison with a particular emphasis on functional genomic data (i.e. microarrays and other high throughput biological data sources). The aim at the basis of this software is to ease knowledge transfer from different species. Networks can be enriched with orthologs from other species, in the desired format.
Orthology assessment is a complex task, user can combine different sources of homology prediction, with different specificity and sensitivity, to allow achieving the desired level of precision and coverage.
The data integration is eased by the possibility of choosing between nearly 30 identifiers formats (Uniprot, RefSeq, Ensembl, etc.) and 71 microarrays platforms identifiers (including Affymetrix, Illumina and Agilent) designed for the 30 organisms supported by the current version. Homology data can be used to enrich existing networks or to create new data visualization that improve external data loading and mapping. A specific interface allows the download of curated data directly from Array Express ATLAS database, and several functionalities ease the comparison of data from different networks. Once data is integrated in the user networks any Cytoscape functionality can be used to analyze, visualize and process the data.

If you are using HOMECAT, please cite the following publication:

  • HOMECAT: consensus homologs mapping for interspecific knowledge transfer and functional genomic data integration.
    Zorzan S., Lorenzetto E., Ettorre M., Pontelli V., Laudanna C., Buffelli M.
    Bioinformatics 2013; doi: 10.1093/bioinformatics/btt189
    Abstract

Documentation
Here you can download HOMECAT manual, detailing the software usage.

Plugin & Components
Here you can download HOMECAT Plugin, along with components, needed to support the different orthology projects supported. You will need Cytoscape 2.8.x. and plugins MetaNodePlugin2 (v.1.6 or greater), and nodeCharts (v. 0.94 or greater), that can be download directly from the plugins->Manage Plugins menu in Cytoscape. Cytoscape 3.0 app development is on-going and will be availabe as soon as the aforementioned necessary plugins will be ported to the new version.
The content of this archive (Homecat.jar and the folder "HcComponents") should be placed into the Cytoscape "plugins" folder. It is also advisable, but not mandatory, to increase Java memory in Cytoscape with virtual machine options -Xmx1G -Xss10M (see Cytoscape website for details). Current version: 1.2


In case you downloaded HOMECAT from within Cytoscape, here is the link to download the components package. Components are needed to support the different orthology projects HOMECAT uses for searches. The content of this archive (the folder "HcComponents") should be placed into the Cytoscape "plugins" folder along wiht the file Homecat.jar you installed from Cytoscape.

Components Development
HOMECAT is designed to search several homology data sources, through files called "components", in order to achieve the desired specificity or sensitivity. Each orthology data source is supported through a software Java class, loaded dynamically at plugin startup. With the link below you can download the source code of all the components available so far, and the documentation to develop new ones (The two necessary classes, Java doc, and a template file).

Creative Commons License
HOMECAT by Simone Zorzan is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.