GeneNetVal: Gene Network Validity based on interaction relevance

This is a Java application for network analysis. The application uses the metabolic pathways stored in kegg to rate the validity of an input network.

The code is on http://fgomezvela.github.com/GeneNetVal/.

This application can be used in linux, mac, and windows. To use this tool, you must first download the GeneNetVal.zip file.

In ExampleData folder there are some gene networks for testing the tool.

Usage information

java -jar GeneNetVal.jar inputFile organismId level outPutFile [classical]

Usage: java -jar GeneNetVal.jar Nariai(2004).txt sce 3 results.txt

ARGUMENTS:

inputFile: -- Notice: The tool uses the relative path from the root -- Specification: geneA;geneB geneC;geneD ...

organismId: -- Denotes the organism prefix. See: http://www.kegg.jp/kegg/catalog/org_list.html -- Example: prefix: hsa organism: Homo sapiens (human) prefix: sce organism: Saccharomyces cerevisiae (budding yeast) ...

accuracyLevel: -- The threshold for the distance level of the methodology. -- This argument indicates the maximun level to calculate the Hits -- The distance level must be a value greater than 1.

outputFile: -- The path to the result file. -- Specification:

    PathwayId : Pathway identifier
    Pathway Description : Pathway functional description     
    Hits level i : Number of Hits with the accuracy level i 
    Cumulative Hits level n : The value of Cumulative Hits level n   
    Cumulative Failures level n : The value of Cumulative Hits level n      
    Network Validity level n: The value of the input network validity with the pathway (level n).

classical:(optional) -- If you want to use the "classical use of KEGG". -- With this option, the pathways will not be transformed into a gene network.
-- Example: java -jar GeneNetVal.jar Nariai(2004).txt sce 3 results.txt classical

Example Data

In the example data folder, there are stored four well-known yeast networks. Network specification:

-- Nariai et al. (2004).txt: This network represents the Saccharomyces cerevisae (SCE) cell cycle
                    and it is composed of 47 relationships between 43 yeast genes. 
                The network is a reconstruction of the cell cylce from time–series microarray 
                data refined using PPI data (Spellman et al., 1998).
-- Batada et al. (2006).txt: The network presented by Batada et al. (2006) where a PPI network is presented
                 in the study of the highly connected proteins in a network (hubs).
-- Cherry et al.(2011)(SGD).txt: This network that provides an access to the complete Saccharomyces cerevisiae genomic sequence. 
                In this study, only the PPI + PDI (protein–DNA interaction) data available were taken. 
-- Lee et al. (2007)(YeastNet v.2).txt: Lee et al. (2007)(YeastNet v.2) which combines PPI, PDI, coexpression, phy- logenetic 
                    conservation and literature information.