Software Resource for Discovery of Cell Cycle Genes

Download from Github or download Hegemon.jar

    git clone https://github.com/sahoo00/Hegemon 
    javac Hegemon/tools/*.java

    export HEGEMON_PATH=≤path to Hegemon directory>
    

Download from Human, Mouse and Plant data from GEO

• GSE119083 - Plant Boolean Implication Network
• GSE119084 - Fly Boolean Implication Network
• GSE119085 - Mouse Boolean Implication Network
• GSE119087 - Human Boolean Implication Network
• GSE119128 - An unbiased Boolean analysis of public gene expression data for core cell cycle gene classification

Download perl script: analyze.pl

Run following commands in your terminal

export JAVA_HOME="path to jre or jdk"
export PATH=$JAVA_HOME/bin:$PATH

java -cp "path to Hegemon.jar or Hegemon dir" tools.BooleanNet closure \
    GPL570/human-gpl570 \
    214710_s_at 3.0 0.1 5 1 > res-global-ccnb1-hs.txt
perl analyze.pl idlist \
    GPL570/human-gpl570-expr.txt \
    res-global-ccnb1-hs.txt > res-global-hs-expr.txt
java -cp "path to Hegemon.jar or Hegemon dir" tools.RankCorrelation rank \
    res-global-hs-expr.txt \
    res-global-ccnb1-hs.txt 214710_s_at > res-rank-hs-score.txt
perl analyze.pl select res-rank-hs-score.txt > res-hs-select.txt
java -cp "path to Hegemon.jar or Hegemon dir" tools.Hegemon corr \
    GPL570/human-gpl570 \
    214710_s_at > res-hs-ccnb1-corr.txt
java -cp "path to Hegemon.jar or Hegemon dir" tools.Hegemon corr3 \
    GPL570/human-gpl570 \
    214710_s_at > res-hs-ccnb1-corr3.txt
    

The ranked list of genes will be present in res-hs-select.txt