Aug 20 2012 Author: Prashanti Manda Email: manda.prashanti@gmail.com Input File Format : One transaction per line. Each Transaction starts with a gene name followed by a list of one or more GO annotations separated by commas. Example Transaction : Run Generalization-Host.pl IMPORTANT NOTE : Before running the following script, you will need to download the GO obo file from geneontology.org and set up a database with different tables. The recommended table design is as follows although you can choose an alternative design. Table 1 :GO ID, Parent GO Term, Relation Table 2 : GO ID, Aspect Table 3: GO ID, Longest Depth You will also need to download the apriori script and place it in the same directory as Generalization-Host.pl. The apriori script belongs to Christian Borgelt can be downloaded from http://www.borgelt.net/apriori.html Usage : perl Generalization-Host.pl Transactionfile.txt bp_cctermination cc_mftermination mf_bptermination support confidence p-value This script will produce Transaction files from different levels. You can ignore the transaction files unless you want to see the generalized transactions at each level. The file called Interestingrules.txt contains the interesting rules mined at each level. This file will contain duplicate rules since the same rules might be mined from different levels. Run the file removeduplicaterules.pl to remove the duplicate rules Usage: perl removeduplicaterules.pl Interestingrules.txt The script will produce a file called Interestingrules_duplicatesremoved.txt. This is the file with the final list of interesting rules.