#!batch commands
#clear the current network
clear_network
#set species to human
species=hsa

#read cell cycle pathway from KEGG (use the proxy server for VisANT so that applet can load the KGML from KEGG
read=http://visant.bu.edu:8080/vserver/DAI?command=time_proxy&target=http://www.genome.jp/kegg/KGML/KGML_v0.6.1/hsa/hsa04110.xml

#need to login so that we can resolve the name of the genes, here we use demo user which has certain restrictions
#Users are advised to use their own login. Note, must resolve node name first, otherwise
#names used in the expression data may not match the gene in the network
login=demo_user

#do not need to solve the name of all genes, as it will be done automatically for GO annotation 
#if no parameters are provided, following command annotated functions for all genes with most specific GO terms available
go_annotation

#clear the node selection to make sure that the GOTEA will be processed as designed
clear_selection

#because GOTEA takes time to finish, let's start with the hypergeometric test, which is fast
#in some cases, one of the problem for the current GO informative term analysis is that it returns
#too much significant terms. However, what we expected usually is the shared functions of the genes
#in the given modues. For this reason, we provides the option to post-process the results
#using informative GO terms, for this specific cell cycle pathway, we set the cutoff for the informative GO term
#to 500 so that the result will be as general as "cell cycle"
gotea=mode:hg, info_2_cutoff:500, alpha:0.6, beta:-0.3, top_cutoff:3, cutoff:0.01

#GOTEA, all parameters are optional, if not specified, VisANT will use whatever value of these
#parameters are availabel (usually last value that being used
#Note that the parameter value used in the following macro will not update 
#the current parameter value in VisANT
gotea=mode:go_tea, info_2_cutoff:500, alpha:0.6, beta:-0.3, top_cutoff:5, cutoff:0.01, iteration:2000