ICSNPathway provides a JAVA template program to access web services directly. To run this program, JAVA environment is required. You can download the JVM software from http://java.sun.com/javase/downloads/index.jsp and set your proper system's environment to make sure the JAVA is executable.


Unzip the downloaded ‘ICSNPathway_v1.1.zip’ file, which includes one jar file ‘ICSNPathway.jar’, one configuration file ‘ICSNPathway_Configuration.properties’, one rs-IDs file ‘top_pRA_assoc.assoc_Pvalue.txt’, and one GWAS SNP P-value file ‘pRA_assoc.assoc_Pvalue.txt.gz’.


ICSNPathway.jar: this jar file is to run the main service of our server with the parameters in the file ‘ICSNPathway_Configuration.properties’.



java –Xmx500m -jar ICSNPathway.jar configurationFile 


configurationFile is optional, ICSNPathway_Configuration.properties on current directory is default. To ensure to run this program properly, please put ICSNPathway.jar, configuration file, rs-IDs file, and GWAS SNP P-value file in the same folder; and modify thee paths and file names of rs-IDs file and GWAS SNP P-value file in configuration file.


The program will send the job to our server and the result file will be sent back to your computer, named ‘result_xxxx.txt’ (xxxx is the job name in configurationFile, and default is ‘untitled’).


You can modify the configuration file ICSNPathway_Configuration.properties as you like. The main content of the configuration file are as follows:


Job Name:                                                               


 /*  Set your job name.  */

Upload GWAS SNP P-value file:


/*  Modify it according to the path and name of your GWAS SNP P-value file,and this parameter can NOT be blank  */

Specify SNPs by P-value:


/*  Specify the SNPs with P-value < the threshold as the most significant SNPs.  */

HapMap population:


/*  Select a HapMap population to help to search the LD neighborhoods of the most significant SNPs.  */

LD cutoff:


/* Choose the LD measurement (r2 or D' respectively) cutoff for defining LD neighborhoods. */

Distance(up to 200kb):


/*  The maximum distance (kb) to search LD neighborhoods. */

Rule of mapping SNPs to genes:


/*  Please select the rule of mapping SNPs to genes: functional, within, 5kb, 20kb, 100kb, 500kb */

Pathway/gene set databases (KEGG):


/*  Put yes or no  */

Pathway/gene set databases (BioCarta):


/*  Put yes or no  */

Pathway/gene set databases (GO biological process):


/*  Put yes or no  */

Pathway/gene set databases (GO molecular function):


/*  Put yes or no  */

Minimum number of genes in gene set:


/*  The default minimum gene number is 5.  */

Maximum Number of genes in gene set:


/*  The default maximum gene number is 100.  */

FDR cutoff for PBA:


/*  The default FDR cutoff for PBA is 0.05  */