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’.
Command:
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:
|
[untitled] |
/* Set your job name. */ |
|
Upload GWAS SNP P-value
file: |
[pRA_assoc.assoc_Pvalue.txt.gz] |
/* 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: |
[1e-5] |
/* Specify the
SNPs with P-value < the threshold as the most significant SNPs. */ |
|
HapMap population: |
[CEU] |
/* Select a HapMap
population to help to search the LD neighborhoods of the most significant
SNPs. */ |
|
LD cutoff: |
[r2:0.8] |
/* Choose the LD measurement (r2 or D' respectively) cutoff
for defining LD neighborhoods. */ |
|
Distance(up to 200kb): |
[200] |
/* The maximum
distance (kb) to search LD neighborhoods. */ |
|
Rule of mapping SNPs to genes: |
[within] |
/* Please select the
rule of mapping SNPs to genes: functional, within, 5kb, 20kb, 100kb, 500kb */ |
|
Pathway/gene set databases (KEGG): |
[yes] |
/* Put yes or
no */ |
|
Pathway/gene set databases (BioCarta): |
[yes] |
/* Put yes or
no */ |
|
Pathway/gene set databases (GO biological process): |
[yes] |
/* Put yes or
no */ |
|
Pathway/gene set databases (GO molecular function): |
[yes] |
/* Put yes or
no */ |
|
Minimum number of genes in gene set: |
[5] |
/* The default minimum
gene number is 5. */ |
|
Maximum Number of genes in gene set: |
[100] |
/* The default
maximum gene number is 100. */ |
|
FDR cutoff for PBA: |
[0.05] |
/* The default FDR
cutoff for PBA is 0.05 */ |