order to use the tool, either you need to register an account or you
can use the tool as a guest user. Registering an account will allow you
to see your old data and results from your previous uses of the web
tool. If you’re already registered, you can click the Log In button
located on the right top corner of the homepage. You will then be
directed to the tools view. Clicking any of the tools will direct you
to the input page where you need to provide the input files or you can
use the sample data provided on the site. Once you introduce the input
files you will be able to run the tool.
RESULT NAME (optional):
can give a name to your analysis. When it is left blank, it will be
named using the date and time of the analysis you are about to perform.
p-value file is a file of p-values the user derived from transcriptome
data analysis (or metabolome in the case of Mx-RPAm tool). The p-value
file must be in an mx2 format where the first column includes m gene
names, and the second column includes corresponding p-values. The file
should include p-values of all available genes, not only the ones below
a certain p-value cut-off value.
network file should be a file that contains four columns. The first
column will be reaction names, the second column the reaction itself
(with all substrates and products separated by “//”), the third column
the gene names (again multiple genes separated by “//”), and the fourth
column the associated pathway names (again multiple pathways separated
by “//”). This file can be obtained from sites/databases such as
BioCyc. In order to help the users, we provide metabolic networks of
ten most commonly used organisms, derived from BioCyc. These networks
are accessible when the user selects “I will use the default network”.