Tutorials

This tool allows you to map your metabolome data on the metabolic network of your organism of interest, and gives you the list of perturbed reporter pathways as an output

This tool allows you to map your transcriptome data on the metabolic network of your organism of interest using the classical approach, and gives you the list of perturbed reporter pathways as an output

This tool allows you to map your transcriptome data on the metabolic network of your organism of interest, and gives you the list of perturbed reporter metabolites as an output. It uses the approach introduced by Patil and Nielsen in 2005.

HOME BUTTON
Clicking this button will return you to the homepage

TUTORIAL
Contains the documentation and tutorial on how to use the tools

FAQ (FREQUENTLY ASKED QUESTIONS)
Contains the most frequently asked questions regarding the tool and the answers to the questions

GUEST BUTTON
Clicking this button will log you in as a guest. You will be able to use all features of the tools. However, your results will not be saved after you leave the website.

LOG IN BUTTON
Clicking this button will redirect you to login page

SIGN UP BUTTON
Clicking this button will redirect you to the registration page to open an account

To register an account, you need to click the Sign-Up button located in the right top corner of the screen, then you will be asked to fill in the sign-up form. In the form, you will be asked to enter your username, email address, password, your first and your last name. Once you’re done filling out the form you will be directed to the Tools page.

When you log in using your account or as a guest user, you will be directed to the tool selection view page. In this page, you can select the tool that you want to analyse your data with. Currently, there are four tools available for use, ranging from Reporter Metabolite Analysis to different forms of Reporter Pathway Analysis.

This tool allows you to map your transcriptome data on the metabolic network of your organism of interest using the novel approach by Çakır et al. (2015), and gives you the list of perturbed reporter pathways as an output

In 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.

INPUT DESCRIPTION:
RESULT NAME (optional):
You 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-VALUES:
The 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 m is the column of gene names and n is the column of 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:
The 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”.