Metabolizer

Metabolizer allows you to simulate knockout (KO) and/or over-expression (OE) of one or several genes or the effect of a drug in metabolic module genes.

2 different usage of Knockout tool exist:

1) Using sample

• Input data
• If you upload expression data for 1 sample, you do not need to upload design data and can not use auto knockout option.
• Species
• Job information

2) Using a dataset (Multiple Samples)

The tool can be accessed from the main menu bar, by clicking on the Knockout button, see Workflow for further information.

The main page of the tool is its filling in form. This form includes all the information and parameters that the tool needs to process a job. The form is divided in different panels:

• Input data
• Design data
• Species
• Job information

Once the form has been filled in, press the Launch job button to launch a job. Your job will be listed in the My jobs panel, see Workflow for further information.

The results page of the Differential signaling tool includes different output results. You can download any table or image showed in the results page by clicking on the name right above it. You can also download calculated module activity values and statistical results by clicking on Module values and Path significance respectively. Using module activity values clustering of the samples are represented with heatmap and Principal component analysis (PCA) plots

The results are divided in different panels:

• Input Parameters
• Module Values
• Pathway viewer