Tutorial : Results visualization using Escher

⚠️ This tutorial ONLY works for results generated using the Human Recon.2.2 or the CHO cell as reference models ⚠️

Users may easily visualize their CellFie tasks using the Escher webtool. For this you will need:

• Reaction Activity Level - File containing the list of essential reactions and their associated scores for each sample
• Escher maps for the CellFie tasks

1. Extracting Reaction Activity Level from CellFie module results

One of the output of the CellFie module is a csv file named detailScoring. This file contains the Reaction Activity Level (i.e. the score of all essential reactions for each metabolic tasks) that can be overlaid on the Escher maps.

1.1 The detailScoring file

The detailScoring.csv file contains 8 columns for each sample with detailed information about the essential reaction scores:

• Column 1: sample ID
• Column 2: task ID
• Column 3: task score for this sample
• Column 4: binary task score for this sample
• Column 5: essential reaction associate with this task
• Column 6: expression score associated with the reaction listed in column 5
• Column 7: gene used to determine the expression of the reaction in column 5
• Column 8: original expression value of the gene listed in column 7

Information is concatenated horizontally therefore columns 9-16 will contain information for sample 2, columns 17-24 will contain information for sample 3, etc. Example : this is the detailScoring file that you should obtain if you run the Cellfie module with the test dataset, the Human Recon2.2 as reference model and the default parameters (local + percentile + minmaxmean + 25 + 75)

1.2 Extracting Reaction Activity Level

The Reaction Activity Level corresponds to the essential reaction and expression score (the columns 5 and 6 of the detailScoring file). This information should be extracted as a separated CSV file for submission to Escher website. To do this, simply copy-paste the columns 5 and 6 of the detailScoring file into a new document. Example: this is the Reaction Activity Level file that you should extract from the detailScoring file.

More information about Escher compatible data format can be found here

2. Visualizing on CellFie Escher maps

2.1 Launching a blank workspace in Escher

When you open the Escher website, you will see a launch page that looks like this:

Select **None **for both Map and Model (you will be uploading your own CellFie maps later). Then click Load map to open the Escher builder.

2.2 Loading the CellFie Escher map

We created 6 CellFie Escher maps that can be used to visualized various metabolic processes:

• amino acid metabolism
• carbohydrate metabolism
• energy & nucleotide metabolism
• glycan metabolism
• lipids metabolism
• vitamin & cofactor metabolism

⚠️ These maps ONLY works for results generated using the Human Recon.2.2 or the CHO cell models ⚠️

Use the Map menu to load a process map:

2.3 Loading the Reaction Activity Level file you want to visualize

Load the Reaction Activity Level file using the Data menu:

Reaction scores are visualized by changing the color, thickness, and labels of reaction arrows. The specific visual styles can be modified in the Settings menu. When data is not present for a specific reaction, then the text label will read “nd” which means “no data.”

This is how the carbohydrate metabolism map looks when overlaid with the example Reaction Activity Level file:

2.4 Saving your CellFie map

You can use the Map menu to export your CellFie visualization as a PNG or SVG file: