Task 2 - Metabolic Pathway Visualization

Integrate and visualize a set of biological data (e.g. genes,proteins,enzymes, …) within metabolic pathways of interest using the MapMan Desktop App. In this task, the user will handle the set of proteins previously annotated in Task 1 - Plant Data Annotation and integrate/visualize them within a lignin biosynthesis metabolic pathway.

Integrating annotated cork oak data in a metabolic pathway of interest

  1. Perform the download and installation of the MapMan Desktop App using the download & installation intructions within this guide.

  2. Launch MapMan, and in the main menu select Show Pathway to visualize your data in the context of metabolic pathways.

../_images/mapman_arrow.png

  1. In the left box, right-click Experiments -> Add Data -> select the corkoak_LogFC_July_April file.

  2. In the left box, right-click Mappings -> New Mapping -> from file, browse and select the corkoak.results file (obtained in Task 1 - Plant Data Annotation) within the CorkOak_UseCase_Data-main folder.

  3. In the left box, right-click Pathways -> Add Pathway -> download, browse and select the file named X4.5_Lignin (select the file with the Microsoft Edge HTML Document extension, the XML Document will not work).

Warning

In the case of error message: service temporarily unavailable, perform these alternative steps:
Go to the Mapman website and under the diagrams compatible with Mercator4 v.5 section, click to download the X4.5 Monolignol biosynthesis custom-made diagram, and unzip it (it should extract two separate files).
Then, in the left box, right-click Pathways -> Add Pathway -> from file, browse and select the file named X4.5_Lignin

  1. In the Pathway Workflow - Choose Pathway box, select the X4.5_Lignin pathway file.

  2. In the Pathway Workflow – Choose Mapping box, select the corkoak.results mapping file.

  3. In the Pathway Workflow – Choose Experimental Data Set, select the corkoak_LogFC_July_April file.

  4. Click Show Pathway.

../_images/mapman_screenshot.PNG

Note

In MapMan, by default, red color indicates gene downregulation while blue indicates upregulation.

  1. Right-click the pathway image and select Options. Under the Coloring Scheme field, select +Red Blue- to invert color mappings.

  2. Download the pathway image by clicking File (leftmost corner) -> Export as Image, renaming it as corkoak_lignin_mapping.
    The Output Annotated Pathway should look like the following:

MapMan Output

../_images/corkoak_lignin_mapping.jpg

  • Pathway Interpretation

The generated pathway illustrates where our query genes are possibly located throughout the several steps of a specified pathway of interest.

In the example shown, some of our cork oak genes of interest are annotated as PMTs and Laccases, intervenients in the latter stages of lignin biosynthesis. These genes are colored in red, which also indicates their upregulation during summer, based on the supplied experimental data.

This visualization can help comprehend the possible role of these genes in cork oak and illustrate their pathway-specific regulation during multiple conditions.

In our case, a hint is provided regarding the important upregulation of cork oak genes, such as CFP56_66243, CFP56_46579 and CFP56_46583, between others.

These putative PMTs and Laccases, acting on the latter stages of lignin biosynthesis, are relevant as cork oak is known to undergo higher secondary growth activity during the summer season, including the further development of lignified tissues in the tree stem and bark (cork layer).

Note

Different visualization options are available by specifying multiple combinations of Pathways (obtained from the MapMan Website), Mappings (Mercator4 results) and Experimental Data (user generated or other publicly availabe data).
Nevertheless, in case of no experimental data available, a dummy file can be provided instead (example here).

Video Guide:


Dummy Experimental Data Example:

Gene

Log2FoldChange

geneID1

1

geneID2

1

geneID3

1

…

…
We now have annotated plant data in the context of a specific metabolic pathway!
For visualization of the annotated data in a dynamic network format, go to the following Task 3 - Dynamic Network Visualization.