pathvisio questions

[Huansheng Cao]

Hi there,

I have create a custom pathway which exists my organism including the organisms I study: cyanobacteria. so these pathways are custom, but not standard pathways from any reference organism. I have many pathways are not standard pathways. I have some gene expression data and some other abundance I would like to map to these pathways. 

can this be done through pathvisio? I tried but did not make it work. I attached the custom pathway in .gpml and mapping data in .csv format for your reference.

your help will be much appreciated!

Best,

Huansheng

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Huansheng Cao, Ph.D. | Assistant Research Professor

Center for Fundamental and Applied Microbiomics

The Biodesign Institute | Arizona State University

727 E. Tyler St. Tempe, AZ 85287

Phone: 480-727-2294 | Email: hsh...@asu.edu

https://biodesign.asu.edu/huansheng-cao

[Alexander Pico]

Hi.

I haven't tried using PathVisio (PV) for a non-supported species, but I think it might work...  First, you'll need to fix you GPML pathway.  I noticed that none of your genes have Xref entries. These are what PV uses to map from your data to the pathway. It does NOT use the label, which can be anything.  For example:

  <DataNode TextLabel="GltBD" GraphId="a6cff" Type="GeneProduct">

    <Graphics CenterX="772.25" CenterY="252.5" Width="90.0" Height="25.0" ZOrder="32768" FontSize="12" Valign="Middle" />

    <Xref Database="" ID="" />

  </DataNode>

The Database should be "O" and the ID should be "GltBD"... just like in your CSV file.

If that still doesn't work, let us know. You might have to make a "fake" gene database via a custom local file, like set 4.2 here: https://www.bigcat.unimaas.nl/data/jib-supplemental/supplemental3_tutorial.pdf. But, I'm not sure that is necessary.

 - Alex

[Martina Summer-Kutmon]

Hi Huansheng,

Alex' description is correct. You can load your data and visualize it on the pathway as long as the identifiers in the pathway (as Alex explains) are exactly the same as in your dataset.

When importing the data, you need to select the same database (or create a system code column). 

At the end of the import, it will tell you that it was not able to import any rows successfully (which just means that they were recognized by the mapping database) but you will still be able to see and visualize the data if there is an exact identifier match.

Hope this helps.

Best, Tina

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Martina Summer-Kutmon, PhD
email: mku...@gmail.com