Hi,

How can I extract a gene ID number that is attached to a specific box in the PageMan graphical output? I can get the functional annotation for each box and the logFC values associated with each, but is there an easy way to determine what gene IDs are attached to each box in the output?

Thanks,
Katie

Hi Katie,

and thanks for your feed back. If i understand you correctly, you want to get a list of all
genes associated to a certain bin that is displayed on a PageMan "heat map" display?

Before answering, please let me clarify one possible misunderstanding - in you post
you mention that you can get the bin functional annotation and log fold change value
by clicking the box you are interested in. The value that is displayed, however, is not
a log fold change value, but the Z-score that was computed in the statistical test you
chose (e.g. Wilcoxon rank sum test). The sign of the value is derived from the general
direction of the response of all genes in the respective bin (i.e. a negative sign would
indicate a general downregulation of the genes in this bin). The magnitude of the Z-score,
however is not reflecting the magnitude of change in gene expression.

Concerning you question: In the current version of PageMan it is unfortunately not possible
to directly display a list of the genes in the selected bin. We will, however, thanks to your
comment, include this feature in the upcoming release of MapMan.

To obtain a list of the genes in the current version of PageMan you could do the
following: Open the mapping you are using by double-clicking it in the list on
the left side of the MapMan main window. All mappings are listed under the "mappings"
category. A new window showing the mapping in a hierarchical tree view will open.

You can arrange the PageMan and mapping window to appear side by side in the
MapMan main window. If you now click an interesting bin in the PageMan window,
the actual bin name will be displayed and you can navigate to this bin in the mapping
window which will show you all genes that are classified in this bin. This is a bit
cumbersome, but it works.

I hope this helps you -
best greetings,
Marc

Hi Marc,

Thank you for your quick and thorough reply and also for clarifying that the values are the z-score from the statistical test, not fold change. And yes, you did understand my question correctly. I am happy to hear that you will add the feature that I was asking for (displaying a list of all genes associated to a certain bin that is displayed on a PageMan "heat map" display) in the next MapMan release. I think this feature would make PageMan even more user friendly and will enable quicker analysis and interpretation of results.

Thank you also for your description of how I can currently get the gene lists associated with the bins. As you noted, this is a bit cumbersome to sort through, so again I think adding the new feature of seeing the associated genes at a click will be a wonderful addition to the program.

Best,
Katie

I have the same question as you but really until now I don't know how to do it, I would be a wordle lot happy if someone would share something at this time.