Table key columns

[Nicolas Wieder]

Hi,

I have a problem with tabels in cytoscape. After importing a .sif file into cytoscape which was created by a software that I use for network analysis, I am trying to run a bingo analysis on a subset of the output nodes. The output of the software are ensembl peptide ids and I convert them to gene symbols in order to feed them into Bingo. When I select nodes of interest and try to run the analysis I get the following error message:

"The selected annotation does not produce any classifications for the selected nodes. Maybe you chose the wrong type of gene identifier?"

I am assuming that even though my table includes gene symbols (which do work with bingo when I manually insert them into the text input) bingo is fed the ensembl peptide ids. This leads to the general question: Which column does bingo (and probably any other app where you cannot specifically select your input columns) uses as input? When I import tables into cytoscape, I can define a "key column", which I assume is the standard identifier for the whole table. In my case, I am adding the desired key column after import, by transforming the ensembl ids into gene symbols.

So, how can I define/change the key column of an existing table in cytoscape?

Thanks,

Nico

[alex.pico]

If I understand the issue, then I think you'll have to re-import the network in order to set the "right" column as the key column (which I think is the "name" column for BiNGO). I don't think BiNGO offers the option to select an alternate column for identifiers. You could also try to copy paste symbols into the 'name' column within Cytoscape, but the Table Panel is usually not a great interface for things that are easier to do in Excel.

 - Alex

[nic]

Thanks for the reply Alex. That's exactly what I did, I wrote a little script that translates my ensembl peptide id .sif file in a gene symbol .sif file. After re-import everything works as expected.

But I don't understand why I need an external work around, while I just want to change the key column of a table. First of all, Bingo should give you the choice of which column to use as an input, second Cytoscape should allow you to change you key (or name) column. This is a very unintuitive limitation which surprises me...

If there is really no build in way to resolve this issue, does anyone know where I could raise this issue for developers?

Thanks,

Nico