ClueGO, Preselected Functions, save result table, Excel, bug

[Jan Söderman]

Hi,

Using ClueGO v. 2.5.6 it is not possible to "Save the result table as Excel sheet" after the Preselected Functions mode. The only result is an empty Excel file, and a pop-up window with a "no entry road sign" on. In the Preselected Functions mode it is possible to "Save ClueGO result table".
In the Functional analysis mode I have no problems with neither "Save the result table as Excel sheet" nor "Save ClueGO result table".
To make sure that my problems was not due to a corrupted installation I uninstall both Cytoscape (v. 3.7.2) and all apps, and then reinstalled Cytoscape and only ClueGO and CluePedia. The result was, however, the same.

Best regards, and thank you in advance,
Jan

[Bernhard]

Hi Jan, this seems to be a bug. We will look into it. Thanks for reporting it.

Best

[Jan Söderman]

Thanks. If I may add an observation with regard to the Preselected functions mode. Opening a saved session takes a really long time. Anywere between 3 min 15 sec and 5 min 50 sec. Also it takes very long time to shift between different analyses tabs in the same session file. This cluego session file contains 104 GO BP terms in 47 groups with 72 connections. As a comparision I have a ClueGO session file with 10 analyses based on the Functional analysis mode. In total this session contains 1861 terms, 768 groups and 5883 connections, and is opened in about 1.5 min.

According to the progress window the step "Initialization of CluePedia (Initialize CluePedia files)" seems to take a long time. However, sometimes the progress window also says "Finalizing" for a long time.

Sincerely/ Jan

[Bernhard]

Hi Jan,

yes we know this problem. The reason for this is that if you start from functions and select to add all genes then it can become very slow because some terms have 500-1000+ genes. If you don't add genes (or few e.g. 50 per term) then it should be much faster, but you will not have kappa score links between the terms. In this case you can use the ontology relations between the terms.

Best

[Jan Söderman]

Hi again Bernard,

I'm unable to find any relevant information on this, neither in the documentation for ClueGO and CluePedia nor in the FAQ or the example files. I note that I can select Tree as a Grouping option, set the number of genes to 0 in the CluePedia option, and in the CluePedia tab of the Table panel select Show ontology relations.

The result I get is very different from that based on Kappa score. Both clusters are grey (instead of red or blue), in the result table there are only a few groupings (as compared to the Kappa score result), and there is little correspondence between groupings according to the table and the ontology relations.

I'm not sure if this is what you mean, and frankly I don't know what I'm doing. Could you please refer me to relevant documentation?

sincerely,

Jan

[Bernhard]

Hi Jan, grouping will only work if you have genes associated to the term (kappascore or tree related)  What I meant was you can connect terms based on the ontology even there are no genes associated. See in the CluePedia panel. Click in the tree icon. You can also grow the ontology up to the root, so all terms under the root will be connected. Sorry the documentation is not up to date because we have not much time to work on this at the moment.

Let me know if it works or if you have other questions.

Best