gene network widget for gene list

[ValWood]

Hi,

We used to have a gene. list network widget but it is now missing:

Is there a list of available widgets anywhere so that we can. see which ones could be useful?

thanks!

Val

@kimrutherford @manulera

[ValWood]

I just. spotted this, which is overlapping. https://github.com/intermine/pombemine/issues/38

[ValWood]

Hi @heralden should this issue be moved onto the bluejeans tracker?

[heralden]

Can you try logging in as an admin on Pombemine bluegenes, then open the user menu at the top-right and click Tools. You should see GO Concept Relation there and be able to install it if it had been removed.

[ValWood]

@kimrutherford could you see if you can resurrect these. I did see them on the list pages a while back...

[ValWood]

Actually the GO Concept relation is there. I think the list I looked at was too large and had no significant hits.

So it is just the cytoscape one.

[kimrutherford]

I've installed the GO Concept Relation plugin. It seems to work.

[ValWood]

OK the cytoscape plug-in is only available from a gene page. You can't use it on a gene list to see how the list members are connected which is a shame. @heralden is it planned to make this available (It's quite a powerful way of interrogating lists. I never find the use case of a spoke model of showing first neighbours particularly as used on the gene pages biologically informative (You could get this more clearly from looking at a list of interactors).

[ValWood]

I have seen esyN used somewhere in a Mine, is it possible to use esyN as a tool to visualise lists of interactors (which is essentially only a cytoscape wrapper).

[ValWood]

Actually it must be possible to view list contents with cytoscape. The above image is a screen shot from when it was available for pombemine.

[ValWood]

I found the intermine tool and installed it to work on lists. However on the GO template query

which provides 20 genes that are in some ways connected, no network resolves.

[ValWood]

It seems that the using the InterMINE plugin a network can only be constructed if the query is an interaction query (previously you could generate a network from a list, for example a GO output which was useful).

Also, there is no key so I am struggling to guess what the unlabelled nodes are:

[heralden]

We have lots of improvements on the roadmap for the cytoscape visualisations (including those you mentioned).

The Gene Interaction Network tool should display for all queries containing genes. You can see this here: https://www.flymine.org/flymine/results/PL%20FlyAtlas_head_top If there aren't any shared nodes, nothing will be displayed (due to shared nodes defaulting to on). You can turn it off but it will just show all the nodes without edges, as they don't share any interactions.

[ValWood]

Currently, it does not appear for all queries containing genes. For example, the GO query template GO term =>genes, using the default term in the template (mitotic spindle assembly).

"Genetic Interaction network" header is present but is not showing any data. These genes definitely have shared genetic and physical interactions.

Also, the label for this tool is "genetic interaction network" but should it be "Genetic or physical interaction network" When it is present there seems to be an option to switch?

[ValWood]

I tried the list from the query I am looking at in esyN. It has lots of genetic and physical interactions, so I think this might not be configured?

[heralden]

I see it crashes on that particular query - I've created an issue for it https://github.com/intermine/bluegenes-interaction-network/issues/24 but won't have time to look into it now.