Loading a network from cytoscape-ReactomeFIVIZ to cluego/cluepedia
148 views
Skip to first unread message
Malela M. Werner
Mar 2, 2016, 9:52:54 AM3/2/16
to cytoscape-helpdesk
Hello,
I have generated a network in cytoscape using the ReactomeFI app. I would like to be able to visualize the network and the associated GO terms from reactome with the cluego/cluepedia visualization. However when I select Analysis Mode Cluepedia and network from cytoscape than input the gene names in the network, the output doesn't have the network that was created with cytoscape-reactome, instead just one cluster and the rest of the genes individually interspesed without connection. I tried reruning with the Cluego analysis mode but none of the connection from reactome are shown even after I select to update with the cluepedia-string-action file.
Thanks for help.
Malela
I have generated a network in cytoscape using the ReactomeFI app. I would like to be able to visualize the network and the associated GO terms from reactome with the cluego/cluepedia visualization. However when I select Analysis Mode Cluepedia and network from cytoscape than input the gene names in the network, the output doesn't have the network that was created with cytoscape-reactome, instead just one cluster and the rest of the genes individually interspesed without connection. I tried reruning with the Cluego analysis mode but none of the connection from reactome are shown even after I select to update with the cluepedia-string-action file.
Thanks for help.
Malela
Bernhard
Mar 2, 2016, 11:16:57 AM3/2/16
to cytoscape-helpdesk
Hi Malela,
if you want to visualize GO terms you will have to create a new ClueGO network based on the genes from the reactome network. You can not visualize the Reactome Visualization together with the ClueGO network because they don't use (technically) the same network visualization. So you have to analyze the data separately. The links from Reactome are not exactly the same than the ones from STRING, so it is normal to see differences. You could try to map the genes on the REACTOME "Ontology", so you will see connections between REACTOME pathways.
Best
Bernhard
if you want to visualize GO terms you will have to create a new ClueGO network based on the genes from the reactome network. You can not visualize the Reactome Visualization together with the ClueGO network because they don't use (technically) the same network visualization. So you have to analyze the data separately. The links from Reactome are not exactly the same than the ones from STRING, so it is normal to see differences. You could try to map the genes on the REACTOME "Ontology", so you will see connections between REACTOME pathways.
Best
Bernhard
Malela M. Werner
Mar 12, 2016, 10:59:57 PM3/12/16
to cytoscape-helpdesk
Hi Bernhard,
Thank you for addressing my question (and sorry for the delay to acknowledge as I thought I'd net notification of response in my inbox through which I log in). I was able to regenerate the networks by using the network genes from reactome to generate a clupedia nested network with directed edges as you suggested. I was able to get most of my networks of interest after updating the interactions of interest. However there are a few genes in the nested network that don't have a link to the other, is it because of low evidence?
Also if I have a nested network, is it possible to change the colors of other nodes of interest (besides the one from my gene list) to a different color.
Again, Thanks!
Malela
Bernhard
Mar 14, 2016, 9:03:47 AM3/14/16
to cytoscape-helpdesk
Hi Malela,
if some links are missing it could be because of low evidence, but also because the provided file from STRING which is probably not on the latest update state compared to the database.
To change the color of a node you can do following 7 steps. After this example the node should be blue. Make sure you change the node with correct id (entrez gene in this case).
But be careful! Just do this only when everything on your network is finished and you want to save the final image! If you click on the "Update" button to refresh the edges the changed node colors will be changed to the initial ones again!
Best
if some links are missing it could be because of low evidence, but also because the provided file from STRING which is probably not on the latest update state compared to the database.
To change the color of a node you can do following 7 steps. After this example the node should be blue. Make sure you change the node with correct id (entrez gene in this case).
But be careful! Just do this only when everything on your network is finished and you want to save the final image! If you click on the "Update" button to refresh the edges the changed node colors will be changed to the initial ones again!
Best
Malela M. Werner
Mar 14, 2016, 3:00:05 PM3/14/16
to cytoscape-helpdesk
Hi Bernhard,
Thanks for the image link to rendering different colors to nodes of interest. It worked perfectly.
Malela
Thanks for the image link to rendering different colors to nodes of interest. It worked perfectly.
Malela
Malela M. Werner
Mar 17, 2016, 2:50:42 PM3/17/16
to cytoscape-helpdesk
Hi Bernhard,
I have another question on Cluepedia. I generated network images containing genes of interest (colored red and blue) from two separate cell lines. However, the nested network can be very crowded and not clearly display the interaction between the genes of interest and other genes in the network. I attach and example for the response to oxidative stress network. Is there a way to only show the colored genes plus other genes in the network to which they form primary and secondary interaction, (other than manually picking and hiding nodes that don't show close intereraction to gene of interest) ei. only show genes immediatedly and secondarily connected to TXNIP, FN1, ATP2A2.
Thank you.
Malela
I have another question on Cluepedia. I generated network images containing genes of interest (colored red and blue) from two separate cell lines. However, the nested network can be very crowded and not clearly display the interaction between the genes of interest and other genes in the network. I attach and example for the response to oxidative stress network. Is there a way to only show the colored genes plus other genes in the network to which they form primary and secondary interaction, (other than manually picking and hiding nodes that don't show close intereraction to gene of interest) ei. only show genes immediatedly and secondarily connected to TXNIP, FN1, ATP2A2.
Thank you.
Malela
Bernhard
Mar 18, 2016, 6:03:23 AM3/18/16
to cytoscape-helpdesk
Hi Malela,
for the moment this is not possible. The only way would be to create a custom edge/link file with only the links you want to show on the network. For this you have to unzip the interaction file that is in the ClueGOSourceFiles/Organism_... folder and open it with excel. Then sort for the gene you are interested in and delete the links(rows) you don't want to show. Save the file with a new name (you don't have to zip it again). Refresh the edges/links in CluePedia and then load the new file. It is a bit of work but that should do it.
Best
Bernhard
for the moment this is not possible. The only way would be to create a custom edge/link file with only the links you want to show on the network. For this you have to unzip the interaction file that is in the ClueGOSourceFiles/Organism_... folder and open it with excel. Then sort for the gene you are interested in and delete the links(rows) you don't want to show. Save the file with a new name (you don't have to zip it again). Refresh the edges/links in CluePedia and then load the new file. It is a bit of work but that should do it.
Best
Bernhard
Reply all
Reply to author
Forward
0 new messages