Edges not present in subnetwork

[seema]

Hello everyone,

I successfully connected to bionetbuilder using a datacard. For demo, I wanted to make Wnt subnetwork. I selected all the interaction databases except HPRD for edges. In the network the edges are simply not coming but the nodes are. In the bionetbuilder tutorial, one could see the wnt subnetwork, but when I try with correct node IDs, they are not being connected. Maybe the bionetbuilder server is having problem, or else tell what to do. Thanks,
Seema

[Kevin Drew]

Hi,

Glad to hear you made the connection. What gene identifier are you
using to build the network? You might want to try GI if possible. If
that does not seem to work and you said you can see the subnetwork of
interest in the tutorial's network, just select the subnetwork and
move it to a new one.

Thanks,

Kevin Drew
Bonneau Lab

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[seema]

Hi, Thanks for your reply. I used GI identifiers which I have checked are all correct. As i would like to make own network, I do not want to use a subnetwork. So, please check if your server is OK as today, even nodes are not coming when I select from nodes with selected annotations, this is proceeding upto Cytoscape GO stage only , and no nodes are present in NumNodes column.

2. How to select different biological processes which are listed far away with those names in bwteen which are not required. When I press shift button on computer to select biological processes, all from one process to the another process get selected when we do not require the in-between biological processes.

[Kevin Drew]

Hi,

Can you send me the organism and gene list (or GO annotation) you are
trying to use so I can test it out on my end?

Thanks,

Kevin Drew
Bonneau Lab