selected nodes but not the network for these selected nodes

[jing lu]

Dear Sir/Madam:

I am a new user of bionetbuilder.
When I used it, I followed the tutorial you provided.
I upload a list of protein ids, and the number of nodes in my
protein list is 164.
And next when I selected the interaction source e.g. Kegg, it always
gave 48012 edges. And the network finally I got has 2200 nodes and
44072 edges.
It seems that the network is not based on the nodes list I uploaded.
It is the network for the organisms I used.
Would you please help me to solve this problem? I don't know, maybe
there is something wrong with click each steps?

Thank you.

Regards
Jing
PhD student
Wageningen University
The Netherlands

[Kevin Drew]

Hi,

There is a checkbox on the Edge source panel called "Add first neighbors of nodes".  This option will add neighbor nodes and their edges when building the network.  Make sure this is unchecked and try to build your network again.

Thanks,

Kevin Drew
Bonneau Lab

--
You received this message because you are subscribed to the Google Groups "BioNetBuilder" group.
To post to this group, send email to bionet...@googlegroups.com.
To unsubscribe from this group, send email to bionetbuilde...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/bionetbuilder?hl=en.

[jing lu]

Dear Kevin:

Here I send you part of my protein list, the organism is bos taurus.
Would you please help me to try if there is still problem? I have done
what you told me, but it didn't work.Thank you in advance.

uniprot: Q08E42
uniprot: P0C7Q4
uniprot: Q95122
uniprot: P13214
uniprot: Q58DS5
uniprot: P48733
uniprot: P84466
uniprot: Q95114
uniprot: Q0VCJ8
uniprot: P48616
uniprot: P62998

Regards
Jing
PhD student
Wageningen University
The Netherlands

> >http://groups.google.com/group/bionetbuilder?hl=en.- Hide quoted text -
>
> - Show quoted text -

[Kevin Drew]

Hi Jing,

I tried your list and am getting the same problem as you described.  I have not figured out exactly what is going wrong but I think it is a problem with the translation of uniprot ids.  I think the best work around is to translate your uniprot ids to gis and use the gis to load the network.  To do this you can use the translator (" Synonym and Ortholog Translator " link on BioNetBuilder's web page).  You may have to strip the "uniprot:" prefix off the list of uniprot ids before you load into the translator.  You can then select "UniProtKB" on the left and "GI"  on the right and press translate.  Save this file and add in the "GI:" prefix to the list.  Load this list into BioNetBuilder. 

I did this translation with your list to get the GI list below and it loaded the proper network into BioNetBuilder. 
-snip-
GI:116003833
GI:158341674
GI:41386760
GI:48374083
GI:66792866
GI:27806359
GI:114053041
GI:41386719
GI:122692341
GI:110347570
GI:27806443
-snip-

Hopefully this helps.  Sorry for the trouble.

Thanks,

Kevin Drew
Bonneau Lab

[jing lu]

Dear Kevin:

 

  I did what you said, and it works. Thank you very much.

 

Regards

Jing