CyThesaurus: expression set ID's to be converted to cPath network ID's

[KER]

Hello,

I am interested in using CyThesaurus to convert by Gene Symbol IDs
from my expression dataset into IDs for genes in a network generated
from cPath. (For example, for the MYCN oncogene, I have "MYCN" from
my expression set and "human_mycn" from the node in the cPath
network.)

However, when I follow the instructions from the CyThesaurus Wiki :
Tab-delimited-text-file based (Note: My expression dataset is a tab-
delimited text file)

1. From menu: File => Import => Network (multiple file types)... =>
Remote/URL => Import the first one, ie. http://chianti.ucsd.edu/kono/data/galFiltered.sif
2. From menu: Plugin => CyThesaurus plugin
3. Click "ID Mapping Resources Configuration" at bottom left size
of the dialog.
4. Right click on node "Local/remote Files" and click "Add an ID
mapping file..."
5.Select "Remote/URL" => input http://tinyurl.com/mergesvn/testData/yeast_id_mapping.txt
=> click "Retrieve" => click "OK" and wait and Click "OK".
6. Select "Ensembl Gene ID" as the source ID type for attribute
"ID"
7. Click "OK" and wait and Click "OK"
8. In the Data Panel, display the new attribute which was just
created

^ I do not have an option to convert my Source ID type (GENE) to the
target ID type, which I would presume to be the cPath ID. In fact, the
options for both Source and Target IDs only include headers from my
expression dataset. Why am I not able to specify IDs in my network?

Thank you in advance for your reply.

[Jianjiong Gao]

Hello,

Let me try to understand your problem. So you have a network generated
from cPath with node IDs such as "human_mycn" and an expression file
with gene symbols such as "MYCN". You would like to import the
expression file into the network. But according to
http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/Expression_Data,
you have to use the same IDs for the network and the expression file.
In short, you had problem to import the expression file into the
network because the different IDs of your network and expression file.
Therefore, you want to map the IDs between the network and the
expression file.

If my understanding is correct, I am not sure if CyThesaurus can solve
you problem unless you have the mapping file. CyThesaurus can be used
to convert IDs of one type in one node attribute to IDs of another
type and save the converted IDs to another node attribute. But it
cannot help you to associate node IDs in the network to IDs in the
expression file.

I am not sure if anyone else has any easy workaround for you. If you
can send me the list of IDs in your network and IDs in the expression
file, I may be able to provide some help.

Thanks,
-JJ

On Aug 17, 7:36 pm, KER <kregan...@gmail.com> wrote:
> Hello,
>
> I am interested in using CyThesaurus to convert by Gene Symbol IDs
> from my expression dataset into IDs for genes in a network generated
> from cPath.  (For example, for the MYCN oncogene, I have "MYCN" from
> my expression set and "human_mycn" from the node in the cPath
> network.)
>
> However, when I follow the instructions from the CyThesaurus Wiki :
> Tab-delimited-text-file based  (Note: My expression dataset is a tab-
> delimited text file)
>
>    1. From menu: File => Import => Network (multiple file types)... =>

> Remote/URL => Import the first one, ie.http://chianti.ucsd.edu/kono/data/galFiltered.sif

>    2. From menu: Plugin => CyThesaurus plugin
>    3. Click "ID Mapping Resources Configuration" at bottom left size
> of the dialog.
>    4. Right click on node "Local/remote Files" and click "Add an ID
> mapping file..."

>    5.Select "Remote/URL" => inputhttp://tinyurl.com/mergesvn/testData/yeast_id_mapping.txt