iRefR question,

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jirivoller

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Mar 16, 2012, 3:55:52 PM3/16/12
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Hello,

a question about iRefR function select_protein
parameter complex_info is described as follows:
complex_info Flag that gives the user the option to retrieve either
all the records of the complex to which such protein belongs to
("full_complex"), or only the record
of the complex where the given protein is present
("not_full_complex"). Default="full_complex"

I am not sure how to understand it:

Is it like:
there is a protein complex of changing composition (may reflect
biological change, or diferent sensitivity of analysis methods)
not_full_complex = I get members of the special case of the complex
that included my query protein
full_complex = I get also members of the complex that were observed
in situations when my query protein was not present/observed
?

How strong the association has to be for a protein to be counted as a
member of a complex? Lets say a kinase is known to phosporylate some
component of a complex (but it was never co-imunoprecipitated) - a
"fleeting" interacation - will it count as a temporary complex member
(and will select_protein function report other/all components of the
complex as interactors)?

Thank you for explanation.
Also thaks for the help with cytoscape plugin.

jiri

Sabry

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Mar 18, 2012, 12:38:55 PM3/18/12
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Hello Jiri,
I have forwarded your question to The iRefR authors and you will get
an answer shortly.

Regards,
Sabry.
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