FILE IMPORT ISSUES CYTOSCAPE

[Rohan Chodankar]

Hi

I am a new cystoscape user and would really appreciate some help. I have the STRING plugin installed and my samples are human.

I have a a CSV file with GENE ENSEMBL number and gene names eg PENK with the log FC and adj P value etc. So I have ESNGXXXX rather than ESNPXXX data. See here 

CSV File

When I enter these in String within Cytoscape I do get a network. IN the shared name and name column. (NODE Table) is get the names as 9606.ESNPXXXX, although the display name tab is correct.

The issue appears when I want to import a CSV file with the fold change values. I need to import with "key ID" as display name rather than shared name. This works fine for linking FC values.

However my network generated using MCODE has over 553 nodes  edges. I wish to filter these, but when I use the degree filter In and out I get no values. 

I have tried BIOMART to convert the ESNG IDs to ESNP IDs, however with over 500 genes, this doesn't seem to work as multiple ESNPs are provided for one ESNG.

Please help!

Rohan

[Nadezhda Doncheva]

Hi Rohan,

When you create a STRING network, your input identifiers are saved in a column called "query term". You should use this one to match to your table with the logFC values. There is no need to do external identifier mapping.

I don't quite understand your question regarding MCODE and the degree-based filtering, but maybe someone else hre can answer that.

Best wishes,

Nadya

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/4df34379-241a-4827-8717-7b0c21a65e56n%40googlegroups.com.

[Rohan Chodankar]

thanks !