exporting network view

Question

exporting network view

reimand0 opened this issue 7 years ago · comments

can we export the network in the network view as a text file, perhaps using the following columns?

target_protein target_site target_site_type target_site_mutation_impact bound_enzyme

Michał Krassowski · Answer 1 · Thu Jul 20 2017 20:05:22 GMT+0800 (China Standard Time)

I started implementing this. Should we duplicate entries for all impacts that we see on given site, or only use the most severe consequence (impact)? I am referring to proposed target_site_mutation_impact column. Let's look at 305 K from TP53; there are two mutations within a range of +/- 7 from this site, one with "proximal" and one with "distal" impact. should this render into:

NM_000546    305K     acetylation,ubiquitination    distal    EP300
NM_000546    305K     acetylation,ubiquitination    proximal    EP300

or just into:

NM_000546    305K     acetylation,ubiquitination    proximal    EP300

Michał Krassowski · Answer 2 · Fri Jul 21 2017 06:53:51 GMT+0800 (China Standard Time)

Did I understand the first column properly anyway - will it always have the same value for a single protein (unless we implement second shell i.e. showing all interactions of kinases)?

reimand0 · Answer 3 · Sat Jul 22 2017 03:46:19 GMT+0800 (China Standard Time)

yes, the first column will be the same. but we should still keep it - this allows users to concatenate multiple networks for example. Also network visualisation with Cytoscape uses this file format.

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On Thu, Jul 20, 2017 at 6:53 PM krassowski ***@***.***> wrote: Did I understand the first column properly anyway - will it always have the same value for a single protein (unless we implement second shell i.e. showing all interactions of kinases)? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#106 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASYC_YydMCsx4ZfCTkyb7zkfKQbV-2G7ks5sP9p_gaJpZM4OXBtB> .

Michał Krassowski · Answer 4 · Sat Jul 22 2017 04:11:44 GMT+0800 (China Standard Time)

So assuming that we only need the most severe impact, it is already implemented and ready to use on production: this is the "TSV file". Should I change the refseq id to gene name?

reimand0 · Answer 5 · Sat Jul 22 2017 04:36:54 GMT+0800 (China Standard Time)

Yes symbols are better for networks. You can keep refseq too as additional columns. Jüri

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On Jul 21, 2017, at 16:11, krassowski ***@***.***> wrote: So assuming that we only need the most severe impact, it is already implemented and ready to use on production: this is the "TSV file". Should I change the refseq id to gene name? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

Michał Krassowski · Answer 6 · Sat Jul 22 2017 05:02:10 GMT+0800 (China Standard Time)

Done. If any amendments are needed, please reopen this issue.