Translation among annotations

nuno-agostinho / psichomics

Interactive R package to quantify, analyse and visualise alternative splicing

http://nuno-agostinho.github.io/psichomics/

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Translation among annotations #420

Closed MiqG closed 3 years ago

MiqG commented 3 years ago

Hi,

thank you for creating such a great package that unifies the field of alternative splicing analysis.

Currently, I am trying to translate the event annotations from Thomas et al. 2020 into VastDB identifiers. So far, I have been able to spot that they used MISO annotations from hg19, but I cannot figure out which event they map to and with which logic. I thought that since you are working at the intersection of all the AS tools, this would be a piece of cake!

For example:

event in Thomas 2020:

se@1:107963765:107973372:+|1:107963765:107979287:+

possible mappings in VastDB annotation from hg19 searching every coordinate separately:

GENE    EVENT   COORD_o LE_o    FULL_CO
NTNG1    HsaEX0044072    chr1:107963706-107963765   60    chr1:107961267,107963706-107963765,108023233
NTNG1    HsaEX0044073    chr1:107973372-107973539    168    chr1:107950330,107973372-107973539,108023233
NTNG1    HsaEX0044074   chr1:107979287-107979421   135    chr1:107973539,107979287-107979421,108023233

Thanks a lot in advance for your help!

Miquel

nuno-agostinho commented 3 years ago

Hey Miquel!

se@1:107963765:107973372:+|1:107963765:107979287:+

I don't think that identifier is from MISO...

Anyway, you can find in Bioconductor an alternativeSplicingEvents.hg19 annotation that I created with the conversion between MISO and VAST-TOOLS identifiers for multiple events (probably not all though).

Please note that:

MISO IDs are in the following format (as according to MISO documentation): chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-
VAST-TOOLS has two different identifiers per event (e.g. HsaEX0000001 and ENSG00000254427_CASSETTE1 correspond to the same identifier). I used the ENSG00000254427_CASSETTE1 format in the annotation table, but you can easily convert those to the HsaEX identifiers by downloading the human VASTDB annotation and going to the file FILES/New_ID-Hsa.txt.gz where you have the conversion between the different VAST-TOOLS identifiers.

If you need further help, feel free to ask me! :)

MiqG commented 3 years ago

Thanks a lot for the quick help! I'll contact the authors then :)

nuno-agostinho commented 3 years ago

Hey Miquel, any news on this? Anything that I can help you with? :)

MiqG commented 3 years ago

Hi Nuno, yes I got back from them!

They explained to me that their exon definition was: first junction|exclusion junction. For example, in se@1:107963765:107973372:+|1:107963765:107979287:+ the first junction goes from 107963765 to 107973372, and when the exon is skipped the junction goes from the second portion of coordinates from 107963765 to 107979287; that's why the first coordinate is the same for both junctions. With this, I was able to use the coordinates to map their events to VastDB identifiers using the REF_CO column of the hg19 annotation :)

Cheers!

nuno-agostinho commented 3 years ago

Glad to hear that you got it working Miquel! 😄 Cheers!