What Does 'Intactid' Stand For In Uniprot Xml Files (Comment Binary Interactions Section) ?

Question

[Pablo Pareja]

Hi all, I was wondering what exactly intactId stands for in uniprot entries. For example in the entry with accession Q9V3W6 you can find:

<comment type="interaction"> 
<interactant intactId="EBI-126914" /> 
<interactant intactId="EBI-213208"> 
<id>P13607-1</id> 
<label>Atpalpha</label> 
</interactant> 
<organismsDiffer>false</organismsDiffer> 
<experiments>1</experiments> 
</comment>

I've been checking the ids in intact db website and sometimes I get the same results as entering the accession of one of the proteins, but not always. I thought as well that they could be specific ids for interactions between two proteins, i.e. a unique id for each pair. I would appreciate any contribution. Regards,

Pablo Pareja

Answer 1

[Samuel Kerrien]

Hi guys,

I will try to explain the reason why some of our proteins do have multiple ACs.

In the case above, molecule B is a splice variant:

$2 ID(s) interactor B : uniprotkb:P15806-2|intact:EBI-413585

The way we are dealing with splice variant (and feature chains for that matter) is that we are creating a dedicated protein in the database and linking it to it's parent (i.e. the uniprot entry where the splice variant is described) by creating a cross reference to the AC of that protein in the database. So what you are seeing line 21 (below) is that specific cross reference and you can also see in parenthesis the protein ID:

$21 Properties interactor B : intact:EBI-81370(tfe2_mouse)|uniprotkb:P15806-2(identity)

I hope that clarifies this one.

Cheers
Sam

Answer 2

[Pierre Lindenbaum]

Hi Pablo, welcome on biostar,

I guess the Id in InAct ( http://www.ebi.ac.uk/intact/search/do/search?binary=EBI-126914,EBI-213208) is just an internal Id for a protein. So, EBI-126914 is just the IntAct-Id for 'prp7'

Update:after I saw Pablo's I grep'ed the IntAct data; there are only eight interactions with EBI-81370:

curl -s "ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.txt"  | cut -d '     ' -f 1,2 | egrep '(#|EBI\-81370)'
#ID(s) interactor A ID(s) interactor B
uniprotkb:Q64279|intact:EBI-81361   uniprotkb:P15806|intact:EBI-81370
uniprotkb:P15806|intact:EBI-81370   uniprotkb:Q61039|intact:EBI-81388
uniprotkb:Q64279|intact:EBI-81361   uniprotkb:P15806|intact:EBI-81370
uniprotkb:Q61039|intact:EBI-81388   uniprotkb:P15806|intact:EBI-81370
uniprotkb:P15806|intact:EBI-81370   uniprotkb:P41136|intact:EBI-309167
uniprotkb:P15806|intact:EBI-81370   uniprotkb:P20067|intact:EBI-309519
uniprotkb:P15806|intact:EBI-81370   uniprotkb:O35437|intact:EBI-309880
uniprotkb:P15806|intact:EBI-81370   uniprotkb:Q62392|intact:EBI-309727

but if you're searching for in all the available fields, you'll get 14 records:

 curl -s  "ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.txt"  | egrep -w  '(#ID|EBI\-81370)' | cut -d '      ' -f 1,2 | cat -n
     1  #ID(s) interactor A ID(s) interactor B
     2  uniprotkb:Q64279|intact:EBI-81361   uniprotkb:P15806|intact:EBI-81370
     3  uniprotkb:P15806|intact:EBI-81370   uniprotkb:Q61039|intact:EBI-81388
     4  uniprotkb:Q64279|intact:EBI-81361   uniprotkb:P15806|intact:EBI-81370
     5  uniprotkb:Q61039|intact:EBI-81388   uniprotkb:P15806|intact:EBI-81370
     6  uniprotkb:P15806|intact:EBI-81370   uniprotkb:P41136|intact:EBI-309167
     7  uniprotkb:P15806|intact:EBI-81370   uniprotkb:P20067|intact:EBI-309519
     8  uniprotkb:P15806|intact:EBI-81370   uniprotkb:O35437|intact:EBI-309880
     9  uniprotkb:P15806|intact:EBI-81370   uniprotkb:Q62392|intact:EBI-309727
    10  uniprotkb:P15806-2|intact:EBI-413585    uniprotkb:P15923-2|intact:EBI-769650
    11  uniprotkb:P15806-2|intact:EBI-413585    uniprotkb:Q9JKN5|intact:EBI-1213712
    12  uniprotkb:P15806-2|intact:EBI-413585    uniprotkb:Q9EQW6|intact:EBI-1213740
    13  uniprotkb:P15806-1|intact:EBI-413581    uniprotkb:Q9JKN5|intact:EBI-1213712
    14  uniprotkb:P15806-1|intact:EBI-413581    uniprotkb:Q9EQW6|intact:EBI-1213740
    15  uniprotkb:P63280|intact:EBI-80180   uniprotkb:P15806-2|intact:EBI-413585

In the case of the interaction: uniprotkb:P63280/ uniprotkb:P15806 ,EBI-81370 appears in the field $21: Properties interactor B. But here I don't know what this property means.... :-/

	$1 #ID(s) interactor A : uniprotkb:P63280|intact:EBI-80180
	$2 ID(s) interactor B : uniprotkb:P15806-2|intact:EBI-413585
	$3 Alt. ID(s) interactor A : uniprotkb:Ubc9(gene name synonym)|uniprotkb:Ubce9(gene name synonym)|uniprotkb:Ubce2i(gene name synonym)|uniprotkb:Ubiquitin carrier prote
	in 9(gene name synonym)|uniprotkb:Ubiquitin-conjugating enzyme E2 I(gene name synonym)|uniprotkb:Ubiquitin-protein ligase I(gene name synonym)|uniprotkb:Ubiquitin carr
	ier protein I(gene name synonym)|uniprotkb:SUMO-protein ligase(gene name synonym)|uniprotkb:ubc9_mouse(shortlabel)|irefindex:0jkqEuU5j4CObv4J5Q8ApQapojc10090(rogid)
	$4 Alt. ID(s) interactor B : uniprotkb:Transcription factor 3(gene name synonym)|uniprotkb:Transcription factor A1(gene name synonym)|uniprotkb:Immunoglobulin enhancer
	-binding factor E12/E47(gene name synonym)|uniprotkb:Me2(gene name synonym)|uniprotkb:Tcfe2a(gene name synonym)|uniprotkb:Alf2(gene name synonym)|uniprotkb:p15806-2(sh
	ortlabel)|irefindex:m8nVMxqgm/YBNpKCgLUhxnt34ZQ10090(rogid)
	$5 Alias(es) interactor A : uniprotkb:Ube2i
	$6 Alias(es) interactor B : uniprotkb:Tcf3
	$7 Interaction detection method(s) : psi-mi:"MI:0018"(two hybrid)
	$8 Publication 1st author(s) : Loveys et al. (1997)
	$9 Publication Identifier(s) : pubmed:9409784
	$10 Taxid interactor A : taxid:10090(Mouse)
	$11 Taxid interactor B : taxid:10090(Mouse)
	$12 Interaction type(s) : psi-mi:"MI:0915"(physical association)
	$13 Source database(s) : psi-mi:"MI:0469"(IntAct)
	$14 Interaction identifier(s) : intact:EBI-1213460|irefindex:TLAGC+G1wHw6Y03Plz+CjRWrygQ(rigid)
	$15 Confidence value(s) : -
	$16 Experimental role(s) interactor A : psi-mi:"MI:0496"(bait)
	$17 Experimental role(s) interactor B : psi-mi:"MI:0498"(prey)
	$18 Biological role(s) interactor A : psi-mi:"MI:0499"(unspecified role)
	$19 Biological role(s) interactor B : psi-mi:"MI:0499"(unspecified role)
	$20 Properties interactor A : ipi:IPI00119227|refseq:NP_001171080.1|refseq:XP_001473151.1|refseq:NP_035795.1|refseq:NP_001171081.1|rcsb pdb:1U9B|rcsb pdb:1U9A|rcsb pdb
	:2UYZ|rcsb pdb:2VRR|interpro:IPR000608(Ubiquitin-conjugating enzyme, E2)|interpro:IPR016135(Ubiquitin-conjugating enzyme/RWD-like)|ensembl:ENSMUSG00000015120|go:"GO:00
	05737"(cytoplasm)|go:"GO:0043687"(post-translational protein modification)|go:"GO:0043398"(HLH domain binding)|go:"GO:0000122"(negative regulation of transcription fro
	m RNA polymerase II promoter)|go:"GO:0005524"(ATP binding)|go:"GO:0051246"(regulation of protein metabolic process)|go:"GO:0007275"(multicellular organismal developmen
	t)|go:"GO:0007067"(mitosis)|go:"GO:0044419"(interspecies interaction between organisms)|go:"GO:0007059"(chromosome segregation)|go:"GO:0051301"(cell division)|uniprotk
	b:Q86VB3(secondary-ac)|uniprotkb:Q6RUT3(secondary-ac)|uniprotkb:Q15698(secondary-ac)|uniprotkb:P50550(secondary-ac)|uniprotkb:P63280(identity)
	$21 Properties interactor B : intact:EBI-81370(tfe2_mouse)|uniprotkb:P15806-2(identity)
	$22 Type(s) interactor A : psi-mi:"MI:0326"(protein)
	$23 Type(s) interactor B : psi-mi:"MI:0326"(protein)
	$24 HostOrganism(s) : taxid:4932(Baker's yeast)
	$25 Expansion method(s) : -
	$26 Dataset name(s) : Cancer - Interactions investigated in the context of cancer
	$27 Annotation(s) interactor A : -
	$28 Annotation(s) interactor B : isoform-comment:"Phosphorylated on Thr-528 (By similarity)"
	$29 Parameter(s) interactor A : -
	$30 Parameter(s) interactor B : -
	$31 Parameter(s) interaction : -

view raw biostars-4666.txt hosted with ❤ by GitHub

[Pablo Pareja]

Hi Pierre,

That's what I thought first but then I came across some examples like this one in protein Q64279:

[?] [?] [?] [?]P15806[?] [?]Tcf3[?] [?] [?]false[?] [?]1[?] [?]

If you search for the interactant 'P15806' in intact db you get 8 interactions; however if you use its intactId 'EBI-81370' you get 14 results. It looks like they use the same intactId for both protein and its isoforms at least in this case...

Answer 3

[Raquel Tobes]

I think that all the information included in the section comments of a Uniprot entry are manual annotations. These curator annotations probably are a selection of the complete set of interactions collected for a specific entry (in this case for the entry Q9V3W6) in the database IntAct. There is a cross-reference to all these interactions in the section of cross-references entitled "Protein-protein interaction databases" (it is a link to the 8 interactions available at the IntAct database) in the Q9V3W6 Uniprot entry.

The manual annotations have not to be equal to the complete set of interactions available at the IntAct database.

In the comments content:

<interactant intactId="EBI-126914" />
<interactant intactId="EBI-213208">
  <id>P13607-1</id>
  <label>Atpalpha</label>
</interactant>

EBI-126914 is the ID of the entry Q9V3W6

EBI-213208 is the ID of the isoform P13607-1 (Sodium/potassium-transporting ATPase subunit alpha)

You can access to the data of the interaction between the two interactant proteins introducing at the Search box at the URL of IntAct:EBI-126914 AND EBI-213208

Answer 4

[Pablo Pareja]

First of all thanks for your answers.

Summing up it seems that intact-ids like 'EBI-213208' are unique identifiers for both proteins and isoforms. The main reason why I was confused was that when I performed some standard searches in the IntAct DB website the number of results I obtained differed depending on whether I used the intact-id or its supposably equivalent uniprot accession. However I've just checked what happens if I search for results specifying the advanced search field Participant Id and I get the same number of results using either of them.

So I guess that if you just use the standard search instead, you'll probably get as results every entry where the string provided is found, regardless of its position/meaning/etc.

We can see how in the example provided by Pierre there is an occurrence of the string provided in a property line #21. which by the way I do not know either what it means... :-|

Answer 5

[Jerven]

The intactid identifies a participant protein. While this may map to a single uniprot protein, in one case it might be expressed in a yeast hybrid experiment or in an experimental setting which can affect real biology. Also the mappings to UniProt sequences are best effort and not guaranteed to be correct for all experiments. For these reasons every interactor in intact has its own id.

Of course you should ask [e-mail] to find out exactly what it means.

[Pablo Pareja]

Thanks for your answer. I already ask at [e-mail] but didn't get any email back yet. I'll post whatever information they provide me as soon as I get it.