IntAct

IntAct Logo
Please wait...
loading   Loading...
What is this view?

Binary interactions

In this tab, we display the list of interactions that you have selected using one of our search features. Despite the fact that our data are annotated to accurately reflect the interactions reported in scientific literature, the data is shown in this view as binary interactions. Whenever the data was reported as a co-complex involving more than two molecules, we store it as such in the IntAct database and post-process it so the portal can show it as binary interaction. This post-processing is the Spoke Expansion model (connects bait to all preys):



sourceExp

At any moment you can choose to display the expansion column in this view in order to see which interaction are spoke expanded and which are not.

Description of what has changed

  • We have added more download options to allow users to retrieve their interaction set using more standard formats such as PSI-MI XML and PSIMITAB (version 2.5, 2.6 or 2.7) but also XGMML, RDF and Biopax (level 2 and 3).
  • We have now four different table views : minimal(molecule names and interaction AC), basic (minimal + molecule links, interaction detection method, negative), standard(minimal + molecule species, confidences, publication details, experiment details), expanded (standard + more experiment details) and complete (all mitab 2.7 columns).

Configuring the view to your need"

In the header of the interaction table you will find a button: ‘Change Column Display’ that will show you all the columns/Table views available and allow you to update the current selected set.

Downloading the data into Standard formats"

In the header of the interaction table you will find a drop down list that contains all the formats currently supported when downloading the interaction data. Select one of them and click the export button next to the list. Please note that PSI-MI XML is only available when the interaction set is no bigger than 1000 interactions.

Opening the interaction details"

Clicking on the magnifying glass in the first column of the interaction table will open the details of the corresponding interaction in the Interaction Details tab, giving you access to more details of the manually curated record.
What is this view?

Browsing (Browse Tab)

This tab is meant to give you access to more content based on the currently selected set of interactions. As you can see, in this tab we have grouped features under the interacting molecule types. Please note that some of these functionalities will only allow you to include up to 200 molecules , if you exceed this number you will see the warning icon (This number has been reduced to 125 molecules for mRNA expression). Now let’s look at the features available to you:

Listing the molecules involved by specific type

Clicking on the ‘List All’ present under each molecule type will open the corresponding list of molecule in the List Tab.

Limiting the scope of the current dataset with the Uniprot Taxonomy ontology

Allows users to browse the Uniprot Taxonomy hierarchy as a tree and select terms in order to narrow down their dataset. Once a term is selected, you are taken back to the interaction tab to review your dataset.

Limiting the scope of the current dataset with the GO ontology

Allows users to browse the GO hierarchy as a tree and select terms in order to narrow down their dataset. Once a term is selected, you are taken back to the interaction tab to review your dataset.

Limiting the scope of the current dataset with the ChEBI ontology

Allows users to browse the ChEBI hierarchy as a tree and select terms in order to narrow down their dataset. Once a term is selected, you are taken back to the interaction tab to review your dataset.

Bulk linking to third party resources by using involved proteins

  • Proteins by Reactome pathway: Sends your proteins to the Reactome SkyPainter that will show you the pathways in which these molecules are know to play a role.
  • Proteins by Chromosomal location: Sends your list of proteins to Ensembl’s Karyotype viewer and overlays the proteins on the chromosomes.
  • Proteins by mRNA expression: Sends your set of proteins to the ArrayExpress Atlas that will show the known gene expression based on experimental studies.
What is this view?

Searching Interactions (Search Tab)

As you can see in this tab we are now trying to give you more targeted choice to do your queries, please note that the examples provided in this tab are live links so you can simply click them to see the resulting interactions sets.

Using the Quick Search

In this search panel you are free to type anything that might relate to interactions, whether it is properties of their interactor (gene name, identifiers, GO term…) or more specific to the interaction like publication, authors, experimental detection method, ...

Some examples:

  • Try the query: imatinib
    This is a drug for which we have curated a number of interactions.
    Once you press the search button you should be taken to the Interaction Tab that lists 130 binary interactions.
    If you want to construct more complex queries we recommend you take a look at the Molecular Interaction Query Language, accessible from the quick search panel.
  • Try the query: species:yeast AND type:"direct interaction"
    This query selects all interactions involving yeast interactors that have been shown to have direct interactions. If you customize the column display of the interaction tab, you will see that not only “direct interaction” have been selected but also children terms in the PSI-MI ontology.

Using the Ontology Search

Open the Rearch Tab. This panel is specialised to give you an easy access to ontology search. So far you can search on 4 ontologies:
  • Gene Ontology
  • InterPro
  • PSI-MI
  • ChEBI

Whenever you start typing a query in this search panel, the system will search as you type and propose a list of matching controlled vocabulary terms. You can then select one of them and select matching interactions.

For example, type: cancer
You will be presented with a few choices, please note that each term is followed by the count of matching interactions in the IntAct database.

Select a term with the mouse or using the keyboard cursor keys and you will be taken to the interaction tab.

Searching the Compound chemical structure

In this panel you will be able to draw all or part of a chemical structure and search for chemical compounds. If you get any matched, you can then see all interactions involving them.

First you have to open up the chemical search panel so that the applet can load, it might take a few seconds. Then you can start drawing your structure, for instance:

Once you have drawn your structure, select Similarity and press Search. You should be presented with a list of matching compound. Now choose one molecule and click the link: IntAct interactions. You will be taken to the interaction tab to review the data.

Complex Expansion

Binary interactions generated by co-complex expansion

Why should you care about complex expansion ?

Some experimental methods such as Tandem Affinity Purification do generate molecular interactions that can involve more than 2 molecules. Despite the fact that IntAct curation team do capture the molecular interaction as they were reported in the corresponding experiment, when you search using the intact web site, the results of your query is always shown as set of binary interactions (i.e. 2 molecules). We would like to draw your attention on the fact that whenever the reported interaction was a co-complex we do apply an expansion algorithm that transform this n-ary interaction into a set of binary interactions. While none of these agorithms is perfect and will very likely generate some false positive interactions, it is useful to present the data in a consistent manner. Bear in mind that we will strive to differentiate in the search results which interactions are a real experimental binary from expanded ones.

Existing expansion algorithm

There are several known algorithm allowing to transform an n-ary interaction into a set of binaries. The illustration below present the two well known expansion model and illustrates why they can be incorrect.

sourceExp

  • Spoke expansion: Links the bait molecule to all prey molecules. If N is the count of molecule in the complex, it generated N-1 binary interactions.
  • Matrix expansion: Links all molecule to all other molecule present in the complex. If N is the count of molecule in the complex, it generated (N*(N-1))/2 binary interactions.

Now the issue (as illustrated at the bottom right of the diagram above) with these two models lies in the fact that the real complex might not be articulated around the experimental bait but instead, this bait might be linked to a smaller complex, hence most binary interaction generated by spoke and matrix expansion result in false positive.

PSICQUIC

How is the number of interactions in other databases obtained?

PSICQUIC is a standard way to access molecular interaction databases across which it repeats the same query. The number of databases providing data may vary, depending on the status of their services and only those that are active are used in this query. By clicking on the number of interactions you will be redirected to the PSICQUIC View, where you can browse the results in those other resources.

The services currently active are:

Check the PSICQUIC site for more information.

Biological Complexes

How is the number of biological complexes in IntAct obtained?

The IntAct Complex Portal is is a manually curate, encyclopaedic resource of macromolecular complexes from a number of key model organisms. All data is freely available for search and download.

Check the Complex Portal Documentation for more information.

IMEx

What is the significance of the IMEx dataset?"

IMEx is a network of databases which have agreed to supply a non-redundant set of data expertly manually annotated to the same consistent detailed standard which, as such, represents a high-quality subset of the data each individually provides. The number of databases providing data may vary, depending on the status of their services and only those that are active are used in this query. By clicking on the number of interactions you will be redirected to the IMEx View, where you can browse the results in those other resources.

The services currently active are:

Check the IMEx site for more information.

What is this view?

Representation of Experimental Features

This section shows the graphical representation of experimental features, where each participant is represented as a white rectangle with a black border and a line for each hundredth amino acid. All available features are attached to their associated participant and their categories are represented in the right side of the legend. The left side of the legend dynamically shows the range statuses occuring in the shown interaction. These are the possible range statuses:

sourceExp

Interacting with the widget

Hover over a feature to see more information in a tooltip.
sourceExp

To display a single interacting region click on it and click again to display all interacting regions.
Displaying all interacting regionsDisplaying one interacting region
sourceExpsourceExp
What is this view?

Dynamic molecular interaction data

This section shows the graphical representation of dynamic molecular interactions. By default it displays all the interactions from one experiment using radio buttons to allow users to highlight interactions in different variable conditions.
spacer

v.4.1.3



MIQL Syntax Reference

Help: Searches in IntAct

To do a search you can use the Molecular Interaction Query Language (MIQL), which is based on Lucene's syntax.
  • Search based on exact word matches.
    • BRCA2 will not match BRCA2B
    • Association will retrieve both physical association and association
    • To retrieve all isoforms of P12345, use P12345*
  • Search will recognize ontologies and synonyms.
    • Eukaryota will retrieve all children of Eukaryota using the Uniprot taxonomy
    • affinity techniques will match affinity technology because it is affinity techniques is a synonym of affinity technology in the PSI-MI ontology
  • Default fields are used when no field is specified (simple search) :
    • Interactor id, alias
    • Interactor species
    • Interaction id
    • Publication id, first author
    • Interaction type
    • Interaction detection method
    • Interactor xrefs (GO, uniprot secondary xrefs, ...)
    • Interaction xrefs (GO, ...)
    .
    For instance, if you put 'P12345' in the simple query box, this will mean the same as identifier:P12345 OR pubid:P12345 OR pubauth:P12345 OR species:P12345 OR type:P12345 OR detmethod:P12345 OR interaction_id:P12345
  • Use OR or space ' ' to search for ANY of the terms in a field
  • Use AND if you want to search for those interactions where ALL of your terms are found
  • Use quotes (") if you look for a specific phrase (group of terms that must be searched together) or terms containing special characters that may otherwise be interpreted by our query engine (eg. ':' in a GO term)
  • Use parenthesis for complex queries (e.g. '(XXX OR YYY) AND ZZZ')
  • Wildcards (*,?) can be used between letters in a term or at the end of terms to do fuzzy queries,
    but never at the beginning of a term
  • Optionally, you can prepend a symbol in from of your term.
    • + (plus): include this term. Equivalent to AND. e.g. +P12345
    • - (minus): do not include this term. Equivalent to NOT. e.g. -P12345
    • Nothing in front of the term. Equivalent to OR. e.g. P12345

MIQL fields

You can find more information about the Molecular Interactions Query Language (MIQL) defined for PSICQUIC Here
Field NameSearches onExample
idAIdentifier AidA:P74565
idBIdentifier BidB:P74565
idIdentifiers (A or B)id:P74565
aliasAliases (A or B)alias:(KHDRBS1 OR HCK)
identifiersIdentifiers and Aliases undistinctivelyidentifier:P74565
pubauthPublication 1st author(s)pubauth:scott
pubidPublication Identifier(s)pubid:(10837477 OR 12029088)
taxidATax ID interactor A: be it the tax ID or the species nametaxidA:mouse
taxidBTax ID interactor B: be it the tax ID or species nametaxidB:9606
speciesSpecies. Tax ID A or Tax ID Bspecies:human
typeInteraction type(s)type:"physical interaction"
detmethodInteraction Detection method(s)detmethod:"two hybrid*"
interaction_idInteraction identifier(s)interaction_id:EBI-761050
pbioroleABiological role(s) interactor ApbioroleA:enzyme
pbioroleBBiological role(s) interactor BpbioroleB:enzyme
pbioroleBiological role(s) interactor (A or B)pbiorole:enzyme
ptypeAInteractor type AptypeA:protein
ptypeBInteractor type BptypeB:protein
ptypeInteractor type (A or B)ptype:protein
pxrefAInteractor xref ApxrefA:"GO:0005794"
pxrefBInteractor xref BpxrefB:"GO:0005794"
pxrefInteractor xref (A or B)pxref:"GO:0005794"
xrefInteraction xref(s)xref:"GO:0005634"
annotAnnotations/Tags Interactionannotation:"imex curation"
udateLast update of the interactionudate:[20110607 TO 20120906]
negativeBoolean value which is true if an interaction is negativenegative:true
complexComplex Expansion method(s)expansion:spoke
ftypeAFeature type(s) AftypeA:"binding site"
ftypeBFeature type(s) BftypeB:"binding site"
ftypeFeature type(s) (A or B)ftype:"binding site"
pmethodAParticipant identification method(s) ApmethodA:"western blot"
pmethodBParticipant identification method(s)) BpmethodB:"western blot"
pmethodParticipant identification method(s) (A or B)pmethod:"western blot"
stcBoolean value to know if Interactor A or B has stoichiometry information.stc:true
paramBoolean value to know if the Interaction has some parameters.param:true

IntAct fields

These field names are specific to IntAct and are not in MIQL definition for PSICQUIC.
Field NameSearches onExample
geneNameGene name for Interactor A or BgeneName:brca2
sourceSource database(s)source:mbinfo
intact-miscoreIntAct MI Score (between 0 and 1), based on number of publications, detection methods and interaction types.intact-miscore:[0.5 TO 1.0]
Search:       Show Advanced Fields »   MIQL syntax reference helpIcon
  • Free text search will look by default for interactor identifier, species, interaction id, detection method, interaction type, publication identifier or author, interactor xrefs, interaction xrefs
  • For a more specific search, use MIQL syntax or advanced search
  • Search based on exact word matches eg. BRCA2 will not match BRCA2B
  • Search for isoforms of 'P12345' by using 'P12345*'
Examples

Publication

Author List: Tang Y., Zhao W., Chen Y., Zhao Y., Gu W.
Journal: Cell (0092-8674)
Year of Publication: 2008
PubMed Id: 18485870
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
Annotations:
Topic
Text
Cancer - Interactions investigated in the context of cancer
Apoptosis - Interactions involving proteins with a function related to apoptosis

Experiment (5 interactions)

Accession: EBI-1799558
Name: tang-2008a-3
Host organism: Homo sapiens lung lymph node carcinoma
Organism: Homo sapiens lung lymph node carcinoma
Accession: EBI-399612

Name: human-h1299

Description: Homo sapiens lung lymph node carcinoma

Cross References:
Database
Identifier
Secondary identifier
Qualifier
human

Annotations:
Topic
Text
ATCC number of the cell line is CRL-5803.
Interaction Detection Method: ch-ip
Interaction detection method: ch-ip
Accession: EBI-705656
Name: ch-ip
Description: chromatin immunoprecipitation assay
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
Annotations:
Topic
Text
Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. An antibody against a protein suspected of binding a given cis-element is used to immunoprecipitate fragmented chromatin fragments. Cells or tissue may first be briefly treated with an agent such formaldehyde to crosslink proteins to DNA. Nucleic acids are then identified by sequencing, for example polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element or next-generation sequencing techniques
Participant Identification Method: primer specific pcr
Participant identification method: primer specific pcr
Accession: EBI-967
Name: primer specific pcr
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
Annotations:
Topic
Text
Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs.
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
Annotations:
Topic
Text
wg8@columbia.edu
Source of p53 taken from PMID: 17189186, ep300 from PMID: 17189186 and inferred by sequence length, CBP from PMID: 9194564 and inferred from sequence length.
Only protein-protein interactions
-
7
imex curation

Interaction

Accession: EBI-1799733
Name: p53-mdm2-3
Description: Binding of TP53 and MDM2 to the CDKN1A (p21) promoter
Type: association
Interaction type: association
Accession: EBI-1813191
Name: association
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
Annotations:
Topic
Text
Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait.
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
Annotations:
Topic
Text
P04637; Q00987 transfection
Mdm2 was only present in the complex when K120, K164, K370, K372, K373, K381, K382, and K386 were all mutated to alanine, preventing acetylation suggesting that TP53 acetylation represses recruitment of MDM2 to the CDKN1A promoter. Mdm2 recruitment at the p21 promoter was strongly repressed upon treatment with the DNA-damaging reagent actinomycin D which correlated with the acetylation levels of wild-type p53
Fig. 4A, 4C, 6D

Participants (3)

#
Name
Links
Primary Identifier
Aliases
Description
Species
Expression system
Experimental role
Biological role
Interactor type
More...
1
EBI-366083
 logo
dastyLogo
TP53
P53
Tumor suppressor p53

[+2]
Cellular tumor antigen p53
Homo sapiens
Organism Details
Accession: EBI-874

Name: human

Description: Homo sapiens

Cross References:
Database
Identifier
Secondary identifier
Qualifier
human

Expressed In Details
Accession:

Name:



-
bait
Experimental role: bait
Accession: EBI-49
Name: bait
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
Annotations:
Topic
Text
Molecule experimentally treated to capture its interacting partners.
unspecified role
Biological role: unspecified role
Accession: EBI-77781
Name: unspecified role
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
Annotations:
Topic
Text
Role not specified or not applicable to the data.
protein
Interactor type: protein
Accession: EBI-619654
Name: protein
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
-
Annotations:
Topic
Text
A linear polymer of amino acids joined by peptide bonds in a specific sequence.
Participant: Cellular tumor antigen p53

Participant: Cellular tumor antigen p53

Accession: EBI-1799739

Name: EBI-366083


A
Participant: Cellular tumor antigen p53

Participant: Cellular tumor antigen p53

Accession: EBI-1799739

Name: EBI-366083

Parameters:
Type
Value
Unit
Base
Exponent
Uncertainty
No records found.
P

Participant: Cellular tumor antigen p53

Participant: Cellular tumor antigen p53

Accession: EBI-1799739

Name: EBI-366083

Stoichiometry: 0.0
S
Participant: Cellular tumor antigen p53

Participant: Cellular tumor antigen p53

Accession: EBI-1799739

Name: EBI-366083

Features:

F
Participant: Cellular tumor antigen p53

Participant: Cellular tumor antigen p53

Accession: EBI-1799739

Name: EBI-366083

Confidences:
Type
Value
No records found.
C
2
EBI-1799539
CDKN1A promoter region - sequence unspecified
Homo sapiens
Organism Details
Accession: EBI-874

Name: human

Description: Homo sapiens

Cross References:
Database
Identifier
Secondary identifier
Qualifier
human

Expressed In Details
Accession:

Name:



-
prey
Experimental role: prey
Accession: EBI-58
Name: prey
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
Annotations:
Topic
Text
Molecule experimentally identified as being captured by a given bait.
unspecified role
Biological role: unspecified role
Accession: EBI-77781
Name: unspecified role
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
Annotations:
Topic
Text
Role not specified or not applicable to the data.
dna
Interactor type: dna
Accession: EBI-619647
Name: dna
Description: deoxyribonucleic acid
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
-
Annotations:
Topic
Text
Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine.
Participant: CDKN1A promoter region - sequence unspecified

Participant: CDKN1A promoter region - sequence unspecified

Accession: EBI-1799737

Name: EBI-1799539


A
Participant: CDKN1A promoter region - sequence unspecified

Participant: CDKN1A promoter region - sequence unspecified

Accession: EBI-1799737

Name: EBI-1799539

Parameters:
Type
Value
Unit
Base
Exponent
Uncertainty
No records found.
P

Participant: CDKN1A promoter region - sequence unspecified

Participant: CDKN1A promoter region - sequence unspecified

Accession: EBI-1799737

Name: EBI-1799539

Stoichiometry: 0.0
S
Participant: CDKN1A promoter region - sequence unspecified

Participant: CDKN1A promoter region - sequence unspecified

Accession: EBI-1799737

Name: EBI-1799539

Features:

F
Participant: CDKN1A promoter region - sequence unspecified

Participant: CDKN1A promoter region - sequence unspecified

Accession: EBI-1799737

Name: EBI-1799539

Confidences:
Type
Value
No records found.
C
3
EBI-389668
 logo
dastyLogo
MDM2
p53-binding protein Mdm2
Oncoprotein Mdm2

[+1]
E3 ubiquitin-protein ligase Mdm2
Homo sapiens
Organism Details
Accession: EBI-874

Name: human

Description: Homo sapiens

Cross References:
Database
Identifier
Secondary identifier
Qualifier
human

Expressed In Details
Accession:

Name:



-
prey
Experimental role: prey
Accession: EBI-58
Name: prey
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
Annotations:
Topic
Text
Molecule experimentally identified as being captured by a given bait.
unspecified role
Biological role: unspecified role
Accession: EBI-77781
Name: unspecified role
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
Annotations:
Topic
Text
Role not specified or not applicable to the data.
protein
Interactor type: protein
Accession: EBI-619654
Name: protein
Cross References:
Database
Identifier
Secondary identifier
Qualifier
-
-
-
Annotations:
Topic
Text
A linear polymer of amino acids joined by peptide bonds in a specific sequence.
Participant: E3 ubiquitin-protein ligase Mdm2

Participant: E3 ubiquitin-protein ligase Mdm2

Accession: EBI-1799738

Name: EBI-389668


A
Participant: E3 ubiquitin-protein ligase Mdm2

Participant: E3 ubiquitin-protein ligase Mdm2

Accession: EBI-1799738

Name: EBI-389668

Parameters:
Type
Value
Unit
Base
Exponent
Uncertainty
No records found.
P

Participant: E3 ubiquitin-protein ligase Mdm2

Participant: E3 ubiquitin-protein ligase Mdm2

Accession: EBI-1799738

Name: EBI-389668

Stoichiometry: 0.0
S
Participant: E3 ubiquitin-protein ligase Mdm2

Participant: E3 ubiquitin-protein ligase Mdm2

Accession: EBI-1799738

Name: EBI-389668

Features:

F
Participant: E3 ubiquitin-protein ligase Mdm2

Participant: E3 ubiquitin-protein ligase Mdm2

Accession: EBI-1799738

Name: EBI-389668

Confidences:
Type
Value
No records found.
C

Legend:
A
Annotation and Cross Reference  
P
Experimental Parameter   
S
Stoichiometry   
F
Experimental Feature
C
Participant Confidence