BioGRID Help and Support Resources

If you don't see an answer to your question listed here, please email us at: biogridadmin@gmail.com and we'll answer your question as quickly as possible. Please be advised that some of this information will change from month to month with our regular updates to our interaction data.

• A - Standard annotation data for search results including official name, aliases, synonyms, organism name, and description. The color surrounding the box (in this case navy blue) represents the organism and is different for each (in this case the blue represents the organism Saccharomyces cerevisiae).
• B - External links to 3rd party databases. These links generally point to model organism databases like SGD, MGI, FlyBase, etc. and also large genome resources such as Entrez-Gene and Ensembl.
• C - Gene Ontology summary for the search result. If you're interested in seeing the full details for this result you can click the “view list” link to expand the GO Summary into a list of mapped GO Entries.
• D - Click here to download a dataset consisting only of interactions listed on this search result page.
• E - A quick summary of the number of interactions represented in the current results. In this case there are 72 protein interactions and 374 genetic interactions listed.
• F - This drop down field, when present, allows you to switch the current view and look at the data in an alternate format.
• G - Experimental system, Role, and Publication listings for each interaction. These results are grouped together to form a non-redundant set of results. Interactions listed in Orange denote physical experimental systems and interactions listed in green denote genetic experimental systems. All results are ordered based on confidence in the experimental systems and the number of times the interaction has been reproduced.
• H - Annotation data for each of the resulting interactors with your search result. As above, the interface provides official names, aliases, descriptions, and Gene Ontology categories.
• I - Each interactor is hyperlinked to allow for circular searching. Simply click on the name and you will automatically pull up all curated interactions involving that particular gene, without having to redo your keyword searching.
• J - Sources show the first authors last name and the date in which the publication was published. You can click on these publications for more details and also to download a dataset of interactions reported by that publication.

BioGRID curators capture experimental evidence supporting interactions from the primary literature. Our aim is to curate all interactions in the literature for major model organisms, and selective topic-driven human datasets. Interactions reported in reviews or as unpublished data are not recorded. The BioGRID curation workflow can be viewed here.

BioGRID uses gene identifiers to describe all biological interactors. For each experiment supporting a particular interaction, the interacting partners are recorded as a pair of gene identifiers. For physical interaction evidence this means that the article describes an experiment which supports an interaction between a product of the bait gene and a product of the prey (hit) gene. Genetic interaction evidence codes record experiments where the phenotypes of two strains, each having a perturbation of one of the interacting genes, are compared with the phenotype of a strain with both genes perturbed. Self-interactions are recorded, as are reciprocal interactions if the bait-prey directionality is clear. To expedite curation we record interactors, experimental evidence codes and pubmed ids but not other potentially useful information such as splice variants, wild type strain background, mutations, specific interaction domains or subcellular localization.

BioGRID interactions are recorded as relationships between two proteins or genes (i.e. they are binary relationships) with an evidence code that supports the interaction and a publication reference. The term “interaction” includes, as well as direct physical binding of two proteins, co-existence in a stable complex and genetic interaction. It should not be assumed that the interaction reported in BioGRID is direct and physical in nature; the experimental system definitions below indicate the nature of the supporting evidence for an interaction between the two biological entities. It should also be noted that some interactions in BioGRID have various levels of evidential support. BioGRID simply curates the result of the experiment from the publication and we do not guarantee that any individual interaction is true, well-established or the current consensus view of the community. Curating all available evidence supporting for an interaction enables orthogonal data from various sources to be collated, allowing users of the database to decide confidence in the existence and/or physiological relevance of that interaction.

Interactions are recorded under the experimental systems described below:

Affinity Capture-Luminescence - An interaction is inferred when a bait protein, tagged with luciferase, is enzymatically detected in immunoprecipitates of the prey protein as light emission. The prey protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag.

Affinity Capture-MS - An interaction is inferred when a “bait” protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.

Affinity Capture-RNA - An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and associated RNA species identified by Northern blot, RT-PCR, affinity labeling, sequencing, or microarray analysis.

Affinity Capture-Western - An interaction is inferred when a Bait protein affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner identified by Western blot with a specific polyclonal antibody or second epitope tag. This category is also used if an interacting protein is visualized directly by dye stain or radioactivity. Note that this differs from any co-purification experiment involving affinity capture in that the co-purification experiment involves at least one extra purification step to get rid of potential contaminating proteins.

Biochemical Activity - An interaction is inferred from the biochemical effect of one protein upon another, for example, GTP-GDP exchange activity or phosphorylation of a substrate by a kinase. The “bait” protein executes the activity on the substrate “hit” protein.

Co-crystal Structure - Interaction directly demonstrated at the atomic level by X-ray crystallography. Also used for NMR or Electron Microscopy (EM) structures. If a structure is demonstrated between 3 or more proteins, one is chosen as the bait and binary interactions are recorded between that protein and the others.

Co-fractionation - Interaction inferred from the presence of two or more protein subunits in a partially purified protein preparation. If co-fractionation is demonstrated between 3 or more proteins, one is chosen as the bait and binary interactions are recorded between that protein and the others.

Co-localization - An interaction is inferred from co-localization of two proteins in the cell, including co-dependent association of proteins with promoter DNA in chromatin immunoprecipitation experiments.

Co-purification - An interaction is inferred from the identification of two or more protein subunits in a purified protein complex, as obtained by classical biochemical fractionation or affinity purification and one or more additional fractionation steps.

Far Western - An interaction is detected between a protein immobilized on a membrane and a purified protein probe.

FRET - An interaction is inferred when close proximity of interaction partners is detected by fluorescence resonance energy transfer between pairs of fluorophore-labeled molecules, such as occurs between CFP (donor) and YFP (acceptor) fusion proteins.

PCA - A protein-protein interaction assay in which a bait protein is expressed as fusion to one of the either N- or C- terminal peptide fragments of a reporter protein and prey protein is expressed as fusion to the complementary N- or C- terminal fragment of the same reporter protein. Interaction of bait and prey proteins bring together complementary fragments, which can then fold into an active reporter.

Protein-peptide - An interaction is detected between a protein and a peptide derived from an interaction partner. This includes phage display experiments.

Protein-RNA - An interaction is detected between and protein and an RNA.

Reconstituted Complex - An interaction is detected between purified proteins in vitro.

Two-hybrid - Bait protein expressed as a DNA binding domain (DBD) fusion and prey expressed as a transcriptional activation domain (TAD) fusion and interaction measured by reporter gene activation.

Dosage Growth Defect - A genetic interaction is inferred when over expression or increased dosage of one gene causes a growth defect in a strain that is mutated or deleted for another gene.

Dosage Lethality - A genetic interaction is inferred when over expression or increased dosage of one gene causes lethality in a strain that is mutated or deleted for another gene.

Dosage Rescue - A genetic interaction is inferred when over expression or increased dosage of one gene rescues the lethality or growth defect of a strain that is mutated or deleted for another gene.

Negative Genetic - Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a more severe fitness defect or lethality under a given condition.

Phenotypic Enhancement - A genetic interaction is inferred when mutation or overexpression of one gene results in enhancement of any phenotype (other than lethality/growth defect) associated with mutation or over expression of another gene.

Phenotypic Suppression - A genetic interaction is inferred when mutation or over expression of one gene results in suppression of any phenotype (other than lethality/growth defect) associated with mutation or over expression of another gene.

Positive Genetic - Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a less severe fitness defect than expected under a given condition.

Synthetic Growth Defect - A genetic interaction is inferred when mutations in separate genes, each of which alone causes a minimal phenotype, result in a significant growth defect under a given condition when combined in the same cell.

Synthetic Haploinsufficiency - A genetic interaction is inferred when mutations or deletions in separate genes, at least one of which is hemizygous, cause a minimal phenotype alone but result in lethality when combined in the same cell under a given condition.

Synthetic Lethality - A genetic interaction is inferred when mutations or deletions in separate genes, each of which alone causes a minimal phenotype, result in lethality when combined in the same cell under a given condition.

Synthetic Rescue - A genetic interaction is inferred when mutations or deletions of one gene rescues the lethality or growth defect of a strain mutated or deleted for another gene.

As well as small-scale curated experiments, BioGRID contains data from papers reporting high throughput screens. Since the experimental setup of high throughput screens for interactions can be adjusted to give variable numbers of “hits”, it is common for publications to report a confidence score for each interaction. Before loading any high throughput data into BioGRID the data is assessed and interactions considered low confidence by the authors are not loaded. Generally, the confidence score used by the author is loaded, and on BioGRID gene pages containing interactions from that publication the scores can be displayed by choosing the publication from the “Displaying:” drop-down list. In addition, the number of interactions in BioGRID for each publication is displayed next to that publication.

While we do support a wide variety of identifiers, our goal of limiting redundancy in our search results means that several large sequence databases such as Genbank and Ensembl do not have all their ID's available in the BioGRID. With each annotation update, our coverage increases by hundreds of thousands of new identifiers so please be patient if your ID is not currently supported. If you have a suggestion for a new identifier type, please let us know at biogridadmin@gmail.com.

The following is a listing of our currently supported identifiers: The BioGRID Database Seperator CDNA Accession, CDNA GI, ECOCYC, EcoGene, Ensembl, ENTREZ_GENE, FLYBASE, HGNC, HPRD, IMGT/GENE-DB, Locus Tag, MGD, MGI, MIM, Official Symbol, PROTEIN Accession, PROTEIN GI, RATMAP, RGD, SGD, Synonym, TAIR, UNIPROTKB, WormBase, Xenbase, ZFIN

The following are some suggestions that may help you find what you're looking for if you're having trouble searching:

• Don't use ambiguous names. When possible, search for unique identifiers or systematic names. Many identifiers across the different species are duplicated, and as a result, may not uniquely identify a specific record. The more unique the identifier, the better your chance of getting a direct hit on searches.
• Try being less specific. For example, if you searched for STE11, try searching for STE and see if more results are returned.
• If you are searching with “ALL ORGANISMS” selected, try being more specific and choosing your organism of interest like Saccharomyces cerevisiae or Homo sapiens. Our search engine always attempt to make a direct match first, before using wild cards so, if you search for KSS for example, you may get KSS in Human when you were really after KSS1 in Yeast. Setting the organism to Saccharomyces cerevisae, however, will result in the yeast hit only.
• Make sure you are using the correct spelling. Sounds simple, but sometimes even the publication's use the incorrect spellings.
• Make sure and use the most common identifier when possible. Many genes have multiple synonyms but using the most common one is your best bet to find a hit.

The PSI MI format is a means of exchanging data on molecular interactions, maintained by the HUPO Proteomics Standards Initiative. For a diagram of the PSI 2.5 XML schema click here . BioGRID interactions are annotated with the terms described in the Evidence Codes section above to distinguish between different types of evidence supporting an interaction. The BioGRID PSI MI 2.5 XML files primarily contain MI ontology terms to describe experimental methods and other interaction details; please see the BioGRID/MI mapping file which explains how the MI terms in the BioGRID PSI MI XML file were chosen.

The original BioGRID evidence code used for the annotation can also be found in the PSI MI XML file in the entrySet/entry/interactionList/interaction/attributeList/attribute XML tag with attribute name = “BioGRID Evidence Code”.

BioGRID is released monthly, the release date can be found in the entrySet/entry/source XML tag, in the attribute “releaseDate”.

Interaction IDs found in the entrySet/entry/interactionList/interaction XML tag as an XML attribute are a references which are meaningful only within the XML file. BioGRID interaction IDs which are found in the entrySet/entry/interactionList/interaction/xref/primaryRef XML tag are created when an interaction is curated (an interaction here being an interaction demonstrated between a pair of interactors with one evidence code in one publication). References to experiments used to support the interaction can be found in the entrySet/entry/interactionList/interaction/experimentList/experimentRef XML tag and the XML elements representing the experiments can be found in entrySet/entry/experimentList/experimentDescription.

References to XML elements for the interactors can be found in entrySet/entry/interactionList/interaction/participantList/participant/interactorRef, and the XML elements representing the interactors can be found in entrySet/entry/interactorList/interactor. Details of the interactor's role in the experiment are found in the following XML tags: entrySet/entry/interactionList/interaction/participantList/participant/participantIdentificationMethodList/participantIdentificationMethod, entrySet/entry/interactionList/interaction/participantList/participant/biologicalRole, entrySet/entry/interactionList/interaction/participantList/participant/experimentalRoleList/experimentalRole.

These are expressed in PSI MI terms mapped from BioGRID terms according to the BioGRID/MI mapping file.

Each experiment contains a reference to the publication (entrySet/entry/experimentList/experimentDescription/bibref), the host organism used in the experiment (entrySet/entry/experimentList/experimentDescription/hostOrganismList/hostOrganism) and interaction detection method (entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod). Interaction detection methods are given according to MI terms chosen using a mapping from BioGRID experimental codes. The original BioGRID evidence code can be found in entrySet/entry/interactionList/interaction/attributeList/attribute.

Curation of all interactors in BioGRID are by reference to Entrez Gene identifiers. However, to allow maximum integration with other interaction databases which also use the PSI MI format the primaryRef of interactors in this XML file is a protein RefSeq ID the primaryXref(entrySet/entry/interactorList/interactor/xref/primaryRef), with the exception of interactors having multiple protein RefSeq IDs. Therefore, if the curated Entrez Gene ID has only one protein RefSeq, that RefSeq ID will be present as a primaryRef and the Entrez Gene ID will be present as a secondaryRef. If the curated Entrez Gene ID has multiple protein RefSeqs, those RefSeq IDs will be present as secondaryRefs and the Entrez Gene ID will be present as the primaryRef. Any curation referencing discontinued Entrez Gene IDs are re-pointed to the appropriate new ID, if possible, and the original ID used for annotation is listed as a secondaryRef; if a discontinued Entrez Gene ID is used as a primaryRef, an annotation can be found in the entrySet/entry/interactorList/interactor/xref/primaryRef/attributeList/attribute XML tag, with XML attribute name =“Discontinued” and contents “This interactor record has been discontinued in its source database”. The release date of the Entrez Gene data used to build the XML file can be found in the entrySet/entry/attributeList/attribute XML tag, with attribute name=”based on entrez gene downloaded on”.