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General

You can search by interaction filters (facets) or any field alone, or together in any combination.
The General Query field is similar to a Google search in that it accepts plus and minus operators before terms. For example a search that must match cancer, but must not match tumor:
+cancer -tumor
The Organism filter has an auto-complete input field that you can use to find and enter an organism name not explicitly listed above it. Select the Show Custom Ranges & Distribution Links to view and use this option.

Downloading Your Interactome

The file formats available for download are:
- as MITAB where first line of the file provides the column headers.
- as list of interaction ids for use in OrthoNets.
Interactions that are supported by evidence only from DIP and HPRD will be excluded from your download. There should be sufficient overlap with public databases in most cases to still provide you with a reasonable set of records.
Should your results contain complexes, they will be expanded into binary records.
Because in some cases records maybe excluded (private databases), and in other cases expanded (complexes), the number of lines in the file will not necessarily be exactly the same as the number interactions that matched your search.

Filters

The Interaction Evidence Filters, even if unselected, tell you just how your search results are distributed across various aspects of an interaction. The number of interactions that match a particular filter item with respect to the current query are displayed in parenthesis beside each item:
Physical or Genetic Interaction > physical interaction (162)
As you refine your search these numbers will change to reflect the other filters selected and/or your search terms.
The filters with radio buttons, when selected are the same as saying the interaction must match.
The filters with check boxes implies must at least match. Thus selecting several items in the same filter means an interaction must at least match one of the selctions; for instance using the Source Database filter and selecting bind, biogrid, and hprd means an interaction must be annotated by at least one of bind or biogrid or hprd.
An interaction can be multi-valued with respect to a filter. For example an interaction can be supported by evidence from several source databases, so it contributes to the match count of each those databases.
Select the Show Custom Ranges & Distribution Links to set your own range for numeric filters.

Obtaining the Complete Data Set

If you wish to have the entire data set, please visit iRefIndex.

Search Results Table

The columns of the search results table, from left to right are:

The interaction id -- click on the number to view that interaction's details.
The interacting proteins, if the interaction is binary. The proteins are coloured by their organism.
The number of proteins in the interaction.*
The number of PubMeds that support the interaction.*
LPR and HPR: Lowest and Highest PubMed Re-use. A publication may be used to support more than one interaction. These scores are the lowest and highest number of unique interactions that are supported by one of the interaction's PMIDs. This can be read as rough measure of 'throughput'. For more information, see the FAQ.*
The number of source databases that annotated the interaction.*
The total number of records (evidence) from all source databases for this interaction.*

* Starred items indicate a sortable column. The cells in these columns are coloured according to their value relative to the whole range of possible values, from red (minimum) to green (maximum).

Search Result Summary Jump to Results

404384 interaction(s) — showing 1 to 20

Page(s): 12 3 4 5 6 7 8 9 10..20220 Next

Search Query

General Query: (Full Text / All Fields)

PubMed ID

Protein Alias

Entrez Gene ID
- Upload file
- Paste list

Your search can consist either of search terms entered in the fields above, the search filters below, or both.

Upload List of Gene IDs

Interaction Evidence Filters - Collapse Filters + Show Custom Ranges & Distribution Links

Search Results Back to Top of Page

Table Legend
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Page: 12 3 4..20220 ›
Results per page.

Intrctn ID	Interacting Proteins		# of Proteins	Number of PubMeds	Lowest PubMed Reuse	Highest PubMed Reuse	# of Reporting DBs	# of Source Records
	Homo sapiens Mus musculus Drosophila melanogaster Caenorhabditis elegans Saccharomyces cerevisiae Other		Min 1 Max 645 Mean 2.3 σ 2.9	Min 0 Max 91 Mean 1.4 σ 1.2	Min 0 Max 58135 Mean 12088.3 σ 18720.4	Min 0 Max 58135 Mean 13868.6 σ 19216	Min 1 Max 10 Mean 1.7 σ 1.4	Min 1 Max 123 Mean 2.3 σ 2.7
1	MYO2	sec9	2	3	12	89	2	4
2	ACTB	XPO6	2	1	7	7	1	1
3	Fbxo3	ACVR1	2	1	1055	1055	1	1
4	MSI1	set3	2	1	9974	9974	4	4
5	RAX2	NUM1	2	1	9631	9631	3	3
6	RTT101	DIA2	2	2	8	4535	1	3
8	SWP82	YDR370C	2	2	4488	4621	5	5
9	KAP104	DBP5	2	1	9631	9631	1	1
10	Arrb2	Pes1	2	1	6564	6564	2	2
13	KRE1	RVS161	2	2	95	3592	2	3
14	DCAF6	ACVR1	2	2	1055	8861	3	4
15	ATP9B	VPS11	2	1	8861	8861	1	1
17	Pwp1	NMD3	2	1	8861	8861	1	1
18	CG13510	CG15403	2	1	24879	24879	6	6
19	EAF1	ACT1	2	4	18	58135	1	4
20	SMTN	BRMS1	2	1	19	19	2	2
21	YKE2	HAP5	2	1	3592	3592	2	2
22	YHR140W	PHO86	2	1	1988	1988	2	2
23	ube2d1	TRIM31	2	1	749	749	1	1
24	RPL27B	PUF6	2	1	8671	8671	1	1

Search Result Summary Jump to Results

404384 interaction(s) — showing 1 to 20

Page(s): 12 3 4 5 6 7 8 9 10..20220 Next

iRefWeb 2.1

+	More than one possible assignment is possible (+). This case may arise in one of three ways. 1) The reference supplied by the interaction record requires updating but more than one possibility exists. For example, Q7XJL8 was found to be a secondary access
D	The source database (D) listed in the interaction record is different than what is expected for the given accession for the protein. In specific cases, this difference is tolerated and the assignment is made.
E	The protein reference was a retired NCBI Identifier. NCBI's eUtils (E) were used to retrieve the current accession and/or sequence.
G	The interaction record's reference for the protein was an EntrezGene (G) identifier. The corresponding products of the gene were used to make the assignment.
I	The protein reference used was an NCBI GenInfo Identifier (I).
L	More than one possible assignment is possible (see + above). The assignment with the largest (L) SEGUID is arbitrarily chosen (see Methods)
M	The protein reference listed by the interaction record was a typographical modification (M) of a known accession. In specific cases, this variation is tolerated and the assignment is made.
N	The protein reference, taxonomy identifier and sequence for the protein as provided in the interaction record are used to make a new entry in the SEGUID table. The protein interactor is assigned the newly (N) generated ROG identifier.
O	More than one possible assignment is possible (see + above). The assignment chosen has a SEGUID that is identical to the SEGUID of the original (O) sequence provided in the interaction record.
P	Primary accession was used
Q	The protein reference used to make the assignment was of the type 'see-also'. See PSI-MI Path: entrySet/entry/interactorList/interactor/xref/primaryRef/refType = 'see-also'.
S	Secondary accession was used
T	The taxonomy (T) identifier for the protein (as supplied by the interaction record) differed from what was found in the protein sequence record. This discrepancy was tolerated and the assignment was made
U	The protein reference listed in the interaction record and used to make the assignment was a secondary UniProt accession and was updated (U) to a primary UniProt accession in order to make the assignment.
V	The protein reference listed by the interaction record contained version (V) information that was ignored. For example, RefSeq accession.version NP_012420.1 was listed but treated as RefSeq accession NP_012420.
X	More than one possible assignment is possible (see + above). The assignment chosen has the same taxonomy (X) identifier as listed in the interaction record
Y	The accession was referring an accession which was removed (deleted) from RefSeq or UniProt