Statistics iRefIndex 6.0

Summary

• Total interactions : 759,742
• Total distinct interactions (based on RIGID):364,708 ( 48% of total interactions)
• Total distinct proteins (based on ROGID) : 80,677

This page lists statistics for our internal version of iRefIndex that includes all of the data from sources used for the current build Sources_iRefIndex_6.0. This full build of the iRefIndex contains data that cannot be redistributed according to usage policies of the source databases (namely, from DIP, HPRD, CORUM and MPact databases). Please contact ian.donaldson at biotek.uio.no if you would like to obtain a copy of the full iRefIndex build under an academic, collaborative agreement.

The data that are freely available at ftp://ftp.no.embnet.org/irefindex/data/archive/release_6.0/ are a subset of the full build that we can freely redistribute according to the usage policies of the source databases. Please refer to http://irefindex.uio.no/wiki/Statistics_iRefIndex_free_6.0 for statistics that are applicable to this free dataset.

Interactions available from major taxonomies

Top 15 uncorrected taxonomy groups in iRefIndex (Taxonomy identifiers as they appear in original source)

NCBI taxonomy identifier	Scientific_name	Number_of_interactions	'
4932	Saccharomyces cerevisiae	116012
9606	Homo sapiens	102673
7227	Drosophila melanogaster	47471
40674	Mammalia	35023
6239	Caenorhabditis elegans	12205
562	Escherichia coli	12071
197	Campylobacter jejuni	12025
4896	Schizosaccharomyces pombe	11853
10090	Mus musculus	11506
3702	Arabidopsis thaliana	5308
10116	Rattus norvegicus	4223
160	Treponema pallidum	3647
83333	Escherichia coli K-12	3503
1142	Synechocystis	3057
36329	Plasmodium falciparum 3D7	2758

• Full list [[1]]

Top 15 corrected taxonomy groups in iRefIndex (Taxonomy identifiers corrected using sequence database information)

NCBI taxonomy identifier	Scientific_name	Number_of_interactions
4932	Saccharomyces cerevisiae	116000
9606	Homo sapiens	112206
7227	Drosophila melanogaster	47475
6239	Caenorhabditis elegans	12205
197	Campylobacter jejuni	12025
4896	Schizosaccharomyces pombe	11872
83333	Escherichia coli K-12	10979
10090	Mus musculus	10121
3702	Arabidopsis thaliana	5314
155864	Escherichia coli O157:H7 EDL933	4928
160	Treponema pallidum	3647
10116	Rattus norvegicus	3395
1148	Synechocystis sp. PCC 6803	3168
36329	Plasmodium falciparum 3D7	2758
83334	Escherichia coli O157:H7	2560

• Full list [[2]]

Interactions (Corresponds to Table 6 in PMID 18823568)

BIND	62319
BIOGRID	22289	163090
DIP	26090	28943	56451
HPRD	2947	8838	831	39966
INTACT	24444	28247	25033	8467	113843
MINT	22342	34515	30275	6641	45828	77919
MPACT	6938	8226	6748	0	6130	6425	13321
MPPI	386	111	40	304	90	73	0	823
OPHID	2228	6169	876	18149	7277	6454	0	186	47495
CORUM	116	71	28	403	125	69	0	9	158	1917
I2D	0	0	0	0	0	0	0	0	0	0	0
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM	I2D
	(24368)	(103151)	(13356)	(14909)	(56201)	(16753)	(1291)	(238)	(26475)	(1392)	(0)

Interactors

BIND	40841
BIOGRID	16602	27409
DIP	15480	13566	20119
HPRD	3357	5205	1215	9750
INTACT	18205	18409	15634	5967	41925
MINT	16446	16206	15025	4787	23640	28904
MPACT	4651	4445	4609	0	4874	4755	4972
MPPI	673	390	284	429	578	509	0	861
OPHID	3252	4619	1205	7438	5817	4808	1	422	9631
CORUM	1561	1414	642	1867	2312	1769	0	321	1850	3581
I2D	0	0	0	0	0	0	0	0	0	0	0
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM	I2D
	(17893)	(5077)	(1838)	(880)	(12034)	(3370)	(18)	(46)	(1273)	(618)	(0)

Summary of mapping interaction records to RIGs (Corresponds to Table 5 in PMID 18823568)

Source	Total records	Protein-only interactors	PPI Assigned to RIGID	Unique RIGIDs
bind	193648	93957	90370(96.1823%)	62319(68.9598%)
grid	239485	238211	237796(99.8258%)	163090(68.5840%)
dip	57675	57675	56614(98.1604%)	56451(99.7121%)
intact	133302	132525	132073(99.6589%)	113843(86.1970%)
mint	110788	110788	109608(98.9349%)	77919(71.0888%)
HPRD	40075	40075	40075(100.0000%)	39966(99.7280%)
ophid	73257	73257	73133(99.8307%)	47495(64.9433%)
MPACT	16504	16504	16286(98.6791%)	13321(81.7942%)
MPPI	1814	1814	1685(92.8886%)	823(48.8427%)
CORUM	2104	2104	2102(99.9049%)	1917(91.1989%)
ALL	868652	766910	759742(99.0653%)	364708(48.0042%)

Assignment of protein interactors to ROGs (Corresponds to Table 3 in PMID 18823568)

Source	Protein_Intractors	Assigned	%	Arbitrary	New	Unassigned	Unique proteins
bind	285482	273657	95.8579	0	7887	3938	40841
CORUM	10316	10314	99.9806	0	2	0	3581
dip	20728	18533	89.4105	1246	485	464	20119
grid	27629	22371	80.9693	5124	1	133	27409
HPRD	9773	9676	99.0075	55	42	0	9750
intact	100752	97661	96.9321	110	2740	241	41925
mint	77936	74931	96.1443	50	2727	228	28904
MPACT	40349	40112	99.4126	0	0	237	4972
MPPI	3628	3457	95.2867	0	32	139	861
ophid	146423	145362	99.2754	103	952	6	9631
All	723016	696074	96.2737	6688	14868	5386	80677

ROG summary (Corresponds to Table 4 in PMID 18823568)

Decimal_score	Binary_flag	String_score	Score_class	Proteins	Percentage	BIND	BioGrid	DIP	MINT	HPRD	OPHID	MPPI	MPACT	IntAct	CORUM
1	000000000000000001	P	1	576699	79.7630%	232419	19992	0	71896	0	125492	3023	30666	93211	0
65	000000000001000001	PD	1	8086	1.1184%	8083	0	0	3	0	0	0	0	0	0
42	000000000000101010	SVG	1	163	0.0225%	0	0	0	0	163	0	0	0	0	0
41	000000000000101001	PVG	1	2362	0.3267%	0	2362	0	0	0	0	0	0	0	0
554	000000001000101010	SVGO	1	624	0.0863%	0	0	0	0	624	0	0	0	0	0
129	000000000010000001	PM	1	522	0.0722%	473	0	0	0	0	0	32	0	17	0
10	000000000000001010	SV	1	240	0.0332%	0	0	2	9	0	0	0	0	229	0
8193	000010000000000001	PI	1	48	0.0066%	0	0	0	0	0	0	0	0	48	0
8194	000010000000000010	SI	1	12336	1.7062%	12336	0	0	0	0	0	0	0	0	0
2	000000000000000010	S	1	29459	4.0745%	0	3	17397	231	4665	0	0	6927	236	0
16449	000100000001000001	PDE	2	116	0.0160%	0	0	0	34	0	0	0	0	82	0
16385	000100000000000001	PE	2	884	0.1223%	0	0	0	199	0	0	0	0	685	0
778	000000001100001010	SVO+	2	1	0.0001%	0	0	0	0	0	0	0	0	1	0
774	000000001100000110	SUO+	2	166	0.0230%	0	0	0	61	0	0	0	0	105	0
16386	000100000000000010	SE	2	5419	0.7495%	5413	0	6	0	0	0	0	0	0	0
1798	000000011100000110	SUOX+	2	382	0.0528%	0	0	0	194	0	0	0	0	188	0
773	000000001100000101	PUO+	2	9	0.0012%	0	0	0	3	0	1	0	0	5	0
5	000000000000000101	PU	2	23087	3.1932%	0	0	0	318	0	19713	320	2519	217	0
6	000000000000000110	SU	2	126	0.0174%	0	0	84	11	5	0	0	0	26	0
145	000000000010010001	PTM	3	170	0.0235%	132	0	0	0	0	0	35	0	3	0
8210	000010000000010010	STI	3	855	0.1183%	855	0	0	0	0	0	0	0	0	0
17	000000000000010001	PT	3	26406	3.6522%	11871	0	0	1620	0	122	47	0	2456	10290
18	000000000000010010	ST	3	5162	0.7140%	0	0	1010	0	4149	0	0	0	3	0
8209	000010000000010001	PTI	3	12	0.0017%	0	0	0	0	0	0	0	0	12	0
81	000000000001010001	PTD	3	1487	0.2057%	1486	0	0	1	0	0	0	0	0	0
26	000000000000011010	SVT	3	1	0.0001%	0	0	0	0	0	0	0	0	1	0
789	000000001100010101	PUTO+	4	11	0.0015%	0	0	0	0	0	0	0	0	11	0
790	000000001100010110	SUTO+	4	4	0.0006%	0	0	0	0	1	0	0	0	3	0
22	000000000000010110	SUT	4	17	0.0024%	0	0	3	0	14	0	0	0	0	0
16401	000100000000010001	PTE	4	4	0.0006%	0	0	0	0	0	0	0	0	4	0
16402	000100000000010010	STE	4	315	0.0436%	315	0	0	0	0	0	0	0	0	0
131089	100000000000010001	PTQ	5	38	0.0053%	0	0	0	0	0	0	0	0	38	0
131073	100000000000000001	PQ	5	1	0.0001%	0	0	0	0	0	0	0	0	1	0
131077	100000000000000101	PUQ	5	1	0.0001%	0	0	0	0	0	0	0	0	1	0
4354	000001000100000010	SL+	5	1202	0.1662%	0	8	1194	0	0	0	0	0	0	0
5386	000001010100001010	SVXL+	5	2	0.0003%	0	0	0	1	0	0	0	0	1	0
4373	000001000100010101	PUTL+	5	9	0.0012%	0	0	0	1	0	0	0	0	8	0
4357	000001000100000101	PUL+	5	84	0.0116%	0	0	0	0	0	84	0	0	0	0
810	000000001100101010	SVGO+	5	55	0.0076%	0	0	0	0	55	0	0	0	0	0
21	000000000000010101	PUT	5	31	0.0043%	0	0	0	2	0	5	0	0	0	24
4374	000001000100010110	SUTL+	5	52	0.0072%	0	0	52	0	0	0	0	0	0	0
4393	000001000100101001	PVGL+	5	5116	0.7076%	0	5116	0	0	0	0	0	0	0	0
4394	000001000100101010	SVGL+	5	52	0.0072%	0	0	0	0	52	0	0	0	0	0
5381	000001010100000101	PUXL+	5	32	0.0044%	0	0	0	2	0	19	0	0	11	0
5382	000001010100000110	SUXL+	5	139	0.0192%	0	0	0	46	3	0	0	0	90	0
147473	100100000000010001	PTEQ	6	1	0.0001%	0	0	0	0	0	0	0	0	1	0
86274	010101000100000010	SLEN+	6	1	0.0001%	0	0	1	0	0	0	0	0	0	0
82034	010100000001110010	STGDEN	6	1	0.0001%	0	1	0	0	0	0	0	0	0	0
81938	010100000000010010	STEN	6	19	0.0026%	19	0	0	0	0	0	0	0	0	0
81937	010100000000010001	PTEN	6	4	0.0006%	2	0	0	0	0	0	2	0	0	0
81922	010100000000000010	SEN	6	5035	0.6964%	4661	0	372	2	0	0	0	0	0	0
81921	010100000000000001	PEN	6	2163	0.2992%	1342	0	0	263	0	324	19	0	215	0
65665	010000000010000001	PMN	6	2	0.0003%	0	0	0	0	0	0	2	0	0	0
32769	001000000000000001	PY	6	696	0.0963%	271	14	0	326	0	29	0	0	56	0
32770	001000000000000010	SY	6	73	0.0101%	0	0	30	23	0	0	0	0	20	0
32785	001000000000010001	PTY	6	2	0.0003%	2	0	0	0	0	0	0	0	0	0
32786	001000000000010010	STY	6	1	0.0001%	0	0	1	0	0	0	0	0	0	0
32833	001000000001000001	PDY	6	1	0.0001%	1	0	0	0	0	0	0	0	0	0
65537	010000000000000001	PN	6	7485	1.0352%	1717	0	112	2462	42	628	7	0	2515	2
65553	010000000000010001	PTN	6	16	0.0022%	6	0	0	0	0	0	0	0	10	0
65601	010000000001000001	PDN	6	142	0.0196%	140	0	0	0	0	0	2	0	0	0
163841	101000000000000001	PYQ	6	1	0.0001%	0	0	0	0	0	0	0	0	1	0

Scores (Corresponds to Table 2 in PMID 18823568)

Character	Description of feature (when the value is 1)	Frequency
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.	9833(1.3702%)
E	The protein reference was a retired NCBI Identifier or a UniProt identifier. NCBI's eUtils (E) were used to retrieve the current accession and/or sequence. For the identifiers still with no sequence after going through eUtils, seeunce information obtained form UniProt	13962(1.9456%)
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.	8373(1.1668%)
L	More than one possible assignment is possible (see + above). (e.g. isoforms for a geneid) In such a situation, references are picked using a ranking system (first look for RefSeq, then UniProt). Even after this ranking if ambiguity exists, the reference with lengthiest sequences selected. (Please note that this score class definition is different from originally published one)	6689(0.9321%)
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.	694(0.0967%)
+	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 accession in three separate UniProt records (Q3EBZ2, Q6DR20, and Q8GWA9). 2) The secondary references supplied by the interaction record point to more than one unique protein sequence. 3) An EntrezGene identifier is provided in the interaction record as a protein reference. This identifier points to more than one protein product. An attempt is made to resolve this ambiguity as indicated by ROG score features O, X or L (see below).	7317(1.0196%)
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.	14868(2.0718%)
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.	1252(0.1745%)
I	The protein reference used was an NCBI GenInfo Identifier (I).	13251(1.8465%)
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.	24150(3.3652%)
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	34618(4.8239%)
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.	8616(1.2006%)
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'.	42(0.0059%)
P	The interaction record's primary (P) reference for the protein was used to make the assignment	655728(91.3741%)
S	One of the interaction record's secondary (S) references for the protein was used to make the assignment	61902(8.6259%)
Y	the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009)	774(0.1079%)
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	555(0.0773%)