Statistics iRefIndex 7.0

Summary

Last updated: 2010-05-20

• Total interaction source records : 926,113
• Total distinct interactions (based on RIGID): 433,617 ( 46.8 % of total interactions)
• Total distinct proteins (based on ROGID) : 83,234

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_7.0. 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_7.0/ 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_7.0 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
9606	Homo sapiens	106497
7227	Drosophila melanogaster	47149
40674	Mammalia	35023
10090	Mus musculus	12974
6239	Caenorhabditis elegans	12973
4896	Schizosaccharomyces pombe	12250
562	Escherichia coli	12117
197	Campylobacter jejuni	12025
3702	Arabidopsis thaliana	6291
10116	Rattus norvegicus	4819
83333	Escherichia coli K-12	3687
160	Treponema pallidum	3647
1142	Synechocystis	3065
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
9606	Homo sapiens	114644
7227	Drosophila melanogaster	47152
6239	Caenorhabditis elegans	12973
4896	Schizosaccharomyces pombe	12270
197	Campylobacter jejuni	12025
83333	Escherichia coli K-12	11179
10090	Mus musculus	11173
3702	Arabidopsis thaliana	6297
155864	Escherichia coli O157:H7 EDL933	4928
10116	Rattus norvegicus	3738
160	Treponema pallidum	3647
1148	Synechocystis sp. PCC 6803	3177
36329	Plasmodium falciparum 3D7	2758
83334	Escherichia coli O157:H7	2560

• Full list [[2]]

Interactions (Corresponds to Table 6 in PMID 18823568)

BIND	62903
BIOGRID	23140	226496
DIP	26433	32865	61680
HPRD	3029	11612	843	39966
INTACT	24214	32627	25059	8652	117840
MINT	22100	37903	30107	6758	46689	79710
MPACT	6953	8271	6847	0	6147	6430	13321
MPPI	376	141	41	304	92	76	0	830
OPHID	2295	8356	882	18093	7330	6482	0	183	47530
CORUM	232	167	64	549	220	107	0	15	236	2607
I2D	0	0	0	0	0	0	0	0	0	0	0
BIND_TRANSLATION	42739	22497	18370	3980	19401	17755	2145	369	2928	193	0	48765
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM	I2D	BIND_TRANSLATION
	(10382)	(157990)	(16953)	(13960)	(58119)	(16958)	(1278)	(240)	(26312)	(1836)	(0)	(2633)

Interactors

BIND	40790
BIOGRID	17313	29090
DIP	15526	14440	20171
HPRD	3407	6005	1236	9750
INTACT	18310	20511	15628	6189	44616
MINT	16422	17286	15000	4935	23979	29217
MPACT	4655	4547	4646	0	4877	4761	4972
MPPI	675	435	289	429	592	520	0	865
OPHID	3307	5444	1226	7453	6036	4918	1	421	9645
CORUM	2028	2064	842	2293	2908	2225	0	415	2245	4365
I2D	0	0	0	0	0	0	0	0	0	0	0
BIND_TRANSLATION	24977	15261	12008	3576	15673	13975	2370	680	3448	1958	0	26792
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM	I2D	BIND_TRANSLATION
	(10653)	(4470)	(1727)	(810)	(13535)	(3380)	(15)	(47)	(1212)	(682)	(0)	(617)

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	91276(97.1466%)	62903(68.9152%)
grid	333977	329642	329185(99.8614%)	226496(68.8051%)
dip	62903	62903	61843(98.3149%)	61680(99.7364%)
intact	140723	139787	139310(99.6588%)	117840(84.5883%)
mint	113258	113258	112159(99.0296%)	79710(71.0688%)
HPRD	40075	40075	40075(100.0000%)	39966(99.7280%)
ophid	73257	73257	73160(99.8676%)	47530(64.9672%)
MPACT	16504	16504	16286(98.6791%)	13321(81.7942%)
MPPI	1814	1814	1701(93.7707%)	830(48.7948%)
CORUM	2844	2844	2844(100.0000%)	2607(91.6667%)
BIND_Translation	140601	61585	58274(94.6237%)	48765(83.6823%)
ALL	1119604	935626	926113(98.9832%)	433617(46.8212%)

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

Source	Protein_Intractors	Assigned	%	Arbitrary	N_and_Y	Unassigned	Unique proteins
bind	285482	272970	95.6172	0	8602	3905	40790
BIND_Translation	187563	173313	92.4026	9625	496	4129	26792
CORUM	12916	12916	100.0000	0	0	0	4365
dip	20785	18536	89.1797	1255	527	467	20171
grid	36333	30255	83.2714	5869	5	204	29090
HPRD	9773	9663	98.8745	64	46	0	9750
intact	108593	105448	97.1039	19	2862	264	44616
mint	79057	75743	95.8081	2	3086	226	29217
MPACT	40349	40112	99.4126	0	0	237	4972
MPPI	3628	3456	95.2591	0	45	125	865
ophid	146423	145330	99.2535	103	984	6	9645
All	930902	887749	95.3644	16937	16653	9563	83234

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	BIND_Translation
1	000000000000000001	P	1	607631	65.2734%	232081	28623	0	73314	0	125683	3023	30666	101306	12916	19
8193	000010000000000001	PI	1	152094	16.3383%	0	0	0	1	0	0	0	0	48	0	152045
2	000000000000000010	S	1	43100	4.6299%	0	44	17426	244	2772	0	0	6927	255	0	15432
8194	000010000000000010	SI	1	12336	1.3252%	12336	0	0	0	0	0	0	0	0	0	0
65	000000000001000001	PD	1	8076	0.8675%	8073	0	0	3	0	0	0	0	0	0	0
41	000000000000101001	PVG	1	1583	0.1701%	0	1583	0	0	0	0	0	0	0	0	0
10	000000000000001010	SV	1	1293	0.1389%	0	0	5	14	0	0	0	0	237	0	1037
129	000000000010000001	PM	1	528	0.0567%	473	0	0	0	0	0	32	0	23	0	0
554	000000001000101010	SVGO	1	477	0.0512%	0	0	0	0	477	0	0	0	0	0	0
42	000000000000101010	SVG	1	171	0.0184%	0	0	12	0	159	0	0	0	0	0	0
66	000000000001000010	SD	1	99	0.0106%	0	4	9	0	0	0	0	0	0	0	86
5	000000000000000101	PU	2	22826	2.4520%	0	0	0	289	0	19519	320	2519	179	0	0
16386	000100000000000010	SE	2	5429	0.5832%	5423	0	6	0	0	0	0	0	0	0	0
16385	000100000000000001	PE	2	1532	0.1646%	0	0	0	202	0	0	0	0	720	0	610
6	000000000000000110	SU	2	815	0.0875%	0	1	58	4	5	0	0	0	10	0	737
16449	000100000001000001	PDE	2	120	0.0129%	0	0	0	34	0	0	0	0	86	0	0
773	000000001100000101	PUO+	2	13	0.0014%	0	0	0	3	0	1	0	0	9	0	0
774	000000001100000110	SUO+	2	1	0.0001%	0	0	0	0	0	0	0	0	1	0	0
778	000000001100001010	SVO+	2	1	0.0001%	0	0	0	0	0	0	0	0	1	0	0
17	000000000000010001	PT	3	16060	1.7252%	11785	0	0	1632	0	122	46	0	2475	0	0
18	000000000000010010	ST	3	8104	0.8706%	0	0	1016	0	6042	0	0	0	3	0	1043
8209	000010000000010001	PTI	3	2052	0.2204%	0	0	0	0	0	0	0	0	13	0	2039
81	000000000001010001	PTD	3	1497	0.1608%	1496	0	0	1	0	0	0	0	0	0	0
8210	000010000000010010	STI	3	855	0.0918%	855	0	0	0	0	0	0	0	0	0	0
145	000000000010010001	PTM	3	184	0.0198%	132	0	0	0	0	0	35	0	17	0	0
26	000000000000011010	SVT	3	1	0.0001%	0	0	0	0	0	0	0	0	1	0	0
16402	000100000000010010	STE	4	317	0.0341%	316	0	1	0	0	0	0	0	0	0	0
16401	000100000000010001	PTE	4	269	0.0289%	0	0	0	0	0	0	0	0	4	0	265
22	000000000000010110	SUT	4	17	0.0018%	0	0	3	0	14	0	0	0	0	0	0
789	000000001100010101	PUTO+	4	14	0.0015%	0	0	0	0	0	0	0	0	14	0	0
790	000000001100010110	SUTO+	4	1	0.0001%	0	0	0	0	1	0	0	0	0	0	0
4393	000001000100101001	PVGL+	5	5854	0.6289%	0	5854	0	0	0	0	0	0	0	0	0
4362	000001000100001010	SVL+	5	5498	0.5906%	0	0	0	0	0	0	0	0	0	0	5498
4354	000001000100000010	SL+	5	5336	0.5732%	0	14	1195	0	0	0	0	0	0	0	4127
810	000000001100101010	SVGO+	5	193	0.0207%	0	0	0	0	193	0	0	0	0	0	0
4357	000001000100000101	PUL+	5	84	0.0090%	0	0	0	0	0	84	0	0	0	0	0
4394	000001000100101010	SVGL+	5	70	0.0075%	0	1	8	0	61	0	0	0	0	0	0
4374	000001000100010110	SUTL+	5	52	0.0056%	0	0	52	0	0	0	0	0	0	0	0
131089	100000000000010001	PTQ	5	39	0.0042%	0	0	0	0	0	0	0	0	39	0	0
5381	000001010100000101	PUXL+	5	29	0.0031%	0	0	0	0	0	19	0	0	10	0	0
4373	000001000100010101	PUTL+	5	9	0.0010%	0	0	0	1	0	0	0	0	8	0	0
21	000000000000010101	PUT	5	7	0.0008%	0	0	0	2	0	5	0	0	0	0	0
1802	000000011100001010	SVOX+	5	4	0.0004%	0	0	0	0	0	0	0	0	4	0	0
5382	000001010100000110	SUXL+	5	3	0.0003%	0	0	0	0	3	0	0	0	0	0	0
5386	000001010100001010	SVXL+	5	2	0.0002%	0	0	0	1	0	0	0	0	1	0	0
131073	100000000000000001	PQ	5	1	0.0001%	0	0	0	0	0	0	0	0	1	0	0
131077	100000000000000101	PUQ	5	1	0.0001%	0	0	0	0	0	0	0	0	1	0	0
32769	001000000000000001	PY	6	8873	0.9532%	3051	4	0	2785	0	731	5	0	2297	0	0
81922	010100000000000010	SEN	6	4524	0.4860%	4515	0	9	0	0	0	0	0	0	0	0
32833	001000000001000001	PDY	6	755	0.0811%	755	0	0	0	0	0	0	0	0	0	0
65537	010000000000000001	PN	6	608	0.0653%	178	1	112	26	46	0	11	0	234	0	0
32770	001000000000000010	SY	6	567	0.0609%	0	0	405	25	0	0	0	0	95	0	42
65601	010000000001000001	PDN	6	559	0.0600%	52	0	0	247	0	253	5	0	2	0	0
81921	010100000000000001	PEN	6	418	0.0449%	0	0	0	3	0	0	22	0	1	0	392
73729	010010000000000001	PIN	6	223	0.0240%	0	0	0	0	0	0	0	0	223	0	0
81937	010100000000010001	PTEN	6	64	0.0069%	0	0	0	0	0	0	2	0	0	0	62
32785	001000000000010001	PTY	6	32	0.0034%	32	0	0	0	0	0	0	0	0	0	0
81938	010100000000010010	STEN	6	19	0.0020%	19	0	0	0	0	0	0	0	0	0	0
65553	010000000000010001	PTN	6	8	0.0009%	0	0	0	0	0	0	0	0	8	0	0
147473	100100000000010001	PTEQ	6	1	0.0001%	0	0	0	0	0	0	0	0	1	0	0
40961	001010000000000001	PIY	6	1	0.0001%	0	0	0	0	0	0	0	0	1	0	0
32786	001000000000010010	STY	6	1	0.0001%	0	0	1	0	0	0	0	0	0	0	0
163841	101000000000000001	PYQ	6	1	0.0001%	0	0	0	0	0	0	0	0	1	0	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.	11106(1.2054%)
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.	12693(1.3777%)
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.	8348(0.9061%)
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)	16937(1.8383%)
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.	712(0.0773%)
+	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).	17164(1.863%)
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.	6423(0.6971%)
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.	704(0.0764%)
I	The protein reference used was an NCBI GenInfo Identifier (I).	167561(18.1868%)
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.	23872(2.591%)
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	29603(3.2131%)
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.	15147(1.644%)
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'.	43(0.0047%)
P	The interaction record's primary (P) reference for the protein was used to make the assignment	832046(90.309%)
S	One of the interaction record's secondary (S) references for the protein was used to make the assignment	89286(9.691%)
Y	the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009)	10230(1.1103%)
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	38(0.0041%)

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