Statistics iRefIndex 6.0

Summary

Last updated : 22 September 2009

• Total interactions : 760,194
• Total distinct interactions (based on RIGID):365,117 ( 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	116014
9606	Homo sapiens	102728
7227	Drosophila melanogaster	47478
40674	Mammalia	35023
6239	Caenorhabditis elegans	12211
562	Escherichia coli	12091
197	Campylobacter jejuni	12025
4896	Schizosaccharomyces pombe	11856
10090	Mus musculus	11524
3702	Arabidopsis thaliana	5309
10116	Rattus norvegicus	4242
160	Treponema pallidum	3647
83333	Escherichia coli K-12	3504
1142	Synechocystis	3057
36329	Plasmodium falciparum 3D7	2758

• Full list [[]]

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	116002
9606	Homo sapiens	112309
7227	Drosophila melanogaster	47482
6239	Caenorhabditis elegans	12211
197	Campylobacter jejuni	12025
4896	Schizosaccharomyces pombe	11876
83333	Escherichia coli K-12	10981
10090	Mus musculus	10139
3702	Arabidopsis thaliana	5315
155864	Escherichia coli O157:H7 EDL933	4928
160	Treponema pallidum	3647
10116	Rattus norvegicus	3414
1148	Synechocystis sp. PCC 6803	3168
36329	Plasmodium falciparum 3D7	2758
83334	Escherichia coli O157:H7	2560

• Full list [[]]

Interactions (Corresponds to Table 6 in PMID 18823568)

BIND	62765
BIOGRID	22284	163090
DIP	26092	28937	56450
HPRD	2947	8838	830	39966
INTACT	24453	28246	24981	8485	113844
MINT	22280	34508	30187	6640	45779	77816
MPACT	6938	8226	6748	0	6132	6427	13321
MPPI	386	111	40	304	90	73	0	825
OPHID	2226	6172	876	18071	7283	6441	0	183	47396
CORUM	116	71	28	403	125	69	0	9	158	1919
I2D	0	0	0	0	0	0	0	0	0	0	0
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM	I2D
	(24824)	(103136)	(13377)	(14959)	(56206)	(16736)	(1291)	(240)	(26441)	(1394)	(0)

Interactors

BIND	40840
BIOGRID	16600	27409
DIP	15481	13567	20118
HPRD	3357	5205	1215	9750
INTACT	18211	18412	15620	5971	41940
MINT	16427	16202	14992	4783	23625	28912
MPACT	4651	4445	4609	0	4874	4756	4972
MPPI	673	390	284	429	579	511	0	861
OPHID	3253	4620	1206	7429	5814	4805	1	421	9646
CORUM	1561	1414	643	1867	2313	1771	0	321	1849	3581
I2D	0	0	0	0	0	0	0	0	0	0	0
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM	I2D
	(17892)	(5070)	(1846)	(883)	(12049)	(3408)	(18)	(46)	(1290)	(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	91057(96.9135%)	62765(68.9294%)
grid	239485	238211	237796(99.8258%)	163090(68.5840%)
dip	57675	57675	56613(98.1586%)	56450(99.7121%)
intact	133302	132525	132071(99.6574%)	113844(86.1991%)
mint	110788	110788	109500(98.8374%)	77816(71.0648%)
HPRD	40075	40075	40075(100.0000%)	39966(99.7280%)
ophid	73257	73257	73004(99.6546%)	47396(64.9225%)
MPACT	16504	16504	16286(98.6791%)	13321(81.7942%)
MPPI	1814	1814	1688(93.0540%)	825(48.8744%)
CORUM	2104	2104	2104(100.0000%)	1919(91.2072%)
ALL	868652	766910	760194(99.1243%)	365117(48.0295%)

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	40840
CORUM	10316	10314	99.9806	0	2	0	3581
dip	20728	18533	89.4105	1246	484	465	20118
grid	27629	22371	80.9693	5124	1	133	27409
HPRD	9773	9676	99.0075	55	42	0	9750
intact	100752	97752	97.0224	19	2740	241	41940
mint	77936	74979	96.2059	2	2727	228	28912
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	9646
All	723016	696213	96.2929	6549	14867	5387	80749

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	577648	79.8942%	232419	19992	0	72231	0	125686	3023	30666	93631	0
2	000000000000000010	S	1	27585	3.8153%	0	3	17416	231	2772	0	0	6927	236	0
8194	000010000000000010	SI	1	12336	1.7062%	12336	0	0	0	0	0	0	0	0	0
65	000000000001000001	PD	1	8086	1.1184%	8083	0	0	3	0	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	242	0.0335%	0	0	2	9	0	0	0	0	231	0
42	000000000000101010	SVG	1	163	0.0225%	0	0	0	0	163	0	0	0	0	0
8193	000010000000000001	PI	1	48	0.0066%	0	0	0	0	0	0	0	0	48	0
5	000000000000000101	PU	2	22841	3.1591%	0	0	0	293	0	19519	320	2519	190	0
16386	000100000000000010	SE	2	5419	0.7495%	5413	0	6	0	0	0	0	0	0	0
16385	000100000000000001	PE	2	884	0.1223%	0	0	0	199	0	0	0	0	685	0
16449	000100000001000001	PDE	2	116	0.0160%	0	0	0	34	0	0	0	0	82	0
6	000000000000000110	SU	2	77	0.0106%	0	0	60	4	5	0	0	0	8	0
773	000000001100000101	PUO+	2	12	0.0017%	0	0	0	3	0	1	0	0	8	0
778	000000001100001010	SVO+	2	1	0.0001%	0	0	0	0	0	0	0	0	1	0
774	000000001100000110	SUO+	2	1	0.0001%	0	0	0	0	0	0	0	0	1	0
17	000000000000010001	PT	3	26406	3.6522%	11871	0	0	1620	0	122	47	0	2456	10290
18	000000000000010010	ST	3	7060	0.9765%	0	0	1015	0	6042	0	0	0	3	0
81	000000000001010001	PTD	3	1487	0.2057%	1486	0	0	1	0	0	0	0	0	0
8210	000010000000010010	STI	3	855	0.1183%	855	0	0	0	0	0	0	0	0	0
145	000000000010010001	PTM	3	170	0.0235%	132	0	0	0	0	0	35	0	3	0
8209	000010000000010001	PTI	3	12	0.0017%	0	0	0	0	0	0	0	0	12	0
26	000000000000011010	SVT	3	1	0.0001%	0	0	0	0	0	0	0	0	1	0
16402	000100000000010010	STE	4	315	0.0436%	315	0	0	0	0	0	0	0	0	0
22	000000000000010110	SUT	4	17	0.0024%	0	0	3	0	14	0	0	0	0	0
789	000000001100010101	PUTO+	4	14	0.0019%	0	0	0	0	0	0	0	0	14	0
16401	000100000000010001	PTE	4	4	0.0006%	0	0	0	0	0	0	0	0	4	0
790	000000001100010110	SUTO+	4	1	0.0001%	0	0	0	0	1	0	0	0	0	0
4393	000001000100101001	PVGL+	5	5116	0.7076%	0	5116	0	0	0	0	0	0	0	0
4354	000001000100000010	SL+	5	1202	0.1662%	0	8	1194	0	0	0	0	0	0	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
4394	000001000100101010	SVGL+	5	52	0.0072%	0	0	0	0	52	0	0	0	0	0
4374	000001000100010110	SUTL+	5	52	0.0072%	0	0	52	0	0	0	0	0	0	0
131089	100000000000010001	PTQ	5	38	0.0053%	0	0	0	0	0	0	0	0	38	0
21	000000000000010101	PUT	5	31	0.0043%	0	0	0	2	0	5	0	0	0	24
5381	000001010100000101	PUXL+	5	29	0.0040%	0	0	0	0	0	19	0	0	10	0
4373	000001000100010101	PUTL+	5	9	0.0012%	0	0	0	1	0	0	0	0	8	0
1802	000000011100001010	SVOX+	5	3	0.0004%	0	0	0	0	0	0	0	0	3	0
5382	000001010100000110	SUXL+	5	3	0.0004%	0	0	0	0	3	0	0	0	0	0
5386	000001010100001010	SVXL+	5	2	0.0003%	0	0	0	1	0	0	0	0	1	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
65537	010000000000000001	PN	6	7476	1.0340%	1678	1	112	2451	42	672	5	0	2515	0
81922	010100000000000010	SEN	6	5574	0.7709%	5200	0	372	2	0	0	0	0	0	0
65601	010000000001000001	PDN	6	1171	0.1620%	668	0	0	248	0	253	0	0	2	0
32769	001000000000000001	PY	6	696	0.0963%	271	14	0	326	0	29	0	0	56	0
81921	010100000000000001	PEN	6	605	0.0837%	314	0	0	26	0	27	23	0	213	2
32770	001000000000000010	SY	6	73	0.0101%	0	0	30	23	0	0	0	0	20	0
81938	010100000000010010	STEN	6	19	0.0026%	19	0	0	0	0	0	0	0	0	0
65553	010000000000010001	PTN	6	17	0.0024%	7	0	0	0	0	0	0	0	10	0
81937	010100000000010001	PTEN	6	3	0.0004%	1	0	0	0	0	0	2	0	0	0
32785	001000000000010001	PTY	6	2	0.0003%	2	0	0	0	0	0	0	0	0	0
65665	010000000010000001	PMN	6	2	0.0003%	0	0	0	0	0	0	2	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
147473	100100000000010001	PTEQ	6	1	0.0001%	0	0	0	0	0	0	0	0	1	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.	10861(1.5135%)
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.	12940(1.8032%)
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.	8372(1.1666%)
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)	6549(0.9126%)
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).	6636(0.9247%)
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.	14867(2.0717%)
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.	711(0.0991%)
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.	23172(3.229%)
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	36515(5.0883%)
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.	8621(1.2013%)
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	655896(91.3976%)
S	One of the interaction record's secondary (S) references for the protein was used to make the assignment	61733(8.6024%)
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	37(0.0052%)