Statistics iRefIndex 8.0

Summary

Last updated: 2010-11-17

• Total interaction source records :
• Total distinct interactions (based on RIGID): ( % of total interactions)
• Total distinct proteins (based on ROGID) :

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_8.0.

Interactions available from major taxonomies

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

• Full list [[1]]

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

• Full list [[2]]

Interactions (Corresponds to Table 6 in PMID 18823568)

BIND	62896
BIOGRID	23631	241088
DIP	26457	29866	68301
HPRD	2530	11000	553	40490
INTACT	24320	30088	25124	6603	130316
MINT	22144	36491	30784	5193	47949	83727
MPACT	6965	8287	6857	0	6175	6470	13328
MPPI	382	114	41	198	94	74	0	832
OPHID	0	0	0	0	0	0	0	0	0
CORUM	231	116	66	311	236	108	0	15	0	2607
I2D	31771	67039	34961	24460	69947	58975	8382	646	0	500	481732
BIND_TRANSLATION	55057	23657	23874	3167	23943	22041	6316	379	0	190	33437	61348
INNATEDB	289	656	236	1186	546	431	0	46	0	73	4122	398	6114
MATRIXDB	2	5	3	20	15	2	0	2	0	0	40	5	4	201
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM	I2D	BIND_TRANSLATION	INNATEDB	MATRIXDB
	(3656)	(156331)	(22561)	(12571)	(47752)	(12213)	(1112)	(91)	(0)	(1807)	(340528)	(2311)	(1838)	(146)

Interactors

BIND	40784
BIOGRID	17136	30716
DIP	15599	13707	21334
HPRD	3205	6004	1081	9846
INTACT	18675	20495	16619	6141	50583
MINT	16570	16738	15432	4534	24840	30382
MPACT	4663	4554	4652	0	4879	4771	4978
MPPI	680	406	291	359	625	524	0	867
OPHID	0	0	0	0	0	0	0	0	0
CORUM	2036	1921	859	1967	3115	2280	0	416	0	4365
I2D	19257	20632	14835	8231	29594	22941	4956	816	0	3843	51871
BIND_TRANSLATION	38396	17468	15289	3592	19247	16899	4379	688	0	2208	20031	40956
INNATEDB	1440	1449	778	1602	2167	1722	0	339	0	1047	2908	1601	2998
MATRIXDB	109	92	57	126	136	111	0	18	0	52	189	115	85	222
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM	I2D	BIND_TRANSLATION	INNATEDB	MATRIXDB
	(1352)	(5320)	(1815)	(728)	(13291)	(2757)	(8)	(14)	(0)	(305)	(14805)	(896)	(62)	(22)

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	91264(97.1338%)	62896(68.9165%)
grid	355947	351586	351145(99.8746%)	241088(68.6577%)
dip	69463	69463	68390(98.4553%)	68301(99.8699%)
intact	154833	153547	152961(99.6184%)	130316(85.1956%)
mint	118153	118153	117679(99.5988%)	83727(71.1486%)
HPRD	40618	40618	40618(100.0000%)	40490(99.6849%)
MPACT	16504	16504	16293(98.7215%)	13328(81.8020%)
MPPI	1814	1814	1703(93.8809%)	832(48.8550%)
CORUM	2844	2844	2844(100.0000%)	2607(91.6667%)
I2D	847845	847845	847837(99.9991%)	481732(56.8189%)
BIND_Translation	213166	89275	83179(93.1717%)	61348(73.7542%)
InnateDB	13609	10595	9970(94.1010%)	6114(61.3240%)
MatrixDB	846	349	321(91.9771%)	201(62.6168%)
ALL	2029290	1796550	1784204(99.3128%)	792679(44.4276%)

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	272821	95.5650	0	8732	3923	40784
BIND_Translation	297101	265324	89.3043	10290	1549	19938	40956
CORUM	12916	12916	100.0000	0	0	0	4365
dip	21970	20290	92.3532	671	532	477	21334
grid	38197	31321	81.9986	6668	2	206	30716
HPRD	9871	9630	97.5585	192	49	0	9846
I2D	52222	52107	99.7798	4	108	3	51871
InnateDB	25172	24386	96.8775	0	0	786	2998
intact	125474	121570	96.8886	38	3553	313	50583
MatrixDB	1123	1077	95.9038	0	0	46	222
mint	82312	78661	95.5644	1	3524	126	30382
MPACT	40349	40118	99.4275	0	1	230	4978
MPPI	3628	3457	95.2867	0	47	124	867
All	995817	933684	93.7606	17864	18097	26172	105435

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
32834	001000000001000010	SDY	-1	193	0.0194%	0	0	0	0	0	0	0	0	0	0	193
770	000000001100000010	SO+	-1	6	0.0006%	0	0	0	0	0	0	0	0	6	0	0
1797	000000011100000101	PUOX+	-1	2	0.0002%	0	0	0	0	0	0	0	0	2	0	0
9	000000000000001001	PV	-1	1	0.0001%	0	0	0	0	0	0	0	0	1	0	0
1	000000000000000001	P	1	568766	57.1155%	231951	19013	0	76612	0	0	3023	30666	117787	12916	19
8193	000010000000000001	PI	1	225108	22.6054%	0	0	0	3	0	0	0	0	51	0	225054
2	000000000000000010	S	1	53213	5.3437%	0	20	19310	254	2267	0	0	6935	317	0	24110
8194	000010000000000010	SI	1	12336	1.2388%	12336	0	0	0	0	0	0	0	0	0	0
65	000000000001000001	PD	1	8074	0.8108%	8073	0	0	1	0	0	0	0	0	0	0
554	000000001000101010	SVGO	1	2195	0.2204%	0	0	0	0	2195	0	0	0	0	0	0
41	000000000000101001	PVG	1	1747	0.1754%	0	1747	0	0	0	0	0	0	0	0	0
10	000000000000001010	SV	1	1419	0.1425%	0	0	5	19	0	0	0	0	253	0	1142
129	000000000010000001	PM	1	678	0.0681%	473	0	0	0	0	0	32	0	36	0	0
42	000000000000101010	SVG	1	198	0.0199%	0	0	12	0	186	0	0	0	0	0	0
66	000000000001000010	SD	1	117	0.0117%	0	4	9	0	0	0	0	0	0	0	88
16386	000100000000000010	SE	2	5420	0.5443%	5405	0	0	0	15	0	0	0	0	0	0
5	000000000000000101	PU	2	3858	0.3874%	0	0	0	114	0	0	320	2517	365	0	0
16385	000100000000000001	PE	2	1488	0.1494%	0	0	0	0	0	0	0	0	155	0	1333
6	000000000000000110	SU	2	978	0.0982%	0	1	58	4	2	0	0	0	13	0	900
773	000000001100000101	PUO+	2	9	0.0009%	0	0	0	0	0	0	0	0	9	0	0
778	000000001100001010	SVO+	2	1	0.0001%	0	0	0	0	0	0	0	0	1	0	0
774	000000001100000110	SUO+	2	1	0.0001%	0	0	0	0	0	0	0	0	1	0	0
17	000000000000010001	PT	3	26504	2.6615%	11784	10516	0	1654	0	0	47	0	2500	0	0
8209	000010000000010001	PTI	3	10393	1.0437%	0	0	0	0	0	0	0	0	13	0	10380
18	000000000000010010	ST	3	6878	0.6907%	0	20	892	0	4347	0	0	0	1	0	1618
81	000000000001010001	PTD	3	1587	0.1594%	1496	0	0	0	0	0	0	0	0	0	0
8210	000010000000010010	STI	3	855	0.0859%	855	0	0	0	0	0	0	0	0	0	0
145	000000000010010001	PTM	3	189	0.0190%	132	0	0	0	0	0	35	0	22	0	0
26	000000000000011010	SVT	3	27	0.0027%	0	0	0	0	0	0	0	0	1	0	26
82	000000000001010010	STD	3	6	0.0006%	0	0	0	0	0	0	0	0	0	0	6
16401	000100000000010001	PTE	4	650	0.0653%	0	0	0	0	0	0	0	0	2	0	648
16402	000100000000010010	STE	4	356	0.0357%	316	0	1	0	39	0	0	0	0	0	0
789	000000001100010101	PUTO+	4	14	0.0014%	0	0	0	0	0	0	0	0	14	0	0
22	000000000000010110	SUT	4	4	0.0004%	0	0	3	0	1	0	0	0	0	0	0
4393	000001000100101001	PVGL+	5	6628	0.6656%	0	6628	0	0	0	0	0	0	0	0	0
4362	000001000100001010	SVL+	5	5936	0.5961%	0	0	0	0	0	0	0	0	0	0	5936
4354	000001000100000010	SL+	5	5004	0.5025%	0	40	610	0	0	0	0	0	0	0	4354
810	000000001100101010	SVGO+	5	578	0.0580%	0	0	0	0	578	0	0	0	0	0	0
4394	000001000100101010	SVGL+	5	201	0.0202%	0	0	9	0	192	0	0	0	0	0	0
4374	000001000100010110	SUTL+	5	52	0.0052%	0	0	52	0	0	0	0	0	0	0	0
5386	000001010100001010	SVXL+	5	21	0.0021%	0	0	0	1	0	0	0	0	20	0	0
131089	100000000000010001	PTQ	5	12	0.0012%	0	0	0	0	0	0	0	0	12	0	0
5381	000001010100000101	PUXL+	5	10	0.0010%	0	0	0	0	0	0	0	0	10	0	0
4373	000001000100010101	PUTL+	5	8	0.0008%	0	0	0	0	0	0	0	0	8	0	0
4357	000001000100000101	PUL+	5	4	0.0004%	0	0	0	0	0	0	0	0	0	0	0
1802	000000011100001010	SVOX+	5	4	0.0004%	0	0	0	0	0	0	0	0	4	0	0
131073	100000000000000001	PQ	5	3	0.0003%	0	0	0	0	0	0	0	0	3	0	0
21	000000000000010101	PUT	5	2	0.0002%	0	0	0	0	0	0	0	0	0	0	0
32769	001000000000000001	PY	6	8505	0.8541%	3325	1	0	2793	0	0	5	0	2337	0	0
81922	010100000000000010	SEN	6	4503	0.4522%	4503	0	0	0	0	0	0	0	0	0	0
65537	010000000000000001	PN	6	1532	0.1538%	35	0	122	451	49	0	11	0	864	0	0
81921	010100000000000001	PEN	6	1270	0.1275%	0	0	0	8	0	0	22	0	43	0	1133
32833	001000000001000001	PDY	6	755	0.0758%	755	0	0	0	0	0	0	0	0	0	0
32770	001000000000000010	SY	6	572	0.0574%	0	1	409	25	0	0	0	1	94	0	42
65601	010000000001000001	PDN	6	306	0.0307%	52	0	0	247	0	0	5	0	2	0	0
73729	010010000000000001	PIN	6	200	0.0201%	0	0	0	0	0	0	0	0	200	0	0
81937	010100000000010001	PTEN	6	179	0.0180%	0	0	0	0	0	0	2	0	0	0	177
32785	001000000000010001	PTY	6	31	0.0031%	31	0	0	0	0	0	0	0	0	0	0
81938	010100000000010010	STEN	6	31	0.0031%	31	0	0	0	0	0	0	0	0	0	0
65553	010000000000010001	PTN	6	13	0.0013%	0	0	0	0	0	0	0	0	13	0	0
40961	001010000000000001	PIY	6	4	0.0004%	0	0	0	0	0	0	0	0	0	0	4
32897	001000000010000001	PMY	6	2	0.0002%	0	0	0	0	0	0	2	0	0	0	0
32786	001000000000010010	STY	6	1	0.0001%	0	0	1	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	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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