Statistics iRefIndex free 4.0

This page lists statistics for the freely available version of iRefIndex distributed at ftp://ftp.no.embnet.org/irefindex/data/current/.

These data are a subset of the full iRefIndex build that we can freely redistribute according to the usage policies of the source databases. Specifically, this data set does not include interactions from DIP, CORUM, HPRD or MPact. Please refer to http://irefindex.uio.no/wiki/Statistics_iRefIndex_4.0 for statistics that are applicable to the full build.

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Interactions (Corresponds to Table 6 in PMID 18823568)

BIND	62921
BIOGRID	20497	163891
DIP	0	0	0
HPRD	0	0	0	0
INTACT	24241	25650	0	0	111334
MINT	22154	32446	0	0	42185	73739
MPACT	0	0	0	0	0	0	0
MPPI	385	26	0	0	89	105	0	829
OPHID	2210	1333	0	0	7197	7142	0	183	47297
CORUM	0	0	0	0	0	0	0	0	0	0
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM
	(31178)	(120963)	(0)	(0)	(58514)	(16176)	(0)	(306)	(35730)	(0)

Interactors

BIND	40801
BIOGRID	14442	27471
DIP	0	0	0
HPRD	0	0	0	0
INTACT	18121	16830	0	0	41601
MINT	16314	14935	0	0	22895	28055
MPACT	0	0	0	0	0	0	0
MPPI	672	212	0	0	575	550	0	863
OPHID	3242	2300	0	0	5747	4808	0	421	9629
CORUM	0	0	0	0	0	0	0	0	0	0
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM
	(20127)	(8594)	(0)	(0)	(13320)	(3408)	(0)	(48)	(2285)	(0)

Summary of mapping interaction records to RIGs (Table 5)

Source	Total records	Protein-only interactors	PPI Assigned to RIGID	Unique RIGIDs
bind	193648	93957	91291(97.1625%)	62921(68.9236%)
grid	240501	240501	240197(99.8736%)	163891(68.2319%)
intact	129236	128470	128037(99.6630%)	111334(86.9546%)
mint	104847	104847	103522(98.7363%)	73739(71.2303%)
ophid	73257	73257	72907(99.5222%)	47297(64.8731%)
MPPI	1813	1813	1696(93.5466%)	829(48.8797%)
ALL	743302	642845	637650(99.1919%)	337379(52.9097%)

Assignment of protein interactors to ROGs (Table 3)

Source	Protein_Intractors	Assigned	%	Arbitrary	New	Unassigned	Unique proteins
bind	285482	273646	95.8540	0	7942	3894	40801
grid	29318	19162	65.3592	10053	5	98	27471
intact	98122	94514	96.3229	18	3354	236	41601
mint	80543	77298	95.9711	6	2760	479	28055
MPPI	3628	3457	95.2867	0	39	132	863
ophid	146423	145362	99.2754	103	699	259	9629
All	643516	613439	95.3261	10180	14799	5098	79750

ROG summary

Decimal_score	Binary_flag	String_score	Score_class	Proteins	Percentage	BIND	BioGrid	DIP	MINT	HPRD	OPHID	MPPI	MPACT	IntAct	CORUM
1	000000000000000001	P	1	535022	83.1404%	232685	7503	0	74838	0	125715	3023	0	91258	0
130	000000000010000010	SM	1	551	0.0856%	0	551	0	0	0	0	0	0	0	0
129	000000000010000001	PM	1	524	0.0814%	473	1	0	0	0	0	32	0	18	0
66	000000000001000010	SD	1	2	0.0003%	0	2	0	0	0	0	0	0	0	0
65	000000000001000001	PD	1	9549	1.4839%	8084	1446	0	19	0	0	0	0	0	0
8193	000010000000000001	PI	1	48	0.0075%	0	2	0	0	0	0	0	0	46	0
8194	000010000000000010	SI	1	12395	1.9261%	12336	59	0	0	0	0	0	0	0	0
10	000000000000001010	SV	1	7	0.0011%	0	0	0	0	0	0	0	0	7	0
2	000000000000000010	S	1	7907	1.2287%	0	7402	0	263	0	0	0	0	242	0
773	000000001100000101	PUO+	2	7	0.0011%	0	0	0	1	0	0	0	0	6	0
16385	000100000000000001	PE	2	189	0.0294%	0	0	0	0	0	0	0	0	189	0
16386	000100000000000010	SE	2	5405	0.8399%	5405	0	0	0	0	0	0	0	0	0
6	000000000000000110	SU	2	672	0.1044%	0	659	0	5	0	0	0	0	8	0
774	000000001100000110	SUO+	2	1	0.0002%	0	0	0	0	0	0	0	0	1	0
5	000000000000000101	PU	2	20462	3.1797%	0	0	0	427	0	19520	320	0	195	0
778	000000001100001010	SVO+	2	1	0.0002%	0	0	0	0	0	0	0	0	1	0
8209	000010000000010001	PTI	3	13	0.0020%	0	0	0	0	0	0	0	0	13	0
8210	000010000000010010	STI	3	903	0.1403%	855	48	0	0	0	0	0	0	0	0
146	000000000010010010	STM	3	1	0.0002%	0	1	0	0	0	0	0	0	0	0
17	000000000000010001	PT	3	16244	2.5243%	11876	0	0	1739	0	122	47	0	2460	0
18	000000000000010010	ST	3	1490	0.2315%	0	1487	0	0	0	0	0	0	3	0
26	000000000000011010	SVT	3	1	0.0002%	0	0	0	0	0	0	0	0	1	0
81	000000000001010001	PTD	3	1486	0.2309%	1486	0	0	0	0	0	0	0	0	0
145	000000000010010001	PTM	3	170	0.0264%	132	0	0	0	0	0	35	0	3	0
16401	000100000000010001	PTE	4	3	0.0005%	0	0	0	0	0	0	0	0	3	0
789	000000001100010101	PUTO+	4	15	0.0023%	0	0	0	0	0	0	0	0	15	0
22	000000000000010110	SUT	4	1	0.0002%	0	1	0	0	0	0	0	0	0	0
16402	000100000000010010	STE	4	314	0.0488%	314	0	0	0	0	0	0	0	0	0
4357	000001000100000101	PUL+	5	84	0.0131%	0	0	0	0	0	84	0	0	0	0
131073	100000000000000001	PQ	5	2	0.0003%	0	0	0	0	0	0	0	0	2	0
131077	100000000000000101	PUQ	5	1	0.0002%	0	0	0	0	0	0	0	0	1	0
131089	100000000000010001	PTQ	5	38	0.0059%	0	0	0	0	0	0	0	0	38	0
12546	000011000100000010	SLI+	5	6660	1.0349%	0	6660	0	0	0	0	0	0	0	0
21	000000000000010101	PUT	5	11	0.0017%	0	0	0	6	0	5	0	0	0	0
5378	000001010100000010	SXL+	5	1	0.0002%	0	0	0	0	0	0	0	0	1	0
4354	000001000100000010	SL+	5	2984	0.4637%	0	2984	0	0	0	0	0	0	0	0
4373	000001000100010101	PUTL+	5	9	0.0014%	0	0	0	1	0	0	0	0	8	0
5381	000001010100000101	PUXL+	5	32	0.0050%	0	0	0	5	0	19	0	0	8	0
5386	000001010100001010	SVXL+	5	1	0.0002%	0	0	0	0	0	0	0	0	1	0
1802	000000011100001010	SVOX+	5	4	0.0006%	0	0	0	0	0	0	0	0	4	0
4482	000001000110000010	SML+	5	409	0.0636%	0	409	0	0	0	0	0	0	0	0
86274	010101000100000010	SLEN+	6	2	0.0003%	0	2	0	0	0	0	0	0	0	0
81938	010100000000010010	STEN	6	24	0.0037%	24	0	0	0	0	0	0	0	0	0
81937	010100000000010001	PTEN	6	5	0.0008%	3	0	0	0	0	0	2	0	0	0
81922	010100000000000010	SEN	6	5456	0.8478%	5452	3	0	1	0	0	0	0	0	0
81921	010100000000000001	PEN	6	2868	0.4457%	2462	0	0	54	0	98	37	0	217	0
65601	010000000001000001	PDN	6	1	0.0002%	1	0	0	0	0	0	0	0	0	0
65553	010000000000010001	PTN	6	10	0.0016%	0	0	0	0	0	0	0	0	10	0
65537	010000000000000001	PN	6	6432	0.9995%	0	0	0	2705	0	601	0	0	3126	0
196625	110000000000010001	PTNQ	6	1	0.0002%	0	0	0	0	0	0	0	0	1	0

Scores (Table 2)

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.	11038(1.729%)
E	The protein reference was a retired NCBI Identifier. NCBI's eUtils (E) were used to retrieve the current accession and/or sequence.	14266(2.2346%)
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.	0(0.0%)
L	More than one possible assignment is possible (see + above). The assignment with the largest (L) SEGUID is arbitrarily chosen (see Methods)	10182(1.5949%)
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.	1655(0.2592%)
+	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).	10210(1.5993%)
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.	14799(2.3181%)
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.	28(0.0044%)
I	The protein reference used was an NCBI GenInfo Identifier (I).	20019(3.1357%)
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.	21295(3.3356%)
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	20739(3.2485%)
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.	14(0.0022%)
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(0.0066%)
P	The interaction record's primary (P) reference for the protein was used to make the assignment	593226(92.9213%)
S	One of the interaction record's secondary (S) references for the protein was used to make the assignment	45192(7.0787%)
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(0.0060%)