Statistics iRefIndex free 6.0

• This is the statistics for the iRefIndex non-proprietary version (downloadable from ftp), for full statistics please visit http://irefindex.uio.no/wiki/Statistics_iRefIndex_6.0

Summary

• Total interactions : 641,424
• Total distinct interactions (based on RIGID): 327,736 (51.1 % of total interactions)
• Total distinct proteins (based on ROGID) : 76,013 (70,963 of them participate in distribute interactions)

Interactions (Corresponds to Table 6 in PMID 18823568)

BIND	62706
BIOGRID	22310	163090
DIP	0	0	0
HPRD	0	0	0	0
INTACT	24410	31812	0	0	112107
MINT	22293	37478	0	0	44319	76322
MPACT	0	0	0	0	0	0	0
MPPI	386	135	0	0	90	73	0	825
OPHID	2226	8303	0	0	7277	6437	0	183	47331
CORUM	0	0	0	0	0	0	0	0	0	0
I2D	0	0	0	0	0	0	0	0	0	0	0
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM	I2D
	(30476)	(109784)	(0)	(0)	(57306)	(17760)	(0)	(304)	(32821)	(0)	(0)

Interactors

BIND	40749
BIOGRID	16881	27409
DIP	0	0	0
HPRD	0	0	0	0
INTACT	18199	19405	0	0	41624
MINT	16426	17053	0	0	23360	28589
MPACT	0	0	0	0	0	0	0
MPPI	672	423	0	0	579	511	0	859
OPHID	3253	5217	0	0	5811	4804	0	421	9629
CORUM	0	0	0	0	0	0	0	0	0	0
I2D	0	0	0	0	0	0	0	0	0	0	0
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM	I2D
	(19525)	(4859)	(0)	(0)	(12981)	(3617)	(0)	(52)	(1966)	(0)	(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	90998(96.8507%)	62706(68.9092%)
grid	239485	238211	237796(99.8258%)	163090(68.5840%)
intact	133302	132525	130303(98.3233%)	112107(86.0356%)
mint	110788	110788	107860(97.3571%)	76322(70.7602%)
ophid	73257	73257	72779(99.3475%)	47331(65.0339%)
MPPI	1814	1814	1688(93.0540%)	825(48.8744%)
ALL	752294	650552	641424(98.5969%)	327736(51.0951%)

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

Source	Protein_Intractors	Assigned	%	Arbitrary	New	Unassigned	Unique proteins
bind	285482	275666	96.5616	0	5572	3938	40749
grid	27629	22417	81.1358	5079	0	133	27409
intact	100752	99219	98.4784	19	449	239	41624
mint	77936	76567	98.2434	2	298	228	28589
MPPI	3628	3459	95.3418	0	27	140	859
ophid	146423	145653	99.4741	103	280	6	9629
All	641850	625337	97.4273	5203	6626	4684	76013

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	546982	85.2196%	232419	19992	0	72231	0	125686	3023	0	93631	0
8194	000010000000000010	SI	1	12336	1.9219%	12336	0	0	0	0	0	0	0	0	0
65	000000000001000001	PD	1	8086	1.2598%	8083	0	0	3	0	0	0	0	0	0
2	000000000000000010	S	1	2877	0.4482%	0	2410	0	231	0	0	0	0	236	0
129	000000000010000001	PM	1	522	0.0813%	473	0	0	0	0	0	32	0	17	0
10	000000000000001010	SV	1	240	0.0374%	0	0	0	9	0	0	0	0	231	0
8193	000010000000000001	PI	1	48	0.0075%	0	0	0	0	0	0	0	0	48	0
5	000000000000000101	PU	2	20322	3.1662%	0	0	0	293	0	19519	320	0	190	0
16386	000100000000000010	SE	2	5413	0.8433%	5413	0	0	0	0	0	0	0	0	0
16385	000100000000000001	PE	2	884	0.1377%	0	0	0	199	0	0	0	0	685	0
16449	000100000001000001	PDE	2	116	0.0181%	0	0	0	34	0	0	0	0	82	0
6	000000000000000110	SU	2	12	0.0019%	0	0	0	4	0	0	0	0	8	0
773	000000001100000101	PUO+	2	12	0.0019%	0	0	0	3	0	1	0	0	8	0
778	000000001100001010	SVO+	2	1	0.0002%	0	0	0	0	0	0	0	0	1	0
774	000000001100000110	SUO+	2	1	0.0002%	0	0	0	0	0	0	0	0	1	0
17	000000000000010001	PT	3	16115	2.5107%	11871	0	0	1620	0	122	46	0	2456	0
81	000000000001010001	PTD	3	1487	0.2317%	1486	0	0	1	0	0	0	0	0	0
8210	000010000000010010	STI	3	855	0.1332%	855	0	0	0	0	0	0	0	0	0
145	000000000010010001	PTM	3	170	0.0265%	132	0	0	0	0	0	35	0	3	0
8209	000010000000010001	PTI	3	12	0.0019%	0	0	0	0	0	0	0	0	12	0
18	000000000000010010	ST	3	3	0.0005%	0	0	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
16402	000100000000010010	STE	4	315	0.0491%	315	0	0	0	0	0	0	0	0	0
789	000000001100010101	PUTO+	4	14	0.0022%	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
4354	000001000100000010	SL+	5	5079	0.7913%	0	5079	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
131089	100000000000010001	PTQ	5	38	0.0059%	0	0	0	0	0	0	0	0	38	0
5381	000001010100000101	PUXL+	5	29	0.0045%	0	0	0	0	0	19	0	0	10	0
4373	000001000100010101	PUTL+	5	9	0.0014%	0	0	0	1	0	0	0	0	8	0
21	000000000000010101	PUT	5	7	0.0011%	0	0	0	2	0	5	0	0	0	0
1802	000000011100001010	SVOX+	5	3	0.0005%	0	0	0	0	0	0	0	0	3	0
5386	000001010100001010	SVXL+	5	2	0.0003%	0	0	0	1	0	0	0	0	1	0
131077	100000000000000101	PUQ	5	1	0.0002%	0	0	0	0	0	0	0	0	1	0
131073	100000000000000001	PQ	5	1	0.0002%	0	0	0	0	0	0	0	0	1	0
32769	001000000000000001	PY	6	5397	0.8409%	1638	15	0	1912	0	320	3	0	1509	0
81922	010100000000000010	SEN	6	4636	0.7223%	4636	0	0	0	0	0	0	0	0	0
65537	010000000000000001	PN	6	1052	0.1639%	750	0	0	47	0	27	4	0	224	0
65601	010000000001000001	PDN	6	674	0.1050%	166	0	0	248	0	253	5	0	2	0
32833	001000000001000001	PDY	6	640	0.0997%	640	0	0	0	0	0	0	0	0	0
32770	001000000000000010	SY	6	59	0.0092%	0	0	0	25	0	0	0	0	34	0
81938	010100000000010010	STEN	6	19	0.0030%	19	0	0	0	0	0	0	0	0	0
81921	010100000000000001	PEN	6	19	0.0030%	0	0	0	3	0	0	16	0	0	0
65553	010000000000010001	PTN	6	9	0.0014%	1	0	0	0	0	0	0	0	8	0
32785	001000000000010001	PTY	6	5	0.0008%	5	0	0	0	0	0	0	0	0	0
81937	010100000000010001	PTEN	6	2	0.0003%	0	0	0	0	0	0	2	0	0	0
147473	100100000000010001	PTEQ	6	1	0.0002%	0	0	0	0	0	0	0	0	1	0
163841	101000000000000001	PYQ	6	1	0.0002%	0	0	0	0	0	0	0	0	1	0
73729	010010000000000001	PIN	6	215	0.0335%	0	0	0	0	0	0	0	0	215	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.	11003(1.7333%)
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.	11409(1.7972%)
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). (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)	5203(0.8196%)
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.	692(0.109%)
+	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).	5234(0.8245%)
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.	6626(1.0438%)
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.	31(0.0049%)
I	The protein reference used was an NCBI GenInfo Identifier (I).	13466(2.1213%)
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.	20491(3.2279%)
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	19066(3.0034%)
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.	247(0.0389%)
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	602958(94.9824%)
S	One of the interaction record's secondary (S) references for the protein was used to make the assignment	31852(5.0176%)
Y	the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009)	6102(0.9612%)
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	34(0.0054%)

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