Statistics iRefIndex 9.0

Interactions

BIND	62884
GRID	24360	263295
DIP	25783	39232	89716
INTACT	24813	37356	38549	155235
MINT	21678	40432	35850	47251	85758
HPRD	1826	8383	1073	5479	4337	40667
OPHID	2418	9274	1462	7537	6911	9927	47479
MPACT	6129	7831	6652	6224	6473	0	0	13328
MPPI	388	153	63	98	93	147	187	0	830
CORUM	247	193	115	244	119	233	237	0	15	2607
BIND_TRANSLATION	56122	24360	24808	24237	21605	2076	2725	5960	344	186	60291
INNATEDB	339	1272	399	783	647	1021	1212	0	52	82	399	6952
MATRIXDB	4	11	2	15	2	14	24	0	2	0	4	5	201
MPILIT	24	0	85	108	32	0	0	0	0	0	24	0	0	745
MPIIMEX	7	0	25	33	14	0	0	0	0	0	7	0	0	30	473
	BIND	GRID	DIP	INTACT	MINT	HPRD	OPHID	MPACT	MPPI	CORUM	BIND_TRANSLATION	INNATEDB	MATRIXDB	MPILIT	MPIIMEX
	(5067)	(187792)	(27732)	(83506)	(19567)	(25104)	(28622)	(1614)	(252)	(1935)	(3110)	(4265)	(156)	(541)	(398)

Interactors

BIND	40843
GRID	17950	33559
DIP	17386	18500	29969
INTACT	18803	23233	24392	52757
MINT	16524	18446	19518	25481	31622
HPRD	2870	5757	3444	5955	4497	9863
OPHID	3398	5928	4220	6976	5398	6165	9577
MPACT	4286	4491	4603	4934	4797	0	1	4978
MPPI	682	476	470	636	564	305	424	0	863
CORUM	2071	2344	2212	3217	2532	1833	2248	0	417	4365
BIND_TRANSLATION	35168	17405	16787	18274	15971	2913	3330	3899	660	1931	37322
INNATEDB	1616	2072	1786	2556	2128	1683	2106	0	358	1144	1617	3387
MATRIXDB	112	111	87	138	116	110	144	0	18	52	111	89	221
MPILIT	88	0	332	441	227	0	0	0	0	0	89	0	0	937
MPIIMEX	33	0	111	128	65	0	0	0	0	0	31	0	0	92	473
	BIND	GRID	DIP	INTACT	MINT	HPRD	OPHID	MPACT	MPPI	CORUM	BIND_TRANSLATION	INNATEDB	MATRIXDB	MPILIT	MPIIMEX
	(4329)	(6404)	(2245)	(15612)	(4048)	(1816)	(944)	(12)	(35)	(521)	(1457)	(264)	(35)	(367)	(282)

Summary of mapping interaction records to RIGs (Table 5)

Source	Total records	Protein-only interactors	PPI Assigned to RIGID	Unique RIGIDs
bind	193648	93957	91249(97.1178%)	62884(68.9147%)
grid	392218	386984	386462(99.8651%)	263295(68.1296%)
dip	90994	90994	89910(98.8087%)	89716(99.7842%)
intact	183079	181384	180718(99.6328%)	155235(85.8990%)
mint	122775	122775	122269(99.5879%)	85758(70.1388%)
HPRD	83022	83022	83022(100.0000%)	40667(48.9834%)
ophid	73257	73257	73160(99.8676%)	47479(64.8975%)
MPACT	16504	16504	16293(98.7215%)	13328(81.8020%)
MPPI	1814	1814	1699(93.6604%)	830(48.8523%)
CORUM	2844	2844	2844(100.0000%)	2607(91.6667%)
BIND_Translation	192923	87081	83347(95.7120%)	60291(72.3373%)
InnateDB	14729	11476	11176(97.3858%)	6952(62.2047%)
MatrixDB	846	349	321(91.9771%)	201(62.6168%)
mpilit	745	745	745(100.0000%)	745(100.0000%)
mpiimex	473	473	473(100.0000%)	473(100.0000%)
ALL	1369871	1153659	1143688(99.1357%)	533807(46.6742%)

Assignment of protein interactors to ROGs (Table 3)

Source	Protein_Intractors	Assigned	%	Arbitrary	N_and_Y	Unassigned	Unique proteins
bind	285482	272483	95.4466	0	9055	3924	40843
BIND_Translation	264346	239986	90.7848	70	15384	8902	37322
CORUM	12916	12909	99.9458	7	0	0	4365
dip	30978	29258	94.4477	787	450	483	29969
grid	41420	34125	82.3877	7065	7	223	33559
HPRD	123812	108048	87.2678	15533	231	0	9863
InnateDB	27209	26833	98.6181	0	0	376	3387
intact	150972	148099	98.0970	38	2433	402	52757
MatrixDB	1123	1077	95.9038	0	0	46	221
mint	87509	83387	95.2896	51	3926	145	31622
MPACT	40349	40118	99.4275	0	1	230	4978
mpiimex	946	946	100.0000	0	0	0	473
mpilit	1490	1487	99.7987	3	0	0	937
MPPI	3628	3455	95.2315	0	42	131	863
ophid	146423	145149	99.1299	265	1003	6	9577
All	1218603	1147384	94.1557	23819	32532	14868	96627

ROG summary

Decimal_score	Binary_flag	String_score	Score_class	Proteins	Percentage	bind	grid	dip	intact	mint	mpiimex	mpilit	HPRD	ophid	InnateDB	MatrixDB	MPACT	BIND_Translation	MPPI	CORUM
786	000000001100010010	STO+	-1	8853	0.7265%	0	0	0	0	0	0	0	8853	0	0	0	0	0	0	0
1938	000000011110010010	STMOX+	-1	496	0.0407%	0	0	0	2	0	0	0	494	0	0	0	0	0	0	0
5506	000001010110000010	SMXL+	-1	79	0.0065%	0	0	0	0	0	0	0	79	0	0	0	0	0	0	0
914	000000001110010010	STMO+	-1	18	0.0015%	0	0	0	16	0	0	0	2	0	0	0	0	0	0	0
217346	110101000100000010	SLENQ+	-1	7	0.0006%	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0
131093	100000000000010101	PUTQ	-1	5	0.0004%	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0
163905	101000000001000001	PDYQ	-1	2	0.0002%	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0
218370	110101010100000010	SXLENQ+	-1	1	0.0001%	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
163921	101000000001010001	PTDYQ	-1	1	0.0001%	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
1	000000000000000001	P	1	666026	54.6549%	127542	28701	0	101092	49820	936	1405	0	124771	26833	828	0	188186	3021	12891
2	000000000000000010	S	1	45077	3.6991%	0	66	22776	12	270	0	0	21388	0	0	0	0	565	0	0
554	000000001000101010	SVGO	1	17263	1.4166%	0	0	0	0	0	0	0	17263	0	0	0	0	0	0	0
8194	000010000000000010	SI	1	12276	1.0074%	12276	0	0	0	0	0	0	0	0	0	0	0	0	0	0
65	000000000001000001	PD	1	7142	0.5861%	7141	0	0	0	1	0	0	0	0	0	0	0	0	0	0
41	000000000000101001	PVG	1	1936	0.1589%	0	1936	0	0	0	0	0	0	0	0	0	0	0	0	0
42	000000000000101010	SVG	1	1123	0.0922%	0	0	122	0	0	0	0	1001	0	0	0	0	0	0	0
131201	100000000010000001	PMQ	1	942	0.0773%	0	0	0	0	0	0	0	0	0	0	0	0	942	0	0
139265	100010000000000001	PIQ	1	295	0.0242%	0	0	0	0	0	0	0	0	0	0	0	0	295	0	0
129	000000000010000001	PM	1	216	0.0177%	0	0	0	47	0	0	0	0	0	0	137	0	0	32	0
10	000000000000001010	SV	1	71	0.0058%	0	0	5	35	31	0	0	0	0	0	0	0	0	0	0
8193	000010000000000001	PI	1	36	0.0030%	0	0	0	28	8	0	0	0	0	0	0	0	0	0	0
66	000000000001000010	SD	1	22	0.0018%	0	4	0	0	0	0	0	0	0	0	18	0	0	0	0
9	000000000000001001	PV	1	5	0.0004%	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0
5	000000000000000101	PU	2	21578	1.7707%	0	0	0	61	235	9	3	0	20246	0	0	0	684	322	18
16386	000100000000000010	SE	2	4866	0.3993%	4866	0	0	0	0	0	0	0	0	0	0	0	0	0	0
6	000000000000000110	SU	2	173	0.0142%	0	0	128	26	5	0	0	13	0	0	0	0	1	0	0
16385	000100000000000001	PE	2	153	0.0126%	0	0	0	144	9	0	0	0	0	0	0	0	0	0	0
147458	100100000000000010	SEQ	2	150	0.0123%	0	0	0	4	0	0	0	0	0	0	0	0	146	0	0
147457	100100000000000001	PEQ	2	52	0.0043%	0	0	0	0	0	0	0	0	0	0	0	0	52	0	0
773	000000001100000101	PUO+	2	17	0.0014%	0	0	0	7	1	0	0	0	9	0	0	0	0	0	0
16514	000100000010000010	SME	2	9	0.0007%	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0
1797	000000011100000101	PUOX+	2	4	0.0003%	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0
774	000000001100000110	SUO+	2	1	0.0001%	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
17	000000000000010001	PT	3	230967	18.9534%	115853	3418	0	46440	32920	1	79	0	118	0	2	30656	1434	46	0
18	000000000000010010	ST	3	45443	3.7291%	0	0	6223	1	18	0	0	32179	0	0	0	7001	21	0	0
131217	100000000010010001	PTMQ	3	27945	2.2932%	0	0	0	0	0	0	0	0	0	0	0	0	27945	0	0
146	000000000010010010	STM	3	23248	1.9078%	0	0	0	0	0	0	0	23248	0	0	0	0	0	0	0
81	000000000001010001	PTD	3	2506	0.2056%	2414	0	0	0	1	0	0	0	0	0	91	0	0	0	0
8210	000010000000010010	STI	3	915	0.0751%	915	0	0	0	0	0	0	0	0	0	0	0	0	0	0
145	000000000010010001	PTM	3	662	0.0543%	605	0	0	23	0	0	0	0	0	0	0	0	0	34	0
139281	100010000000010001	PTIQ	3	84	0.0069%	0	0	0	0	0	0	0	0	0	0	0	0	84	0	0
163985	101000000010010001	PTMYQ	3	58	0.0048%	0	0	0	0	0	0	0	0	0	0	0	0	58	0	0
8209	000010000000010001	PTI	3	16	0.0013%	0	0	0	16	0	0	0	0	0	0	0	0	0	0	0
82	000000000001010010	STD	3	10	0.0008%	0	0	0	0	9	0	0	0	0	0	1	0	0	0	0
16530	000100000010010010	STME	3	7	0.0006%	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0
26	000000000000011010	SVT	3	1	0.0001%	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
147474	100100000000010010	STEQ	4	2496	0.2048%	0	0	0	2	0	0	0	0	0	0	0	0	2494	0	0
16402	000100000000010010	STE	4	856	0.0702%	855	0	1	0	0	0	0	0	0	0	0	0	0	0	0
22	000000000000010110	SUT	4	137	0.0112%	0	0	3	0	0	0	0	134	0	0	0	0	0	0	0
790	000000001100010110	SUTO+	4	48	0.0039%	0	0	0	19	27	0	0	2	0	0	0	0	0	0	0
789	000000001100010101	PUTO+	4	32	0.0026%	0	0	0	28	4	0	0	0	0	0	0	0	0	0	0
16401	000100000000010001	PTE	4	3	0.0002%	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0
131073	100000000000000001	PQ	5	16324	1.3396%	0	0	0	6	0	0	0	0	0	0	0	0	16318	0	0
5378	000001010100000010	SXL+	5	13950	1.1448%	0	0	0	15	1	0	0	13934	0	0	0	0	0	0	0
4393	000001000100101001	PVGL+	5	7049	0.5784%	0	7049	0	0	0	0	0	0	0	0	0	0	0	0	0
810	000000001100101010	SVGO+	5	3471	0.2848%	0	0	0	0	0	0	0	3471	0	0	0	0	0	0	0
21	000000000000010101	PUT	5	2521	0.2069%	0	0	0	28	23	0	0	0	5	0	0	2461	4	0	0
4394	000001000100101010	SVGL+	5	1621	0.1330%	0	0	112	0	0	0	0	1509	0	0	0	0	0	0	0
131089	100000000000010001	PTQ	5	860	0.0706%	0	0	0	48	0	0	0	0	0	0	0	0	812	0	0
4354	000001000100000010	SL+	5	670	0.0550%	0	16	652	2	0	0	0	0	0	0	0	0	0	0	0
4357	000001000100000101	PUL+	5	241	0.0198%	0	0	0	0	0	0	3	0	222	0	0	0	9	0	7
4373	000001000100010101	PUTL+	5	70	0.0057%	0	0	0	8	3	0	0	0	4	0	0	0	55	0	0
5381	000001010100000101	PUXL+	5	56	0.0046%	0	0	0	12	5	0	0	0	39	0	0	0	0	0	0
5386	000001010100001010	SVXL+	5	43	0.0035%	0	0	0	1	42	0	0	0	0	0	0	0	0	0	0
4374	000001000100010110	SUTL+	5	30	0.0025%	0	0	17	0	0	0	0	7	0	0	0	0	6	0	0
4358	000001000100000110	SUL+	5	6	0.0005%	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0
5382	000001010100000110	SUXL+	5	4	0.0003%	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0
32769	001000000000000001	PY	6	15958	1.3095%	3658	5	0	1873	3388	0	0	0	750	0	0	0	6279	5	0
65601	010000000001000001	PDN	6	8727	0.7161%	52	0	0	2	247	0	0	0	253	0	0	0	8168	5	0
81922	010100000000000010	SEN	6	4426	0.3632%	4426	0	0	0	0	0	0	0	0	0	0	0	0	0	0
65537	010000000000000001	PN	6	959	0.0787%	35	0	190	263	256	0	0	204	0	0	0	0	0	11	0
32833	001000000001000001	PDY	6	769	0.0631%	769	0	0	0	0	0	0	0	0	0	0	0	0	0	0
32770	001000000000000010	SY	6	420	0.0345%	0	2	258	88	25	0	0	0	0	0	0	1	46	0	0
163969	101000000010000001	PMYQ	6	396	0.0325%	0	0	0	0	0	0	0	0	0	0	0	0	396	0	0
212993	110100000000000001	PENQ	6	291	0.0239%	0	0	0	0	0	0	0	0	0	0	0	0	291	0	0
73729	010010000000000001	PIN	6	198	0.0162%	0	0	0	198	0	0	0	0	0	0	0	0	0	0	0
32785	001000000000010001	PTY	6	164	0.0135%	104	0	0	2	0	0	0	0	0	0	0	0	58	0	0
65553	010000000000010001	PTN	6	31	0.0025%	0	0	0	4	0	0	0	27	0	0	0	0	0	0	0
196609	110000000000000001	PNQ	6	31	0.0025%	0	0	0	0	0	0	0	0	0	0	0	0	31	0	0
81921	010100000000000001	PEN	6	27	0.0022%	0	0	0	1	10	0	0	0	0	0	0	0	0	16	0
65617	010000000001010001	PTDN	6	23	0.0019%	0	0	0	0	0	0	0	0	0	0	0	0	23	0	0
196625	110000000000010001	PTNQ	6	22	0.0018%	0	0	0	0	0	0	0	0	0	0	0	0	22	0	0
81938	010100000000010010	STEN	6	9	0.0007%	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0
147473	100100000000010001	PTEQ	6	3	0.0002%	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0
213009	110100000000010001	PTENQ	6	2	0.0002%	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0
32786	001000000000010010	STY	6	2	0.0002%	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0
32897	001000000010000001	PMY	6	2	0.0002%	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
81937	010100000000010001	PTEN	6	2	0.0002%	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
163857	101000000000010001	PTYQ	6	1	0.0001%	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
32913	001000000010010001	PTMY	6	1	0.0001%	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
40978	001010000000010010	STIY	6	1	0.0001%	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
81986	010100000001000010	SDEN	6	1	0.0001%	1	0	0	0	0	0	0	0	0	0	0	0	0	0	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.	19203(1.5953%)
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, sequence information obtained from UniProt.	13361(1.11%)
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.	32463(2.6969%)
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)	23827(1.9795%)
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.	54079(4.4927%)
+	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).	36767(3.0545%)
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.	14757(1.226%)
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.	30203(2.5092%)
I	The protein reference used was an NCBI GenInfo Identifier (I).	13821(1.1482%)
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.	24923(2.0705%)
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	348549(28.9562%)
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.	32583(2.7069%)
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'.	49968(4.1512%)
P	The interaction record's primary (P) reference for the protein was used to make the assignment	1015411(84.3567%)
S	One of the interaction record's secondary (S) references for the protein was used to make the assignment	188300(15.6433%)
Y	the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009)	17775(1.4767%)
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	14633(1.2157%)