Statistics iRefIndex 9.0

Interactions

BIND	62901
GRID	24424	263295
DIP	25910	38242	89716
INTACT	25434	37330	39017	155235
MINT	22278	40367	36677	47248	85758
HPRD	1955	8695	1125	5667	4489	40460
OPHID	2418	9274	1462	7537	6911	10267	47479
MPACT	6714	7768	6992	6210	6464	0	0	13311
MPPI	387	153	63	98	93	160	187	0	830
CORUM	248	193	115	244	119	248	237	0	15	2607
BIND_TRANSLATION	56114	24426	25078	24832	22203	2206	2725	6542	344	186	60212
INNATEDB	339	1273	403	789	654	1045	1221	0	52	82	399	7000
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	744
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
	(5184)	(188537)	(27825)	(83340)	(19066)	(24359)	(28562)	(1588)	(248)	(1932)	(3054)	(4297)	(156)	(540)	(398)

Interactors

BIND	40790
GRID	17983	33559
DIP	17562	18347	29969
INTACT	19129	23211	24531	52751
MINT	16844	18434	19654	25479	31621
HPRD	2926	5803	3484	6005	4536	9824
OPHID	3400	5928	4220	6976	5398	6218	9577
MPACT	4585	4477	4730	4932	4795	0	1	4976
MPPI	682	476	470	636	564	316	424	0	864
CORUM	2072	2344	2212	3217	2532	1858	2248	0	417	4365
BIND_TRANSLATION	35081	17444	16970	18582	16279	2960	3333	4189	660	1932	37155
INNATEDB	1620	2076	1791	2564	2136	1707	2112	0	359	1148	1622	3403
MATRIXDB	112	111	87	138	116	111	144	0	18	52	111	89	221
MPILIT	92	0	332	440	227	0	0	0	0	0	92	0	0	936
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
	(4337)	(6423)	(2236)	(15606)	(4032)	(1718)	(943)	(11)	(35)	(521)	(1398)	(269)	(35)	(366)	(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	91268(97.1381%)	62901(68.9190%)
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%)	40460(48.7341%)
ophid	73257	73257	73160(99.8676%)	47479(64.8975%)
MPACT	16504	16504	16273(98.6003%)	13311(81.7981%)
MPPI	1814	1814	1699(93.6604%)	830(48.8523%)
CORUM	2844	2844	2844(100.0000%)	2607(91.6667%)
BIND_Translation	192923	87081	83349(95.7143%)	60212(72.2408%)
InnateDB	14729	11476	11248(98.0132%)	7000(62.2333%)
MatrixDB	846	349	321(91.9771%)	201(62.6168%)
mpilit	745	745	745(100.0000%)	744(99.8658%)
mpiimex	473	473	473(100.0000%)	473(100.0000%)
ALL	1369871	1153659	1143761(99.1420%)	532634(46.5686%)

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	9075	3924	40790
BIND_Translation	264346	239988	90.7856	73	15383	8902	37155
CORUM	12916	12909	99.9458	7	0	0	4365
dip	30978	29401	94.9093	640	454	483	29969
grid	41420	34125	82.3877	7065	7	223	33559
HPRD	123812	103372	83.4911	20209	231	0	9824
InnateDB	27209	26914	98.9158	0	0	295	3403
intact	150972	148103	98.0996	34	2433	402	52751
MatrixDB	1123	1077	95.9038	0	0	46	221
mint	87509	83389	95.2919	48	3927	145	31621
MPACT	40349	40098	99.3779	0	1	250	4976
mpiimex	946	946	100.0000	0	0	0	473
mpilit	1490	1486	99.7315	3	1	0	936
MPPI	3628	3456	95.2591	0	42	130	864
ophid	146423	145149	99.1299	265	1003	6	9577
All	1218603	1142896	93.7874	28344	32557	14806	96059

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	8850	0.7262%	0	0	0	0	0	0	0	8850	0	0	0	0	0	0	0
898	000000001110000010	SMO+	-1	20	0.0016%	0	0	0	16	0	0	0	4	0	0	0	0	0	0	0
1794	000000011100000010	SOX+	-1	8	0.0007%	0	0	0	6	2	0	0	0	0	0	0	0	0	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
914	000000001110010010	STMO+	-1	2	0.0002%	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0
1922	000000011110000010	SMOX+	-1	2	0.0002%	0	0	0	2	0	0	0	0	0	0	0	0	0	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	809581	66.4352%	229929	21809	0	147356	81034	934	1472	0	124771	26914	828	30649	127973	3021	12891
2	000000000000000010	S	1	51662	4.2394%	0	41	28210	15	294	0	0	13141	0	0	0	9375	586	0	0
131201	100000000010000001	PMQ	1	23587	1.9356%	0	0	0	0	0	0	0	0	0	0	0	0	23587	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	12336	1.0123%	12336	0	0	0	0	0	0	0	0	0	0	0	0	0	0
65	000000000001000001	PD	1	8057	0.6612%	8055	0	0	0	2	0	0	0	0	0	0	0	0	0	0
130	000000000010000010	SM	1	6594	0.5411%	0	0	0	0	0	0	0	6594	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
129	000000000010000001	PM	1	688	0.0565%	470	0	0	49	0	0	0	0	0	0	137	0	0	32	0
139265	100010000000000001	PIQ	1	337	0.0277%	0	0	0	0	0	0	0	0	0	0	0	0	337	0	0
10	000000000000001010	SV	1	84	0.0069%	0	0	5	44	35	0	0	0	0	0	0	0	0	0	0
8193	000010000000000001	PI	1	37	0.0030%	0	0	0	29	8	0	0	0	0	0	0	0	0	0	0
66	000000000001000010	SD	1	35	0.0029%	0	4	0	0	13	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	21571	1.7701%	0	0	0	61	234	9	2	0	20246	0	0	0	679	322	18
16386	000100000000000010	SE	2	5377	0.4412%	5377	0	0	0	0	0	0	0	0	0	0	0	0	0	0
770	000000001100000010	SO+	2	3486	0.2861%	0	0	0	4	0	0	0	3482	0	0	0	0	0	0	0
147458	100100000000000010	SEQ	2	1985	0.1629%	0	0	0	4	0	0	0	0	0	0	0	0	1981	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
147457	100100000000000001	PEQ	2	53	0.0043%	0	0	0	0	0	0	0	0	0	0	0	0	53	0	0
773	000000001100000101	PUO+	2	17	0.0014%	0	0	0	7	1	0	0	0	9	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
16514	000100000010000010	SME	2	3	0.0002%	3	0	0	0	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	87494	7.1799%	13466	10310	0	176	1706	3	12	0	118	0	2	7	61647	47	0
18	000000000000010010	ST	3	33709	2.7662%	0	25	931	1	0	0	0	32752	0	0	0	0	0	0	0
146	000000000010010010	STM	3	16663	1.3674%	0	0	0	0	0	0	0	16663	0	0	0	0	0	0	0
131217	100000000010010001	PTMQ	3	5300	0.4349%	0	0	0	0	0	0	0	0	0	0	0	0	5300	0	0
81	000000000001010001	PTD	3	1591	0.1306%	1500	0	0	0	0	0	0	0	0	0	91	0	0	0	0
8210	000010000000010010	STI	3	855	0.0702%	855	0	0	0	0	0	0	0	0	0	0	0	0	0	0
145	000000000010010001	PTM	3	190	0.0156%	135	0	0	21	0	0	0	0	0	0	0	0	0	34	0
163985	101000000010010001	PTMYQ	3	57	0.0047%	0	0	0	0	0	0	0	0	0	0	0	0	57	0	0
139281	100010000000010001	PTIQ	3	42	0.0034%	0	0	0	0	0	0	0	0	0	0	0	0	42	0	0
8209	000010000000010001	PTI	3	15	0.0012%	0	0	0	15	0	0	0	0	0	0	0	0	0	0	0
16530	000100000010010010	STME	3	13	0.0011%	13	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
82	000000000001010010	STD	3	1	0.0001%	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
147474	100100000000010010	STEQ	4	668	0.0548%	0	0	0	2	0	0	0	0	0	0	0	0	666	0	0
16402	000100000000010010	STE	4	345	0.0283%	344	0	1	0	0	0	0	0	0	0	0	0	0	0	0
22	000000000000010110	SUT	4	138	0.0113%	0	0	4	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	19	0.0016%	0	0	0	18	1	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
5378	000001010100000010	SXL+	5	18701	1.5346%	0	0	0	11	1	0	0	18689	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
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
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	528	0.0433%	0	16	510	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
21	000000000000010101	PUT	5	108	0.0089%	0	0	0	20	12	0	0	0	5	0	0	67	4	0	0
4373	000001000100010101	PUTL+	5	70	0.0057%	0	0	0	8	0	0	0	0	4	0	0	0	58	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	25	0.0021%	0	0	12	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
1802	000000011100001010	SVOX+	5	1	0.0001%	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
32769	001000000000000001	PY	6	15999	1.3129%	3696	5	0	1873	3389	0	1	0	750	0	0	0	6280	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	4417	0.3625%	4417	0	0	0	0	0	0	0	0	0	0	0	0	0	0
65537	010000000000000001	PN	6	969	0.0795%	35	0	189	263	256	0	0	215	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	424	0.0348%	0	2	262	88	25	0	0	0	0	0	0	1	46	0	0
163969	101000000010000001	PMYQ	6	401	0.0329%	0	0	0	0	0	0	0	0	0	0	0	0	401	0	0
212993	110100000000000001	PENQ	6	279	0.0229%	0	0	0	0	0	0	0	0	0	0	0	0	279	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	147	0.0121%	86	0	0	2	0	0	0	0	0	0	0	0	59	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
65553	010000000000010001	PTN	6	21	0.0017%	0	0	1	4	0	0	0	16	0	0	0	0	0	0	0
81938	010100000000010010	STEN	6	19	0.0016%	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0
213009	110100000000010001	PTENQ	6	14	0.0011%	0	0	0	0	0	0	0	0	0	0	0	0	14	0	0
32897	001000000010000001	PMY	6	2	0.0002%	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
32786	001000000000010010	STY	6	2	0.0002%	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0
81937	010100000000010001	PTEN	6	2	0.0002%	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
147473	100100000000010001	PTEQ	6	2	0.0002%	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0
163857	101000000000010001	PTYQ	6	1	0.0001%	0	0	0	1	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
32913	001000000010010001	PTMY	6	1	0.0001%	0	0	0	0	0	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.	19207(1.5955%)
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.	13362(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(2.6967%)
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)	28345(2.3546%)
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.	53523(4.4462%)
+	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).	44274(3.6779%)
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.	14751(1.2254%)
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.	33192(2.7573%)
I	The protein reference used was an NCBI GenInfo Identifier (I).	13820(1.148%)
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.	22486(1.8679%)
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	157327(13.0692%)
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.	32597(2.7078%)
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'.	49972(4.1512%)
P	The interaction record's primary (P) reference for the protein was used to make the assignment	1013088(84.1577%)
S	One of the interaction record's secondary (S) references for the protein was used to make the assignment	190709(15.8423%)
Y	the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009)	17806(1.4792%)
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	18820(1.5634%)