Statistics iRefIndex 9.0

Interactions available from major taxonomies

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

NCBI taxonomy identifier	Scientific_name	Number_of_interactions
559292	Saccharomyces cerevisiae S288c	216326
9606	Homo sapiens	145971
7227	Drosophila melanogaster	47389
4932	Saccharomyces cerevisiae	46966
40674	Mammalia	36307
10090	Mus musculus	21487
83333	Escherichia coli K-12	17673
4896	Schizosaccharomyces pombe	15493
6239	Caenorhabditis elegans	14020
197	Campylobacter jejuni	12028
3702	Arabidopsis thaliana	9911
10116	Rattus norvegicus	6917
562	Escherichia coli	5366
632	Yersinia pestis	3823
243276	Treponema pallidum subsp. pallidum str. Nichols	3642

• Full list [[1]]

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

NCBI taxonomy identifier	Scientific_name	Number_of_interactions
559292	Saccharomyces cerevisiae S288c	225644
9606	Homo sapiens	156006
7227	Drosophila melanogaster	47388
10090	Mus musculus	18312
83333	Escherichia coli K-12	17408
284812	Schizosaccharomyces pombe 972h-	15693
6239	Caenorhabditis elegans	14020
197	Campylobacter jejuni	12028
3702	Arabidopsis thaliana	9911
10116	Rattus norvegicus	5383
155864	Escherichia coli O157 H7 str. EDL933	4953
632	Yersinia pestis	3823
243276	Treponema pallidum subsp. pallidum str. Nichols	3643
1148	Synechocystis sp. PCC 6803	3240
1392	Bacillus anthracis	3090

• Full list [[2]]

Interactions

BIND	62923
GRID	24380	277531
DIP	25785	39323	89715
INTACT	25260	38185	39031	156451
MINT	21992	41551	36676	47296	85755
HPRD	1949	8718	1124	5716	4482	40488
OPHID	2414	9264	1463	7578	6912	10286	47479
MPACT	6480	8513	7019	6231	6480	0	0	13331
MPPI	420	153	65	97	93	158	187	0	830
CORUM	263	199	116	248	119	246	237	0	15	2607
BIND_TRANSLATION	56109	24375	24813	24559	21875	2200	2722	6282	391	196	60227
INNATEDB	357	1310	409	811	654	1036	1222	0	52	82	419	7000
MATRIXDB	5	11	2	15	2	14	24	0	2	0	5	5	201
MPILIT	24	0	85	114	32	0	0	0	0	0	24	0	0	745
MPIIMEX	6	0	25	34	14	0	0	0	0	0	6	0	0	30	473
	BIND	GRID	DIP	INTACT	MINT	HPRD	OPHID	MPACT	MPPI	CORUM	BIND_TRANSLATION	INNATEDB	MATRIXDB	MPILIT	MPIIMEX
	(5070)	(200591)	(27502)	(83929)	(18731)	(24349)	(28544)	(1120)	(221)	(1915)	(3055)	(4240)	(156)	(536)	(399)

Interactors

BIND	40897
GRID	18036	34410
DIP	17437	18640	29961
INTACT	19107	23866	24585	53546
MINT	16751	18749	19671	25563	31615
HPRD	2920	5853	3489	6050	4539	9825
OPHID	3397	6004	4220	7030	5398	6228	9574
MPACT	4419	4625	4734	4936	4800	0	1	4979
MPPI	705	498	479	638	565	316	425	0	865
CORUM	2140	2449	2230	3239	2535	1859	2248	0	418	4365
BIND_TRANSLATION	35150	17491	16835	18553	16180	2957	3331	4014	687	2001	37247
INNATEDB	1685	2178	1813	2614	2137	1709	2112	0	359	1148	1687	3403
MATRIXDB	115	111	88	138	116	111	144	0	18	52	114	89	221
MPILIT	89	0	332	442	227	0	0	0	0	0	90	0	0	937
MPIIMEX	32	0	111	129	65	0	0	0	0	0	30	0	0	92	473
	BIND	GRID	DIP	INTACT	MINT	HPRD	OPHID	MPACT	MPPI	CORUM	BIND_TRANSLATION	INNATEDB	MATRIXDB	MPILIT	MPIIMEX
	(4387)	(6793)	(2208)	(16016)	(3969)	(1708)	(921)	(10)	(33)	(494)	(1401)	(244)	(34)	(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	91245(97.1136%)	62923(68.9605%)
grid	416648	411219	410641(99.8594%)	277531(67.5848%)
dip	90994	90994	89910(98.8087%)	89715(99.7831%)
intact	184959	183032	182359(99.6323%)	156451(85.7929%)
mint	122775	122775	122269(99.5879%)	85755(70.1363%)
HPRD	83022	83022	83022(100.0000%)	40488(48.7678%)
ophid	73257	73257	73160(99.8676%)	47479(64.8975%)
MPACT	16504	16504	16296(98.7397%)	13331(81.8054%)
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%)	60227(72.2605%)
InnateDB	14729	11476	11248(98.0132%)	7000(62.2333%)
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	1396181	1179542	1169579(99.1554%)	545743(46.6615%)

Assignment of protein interactors to ROGs (Table 3)

Source	Protein_Intractors	Assigned	%	Arbitrary	N_and_Y	Unassigned	Unique proteins
bind	285482	272457	95.4375	0	9077	3930	40897
BIND_Translation	264346	239976	90.7810	74	15390	8902	37247
CORUM	12916	12909	99.9458	7	0	0	4365
dip	30978	29436	95.0223	609	450	483	29961
grid	45569	37348	81.9592	7948	15	258	34410
HPRD	123812	103344	83.4685	20255	213	0	9825
InnateDB	27209	26914	98.9158	0	0	295	3403
intact	154359	151337	98.0422	36	2581	405	53546
MatrixDB	1123	1077	95.9038	0	0	46	221
mint	87509	83380	95.2816	51	3933	145	31615
MPACT	40349	40121	99.4349	0	1	227	4979
mpiimex	946	946	100.0000	0	0	0	473
mpilit	1490	1487	99.7987	3	0	0	937
MPPI	3628	3456	95.2591	0	42	130	865
ophid	146423	145149	99.1299	265	1003	6	9574
All	1226139	1149359	93.7381	29248	32705	14827	97139

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	0.7218%	0	0	0	0	0	0	0	8850	0	0	0	0	0	0	0
1938	000000011110010010	STMOX+	-1	29	0.0024%	0	0	0	0	0	0	0	29	0	0	0	0	0	0	0
898	000000001110000010	SMO+	-1	21	0.0017%	0	0	0	17	0	0	0	4	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
1922	000000011110000010	SMOX+	-1	2	0.0002%	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0
914	000000001110010010	STMO+	-1	2	0.0002%	0	0	0	0	0	0	0	2	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
163921	101000000001010001	PTDYQ	-1	1	0.0001%	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
218370	110101010100000010	SXLENQ+	-1	1	0.0001%	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
1	000000000000000001	P	1	745949	60.8372%	155411	31550	0	150559	49666	932	1400	0	124701	26914	828	0	188079	3021	12888
2	000000000000000010	S	1	36416	2.9700%	0	65	22378	13	267	0	0	13128	0	0	0	0	565	0	0
131201	100000000010000001	PMQ	1	24630	2.0087%	0	0	0	0	0	0	0	0	0	0	0	0	24630	0	0
554	000000001000101010	SVGO	1	17303	1.4112%	0	0	0	0	0	0	0	17303	0	0	0	0	0	0	0
8194	000010000000000010	SI	1	12319	1.0047%	12319	0	0	0	0	0	0	0	0	0	0	0	0	0	0
65	000000000001000001	PD	1	7080	0.5774%	7079	0	0	0	1	0	0	0	0	0	0	0	0	0	0
130	000000000010000010	SM	1	6593	0.5377%	0	0	0	0	0	0	0	6593	0	0	0	0	0	0	0
41	000000000000101001	PVG	1	2223	0.1813%	0	2223	0	0	0	0	0	0	0	0	0	0	0	0	0
42	000000000000101010	SVG	1	1108	0.0904%	0	0	122	0	0	0	0	986	0	0	0	0	0	0	0
129	000000000010000001	PM	1	714	0.0582%	468	0	0	77	0	0	0	0	0	0	137	0	0	32	0
139265	100010000000000001	PIQ	1	372	0.0303%	0	0	0	0	0	0	0	0	0	0	0	0	372	0	0
10	000000000000001010	SV	1	43	0.0035%	0	0	5	3	35	0	0	0	0	0	0	0	0	0	0
8193	000010000000000001	PI	1	35	0.0029%	0	0	0	27	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	21909	1.7868%	0	0	0	289	253	9	7	0	20314	0	0	10	684	322	21
16386	000100000000000010	SE	2	4888	0.3986%	4888	0	0	0	0	0	0	0	0	0	0	0	0	0	0
770	000000001100000010	SO+	2	3478	0.2837%	0	0	0	0	0	0	0	3478	0	0	0	0	0	0	0
147458	100100000000000010	SEQ	2	2242	0.1829%	0	0	0	4	0	0	0	0	0	0	0	0	2238	0	0
6	000000000000000110	SU	2	194	0.0158%	0	1	147	27	5	0	0	13	0	0	0	0	1	0	0
16385	000100000000000001	PE	2	156	0.0127%	0	0	0	147	9	0	0	0	0	0	0	0	0	0	0
147457	100100000000000001	PEQ	2	55	0.0045%	0	0	0	0	0	0	0	0	0	0	0	0	55	0	0
773	000000001100000101	PUO+	2	21	0.0017%	0	0	0	8	2	0	0	0	11	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	156757	12.7846%	87968	3505	0	19	32901	4	79	0	118	0	2	30590	1524	47	0
18	000000000000010010	ST	3	46525	3.7944%	0	0	6773	1	18	0	0	32718	0	0	0	6994	21	0	0
146	000000000010010010	STM	3	16664	1.3591%	0	0	0	0	0	0	0	16664	0	0	0	0	0	0	0
131217	100000000010010001	PTMQ	3	4257	0.3472%	0	0	0	0	0	0	0	0	0	0	0	0	4257	0	0
81	000000000001010001	PTD	3	2567	0.2094%	2472	0	0	3	1	0	0	0	0	0	91	0	0	0	0
8210	000010000000010010	STI	3	872	0.0711%	872	0	0	0	0	0	0	0	0	0	0	0	0	0	0
145	000000000010010001	PTM	3	171	0.0139%	137	0	0	0	0	0	0	0	0	0	0	0	0	34	0
163985	101000000010010001	PTMYQ	3	52	0.0042%	0	0	0	0	0	0	0	0	0	0	0	0	52	0	0
16530	000100000010010010	STME	3	13	0.0011%	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0
8209	000010000000010001	PTI	3	13	0.0011%	0	0	0	13	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
139281	100010000000010001	PTIQ	3	7	0.0006%	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0
26	000000000000011010	SVT	3	1	0.0001%	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
16402	000100000000010010	STE	4	828	0.0675%	827	0	1	0	0	0	0	0	0	0	0	0	0	0	0
147474	100100000000010010	STEQ	4	411	0.0335%	0	0	0	2	0	0	0	0	0	0	0	0	409	0	0
22	000000000000010110	SUT	4	144	0.0117%	0	0	10	0	0	0	0	134	0	0	0	0	0	0	0
790	000000001100010110	SUTO+	4	47	0.0038%	0	0	0	18	27	0	0	2	0	0	0	0	0	0	0
789	000000001100010101	PUTO+	4	32	0.0026%	0	0	0	27	5	0	0	0	0	0	0	0	0	0	0
16401	000100000000010001	PTE	4	2	0.0002%	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0
5378	000001010100000010	SXL+	5	18721	1.5268%	0	0	0	14	1	0	0	18706	0	0	0	0	0	0	0
131073	100000000000000001	PQ	5	16324	1.3313%	0	0	0	6	0	0	0	0	0	0	0	0	16318	0	0
4393	000001000100101001	PVGL+	5	7931	0.6468%	0	7931	0	0	0	0	0	0	0	0	0	0	0	0	0
810	000000001100101010	SVGO+	5	3440	0.2806%	0	0	0	0	0	0	0	3440	0	0	0	0	0	0	0
21	000000000000010101	PUT	5	2721	0.2219%	0	0	0	15	168	1	1	0	5	0	0	2527	4	0	0
4394	000001000100101010	SVGL+	5	1650	0.1346%	0	0	112	0	0	0	0	1538	0	0	0	0	0	0	0
131089	100000000000010001	PTQ	5	859	0.0701%	0	0	0	47	0	0	0	0	0	0	0	0	812	0	0
4354	000001000100000010	SL+	5	493	0.0402%	0	17	474	2	0	0	0	0	0	0	0	0	0	0	0
4357	000001000100000101	PUL+	5	241	0.0197%	0	0	0	0	0	0	3	0	222	0	0	0	9	0	7
4373	000001000100010101	PUTL+	5	74	0.0060%	0	0	0	8	3	0	0	0	4	0	0	0	59	0	0
5381	000001010100000101	PUXL+	5	55	0.0045%	0	0	0	11	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	0.0024%	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	16102	1.3132%	3687	12	0	1963	3392	0	0	0	750	0	0	0	6293	5	0
65601	010000000001000001	PDN	6	8727	0.7117%	52	0	0	2	247	0	0	0	253	0	0	0	8168	5	0
81922	010100000000000010	SEN	6	4421	0.3606%	4421	0	0	0	0	0	0	0	0	0	0	0	0	0	0
65537	010000000000000001	PN	6	970	0.0791%	35	0	190	299	256	0	0	179	0	0	0	0	0	11	0
32833	001000000001000001	PDY	6	773	0.0630%	773	0	0	0	0	0	0	0	0	0	0	0	0	0	0
32770	001000000000000010	SY	6	427	0.0348%	0	3	258	92	28	0	0	0	0	0	0	0	46	0	0
163969	101000000010000001	PMYQ	6	402	0.0328%	0	0	0	0	0	0	0	0	0	0	0	0	402	0	0
212993	110100000000000001	PENQ	6	293	0.0239%	0	0	0	0	0	0	0	0	0	0	0	0	293	0	0
73729	010010000000000001	PIN	6	204	0.0166%	0	0	0	204	0	0	0	0	0	0	0	0	0	0	0
32785	001000000000010001	PTY	6	164	0.0134%	93	0	0	14	0	0	0	0	0	0	0	0	57	0	0
65553	010000000000010001	PTN	6	38	0.0031%	0	0	0	4	0	0	0	34	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	29	0.0024%	0	0	0	1	10	0	0	0	0	0	0	0	0	18	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	14	0.0011%	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0
32786	001000000000010010	STY	6	3	0.0002%	0	0	2	0	0	0	0	0	0	0	0	1	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
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
163857	101000000000010001	PTYQ	6	1	0.0001%	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
40978	001010000000010010	STIY	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.	19206(1.5856%)
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.	13357(1.1027%)
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.	33655(2.7784%)
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)	29249(2.4147%)
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.	53556(4.4214%)
+	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).	45176(3.7296%)
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.	14774(1.2197%)
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.	33230(2.7434%)
I	The protein reference used was an NCBI GenInfo Identifier (I).	13823(1.1412%)
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.	25488(2.1042%)
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	242211(19.9961%)
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.	33747(2.786%)
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'.	49967(4.1251%)
P	The interaction record's primary (P) reference for the protein was used to make the assignment	1023006(84.4559%)
S	One of the interaction record's secondary (S) references for the protein was used to make the assignment	188284(15.5441%)
Y	the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009)	17931(1.4803%)
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	18859(1.5569%)