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From Donaldson Group

Contents 1 Summary 2 Interactions available from major taxonomies 2.1 Top 15 uncorrected taxonomy groups in iRefIndex (Taxonomy identifiers as they appear in original source) 2.2 Top 15 corrected taxonomy groups in iRefIndex (Taxonomy identifiers corrected using sequence database information) 3 Interactions (Corresponds to Table 6 in PMID 18823568) 4 Interactors 5 Summary of mapping interaction records to RIGs (Corresponds to Table 5 in PMID 18823568) 6 Assignment of protein interactors to ROGs (Corresponds to Table 3 in PMID 18823568) 7 ROG summary (Corresponds to Table 4 in PMID 18823568) 8 Scores (Corresponds to Table 2 in PMID 18823568) 9 All iRefIndex Pages

Summary

Last updated: 2011-01-12

• Total interaction source records : 1,057,642
• Total distinct interactions (based on RIGID)  : 480,368 (45.42 % of total interactions)
• Total distinct proteins (based on ROGID)  : 91,936
• Distinct proteins used in consolidated interactions : 86, 757
• Although 91,936 proteins were mapped to a ROGID, not all of them appear in iRefIndex interactions. This may be due to two reasons;

1. When not all components of an interaction was mapped to a ROGID, that interaction is not included (as it would not have a RIGID). If a protein occurred only in interactions that were not included this will not appear as part of any interaction in iRefIndex.
2. Proteins interacting with only none-proteins (DNA, small molecules etc..) will not appear in iRefIndex.

This page lists statistics for of iRefIndex that includes all of the data from sources used for the current build Sources_iRefIndex_8.0.

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	162083
9606	Homo sapiens	130732
4932	Saccharomyces cerevisiae	60164
7227	Drosophila melanogaster	46917
40674	Mammalia	36385
10090	Mus musculus	18085
83333	Escherichia coli K-12	17224
6239	Caenorhabditis elegans	13831
4896	Schizosaccharomyces pombe	13460
197	Campylobacter jejuni	12025
3702	Arabidopsis thaliana	7994
10116	Rattus norvegicus	6688
562	Escherichia coli	5294
632	Yersinia pestis	3818
160	Treponema pallidum	3647

• 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
4932	Saccharomyces cerevisiae	186503
9606	Homo sapiens	138480
7227	Drosophila melanogaster	46921
83333	Escherichia coli K-12	17008
10090	Mus musculus	14615
6239	Caenorhabditis elegans	13831
4896	Schizosaccharomyces pombe	13471
197	Campylobacter jejuni	12025
3702	Arabidopsis thaliana	7996
10116	Rattus norvegicus	5057
155864	Escherichia coli O157:H7 str. EDL933	4924
632	Yersinia pestis	3822
160	Treponema pallidum	3647
1148	Synechocystis sp. PCC 6803	3229
1392	Bacillus anthracis	3087

• Full list [[2]]

Interactions (Corresponds to Table 6 in PMID 18823568)

BIND	62862
GRID	24223	245516
DIP	26437	38962	89630
INTACT	24797	34903	37889	131339
MINT	22660	41142	36873	48037	85802
HPRD	2653	11892	1574	6777	5537	40569
OPHID	2346	8736	1442	7366	6822	13071	47522
MPACT	7084	8466	7002	6171	6470	0	0	13328
MPPI	381	145	63	95	93	212	183	0	830
CORUM	238	172	114	238	119	342	236	0	15	2607
BIND_TRANSLATION	47304	22231	25048	22972	21585	2	0	6883	113	14	49527
	BIND	GRID	DIP	INTACT	MINT	HPRD	OPHID	MPACT	MPPI	CORUM	BIND_TRANSLATION
	(9440)	(170793)	(27921)	(61935)	(18079)	(19394)	(28503)	(1152)	(267)	(1918)	(1812)

Interactors

BIND	40752
GRID	17804	31832
DIP	17676	18297	29980
INTACT	18892	22275	24274	51140
MINT	16979	18412	19687	25467	31660
HPRD	3288	6324	3868	6321	4934	9851
OPHID	3377	5783	4203	6770	5379	6712	9642
MPACT	4718	4610	4725	4880	4796	0	1	4978
MPPI	679	454	469	626	562	369	422	0	864
CORUM	2049	2246	2208	3137	2528	2032	2244	0	416	4365
BIND_TRANSLATION	28781	14239	14973	15386	14073	758	794	4303	292	659	30021
	BIND	GRID	DIP	INTACT	MINT	HPRD	OPHID	MPACT	MPPI	CORUM	BIND_TRANSLATION
	(6570)	(5419)	(2336)	(15150)	(3987)	(1185)	(1080)	(15)	(39)	(555)	(1003)

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	91228(97.0955%)	62862(68.9065%)
grid	362355	357976	357524(99.8737%)	245516(68.6712%)
dip	90994	90994	89911(98.8098%)	89630(99.6875%)
intact	156558	154962	154305(99.5760%)	131339(85.1165%)
mint	122775	122775	122298(99.6115%)	85802(70.1581%)
HPRD	83022	83022	83022(100.0000%)	40569(48.8654%)
ophid	73257	73257	73160(99.8676%)	47522(64.9563%)
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	149918	66583	65358(98.1602%)	49527(75.7780%)
ALL	1253689	1064688	1057642(99.3382%)	480368(45.4188%)

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

Source	Protein_Intractors	Assigned	%	Arbitrary	N_and_Y	Unassigned	Unique proteins
bind	285482	272804	95.5591	0	8705	3924	40752
BIND_Translation	201856	186453	92.3693	61	13807	1497	30021
CORUM	12916	12916	100.0000	0	0	0	4365
dip	30978	29430	95.0029	641	425	478	29980
grid	39352	32304	82.0899	6833	3	212	31832
HPRD	123812	120541	97.3581	3115	156	0	9851
intact	129043	124852	96.7522	37	3780	328	51140
mint	87509	83727	95.6782	2	3639	138	31660
MPACT	40349	40118	99.4275	0	1	230	4978
MPPI	3628	3457	95.2867	0	41	130	864
ophid	146423	145174	99.1470	241	1002	6	9642
All	1101348	1051916	95.5117	10930	31559	6943	91936

ROG summary (Corresponds to Table 4 in PMID 18823568)

Decimal_score	Binary_flag	String_score	Score_class	Proteins	Percentage	bind	grid	dip	intact	mint	HPRD	ophid	MPACT	BIND_Translation	MPPI	CORUM
1	000000000000000001	P	1	708614	64.3406%	231926	19822	0	121076	81586	0	125682	30666	81917	3023	12916
2	000000000000000010	S	1	57858	5.2534%	0	5	28292	361	268	21415	0	6935	582	0	0
554	000000001000101010	SVGO	1	33637	3.0542%	0	0	2	0	0	33635	0	0	0	0	0
131201	100000000010000001	PMQ	1	21014	1.9080%	0	0	0	0	0	0	0	0	21014	0	0
8194	000010000000000010	SI	1	12336	1.1201%	12336	0	0	0	0	0	0	0	0	0	0
65	000000000001000001	PD	1	8075	0.7332%	8073	0	0	0	2	0	0	0	0	0	0
42	000000000000101010	SVG	1	2422	0.2199%	0	0	104	0	0	2318	0	0	0	0	0
41	000000000000101001	PVG	1	1895	0.1721%	0	1895	0	0	0	0	0	0	0	0	0
129	000000000010000001	PM	1	548	0.0498%	473	0	0	43	0	0	0	0	0	32	0
139265	100010000000000001	PIQ	1	234	0.0212%	0	0	0	0	0	0	0	0	234	0	0
10	000000000000001010	SV	1	172	0.0156%	0	0	5	144	23	0	0	0	0	0	0
8193	000010000000000001	PI	1	59	0.0054%	0	0	0	51	8	0	0	0	0	0	0
9	000000000000001001	PV	1	6	0.0005%	0	0	0	1	5	0	0	0	0	0	0
66	000000000001000010	SD	1	4	0.0004%	0	4	0	0	0	0	0	0	0	0	0
130	000000000010000010	SM	1	1	0.0001%	0	0	0	0	0	1	0	0	0	0	0
5	000000000000000101	PU	2	23266	2.1125%	0	0	0	372	116	0	19356	2517	585	320	0
16386	000100000000000010	SE	2	5405	0.4908%	5405	0	0	0	0	0	0	0	0	0	0
147458	100100000000000010	SEQ	2	1873	0.1701%	0	0	0	0	0	0	0	0	1873	0	0
16385	000100000000000001	PE	2	156	0.0142%	0	0	0	147	9	0	0	0	0	0	0
6	000000000000000110	SU	2	129	0.0117%	0	0	100	17	4	8	0	0	0	0	0
147457	100100000000000001	PEQ	2	44	0.0040%	0	0	0	0	0	0	0	0	44	0	0
773	000000001100000101	PUO+	2	18	0.0016%	0	0	0	9	0	0	9	0	0	0	0
770	000000001100000010	SO+	2	6	0.0005%	0	0	0	6	0	0	0	0	0	0	0
16514	000100000010000010	SME	2	3	0.0003%	3	0	0	0	0	0	0	0	0	0	0
1797	000000011100000101	PUOX+	2	2	0.0002%	0	0	0	2	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
778	000000001100001010	SVO+	2	1	0.0001%	0	0	0	1	0	0	0	0	0	0	0
17	000000000000010001	PT	3	89640	8.1391%	11776	10558	0	2543	1706	0	122	0	62888	47	0
18	000000000000010010	ST	3	56632	5.1421%	0	20	925	1	0	55686	0	0	0	0	0
131217	100000000010010001	PTMQ	3	3856	0.3501%	0	0	0	0	0	0	0	0	3856	0	0
81	000000000001010001	PTD	3	1496	0.1358%	1496	0	0	0	0	0	0	0	0	0	0
8210	000010000000010010	STI	3	855	0.0776%	855	0	0	0	0	0	0	0	0	0	0
145	000000000010010001	PTM	3	189	0.0172%	132	0	0	22	0	0	0	0	0	35	0
139281	100010000000010001	PTIQ	3	41	0.0037%	0	0	0	0	0	0	0	0	41	0	0
163985	101000000010010001	PTMYQ	3	27	0.0025%	0	0	0	0	0	0	0	0	27	0	0
8209	000010000000010001	PTI	3	13	0.0012%	0	0	0	13	0	0	0	0	0	0	0
16530	000100000010010010	STME	3	13	0.0012%	13	0	0	0	0	0	0	0	0	0	0
146	000000000010010010	STM	3	3	0.0003%	0	0	0	0	0	3	0	0	0	0	0
26	000000000000011010	SVT	3	1	0.0001%	0	0	0	1	0	0	0	0	0	0	0
147474	100100000000010010	STEQ	4	507	0.0460%	0	0	0	1	0	0	0	0	506	0	0
16402	000100000000010010	STE	4	317	0.0288%	316	0	1	0	0	0	0	0	0	0	0
789	000000001100010101	PUTO+	4	14	0.0013%	0	0	0	14	0	0	0	0	0	0	0
22	000000000000010110	SUT	4	9	0.0008%	0	0	1	0	0	8	0	0	0	0	0
16401	000100000000010001	PTE	4	2	0.0002%	0	0	0	2	0	0	0	0	0	0	0
131073	100000000000000001	PQ	5	12109	1.0995%	0	0	0	6	0	0	0	0	12103	0	0
810	000000001100101010	SVGO+	5	7467	0.6780%	0	0	0	0	0	7467	0	0	0	0	0
4393	000001000100101001	PVGL+	5	6826	0.6198%	0	6826	0	0	0	0	0	0	0	0	0
4394	000001000100101010	SVGL+	5	3219	0.2923%	0	0	104	0	0	3115	0	0	0	0	0
131089	100000000000010001	PTQ	5	816	0.0741%	0	0	0	12	0	0	0	0	804	0	0
4354	000001000100000010	SL+	5	535	0.0486%	0	7	526	2	0	0	0	0	0	0	0
4357	000001000100000101	PUL+	5	226	0.0205%	0	0	0	0	0	0	222	0	4	0	0
4373	000001000100010101	PUTL+	5	65	0.0059%	0	0	0	8	0	0	0	0	57	0	0
5381	000001010100000101	PUXL+	5	29	0.0026%	0	0	0	9	1	0	19	0	0	0	0
5386	000001010100001010	SVXL+	5	18	0.0016%	0	0	0	17	1	0	0	0	0	0	0
21	000000000000010101	PUT	5	11	0.0010%	0	0	0	2	0	0	5	0	4	0	0
4374	000001000100010110	SUTL+	5	10	0.0009%	0	0	10	0	0	0	0	0	0	0	0
1802	000000011100001010	SVOX+	5	4	0.0004%	0	0	0	4	0	0	0	0	0	0	0
4358	000001000100000110	SUL+	5	1	0.0001%	0	0	1	0	0	0	0	0	0	0	0
5378	000001010100000010	SXL+	5	1	0.0001%	0	0	0	1	0	0	0	0	0	0	0
32769	001000000000000001	PY	6	14728	1.3373%	3325	1	0	2548	2824	0	732	0	5293	5	0
65601	010000000001000001	PDN	6	8195	0.7441%	52	0	0	2	247	0	253	0	7636	5	0
81922	010100000000000010	SEN	6	4422	0.4015%	4422	0	0	0	0	0	0	0	0	0	0
65537	010000000000000001	PN	6	1973	0.1791%	96	0	189	923	529	153	17	0	55	11	0
32833	001000000001000001	PDY	6	755	0.0686%	755	0	0	0	0	0	0	0	0	0	0
32770	001000000000000010	SY	6	386	0.0350%	0	2	232	94	25	0	0	1	32	0	0
212993	110100000000000001	PENQ	6	258	0.0234%	0	0	0	0	0	0	0	0	258	0	0
163969	101000000010000001	PMYQ	6	211	0.0192%	0	0	0	0	0	0	0	0	211	0	0
73729	010010000000000001	PIN	6	202	0.0183%	0	0	0	202	0	0	0	0	0	0	0
163841	101000000000000001	PYQ	6	117	0.0106%	0	0	0	0	0	0	0	0	117	0	0
32785	001000000000010001	PTY	6	81	0.0074%	35	0	0	0	0	0	0	0	46	0	0
196737	110000000010000001	PMNQ	6	40	0.0036%	0	0	0	0	0	0	0	0	40	0	0
81921	010100000000000001	PEN	6	28	0.0025%	0	0	0	1	11	0	0	0	0	16	0
196625	110000000000010001	PTNQ	6	23	0.0021%	0	0	0	1	0	0	0	0	22	0	0
65617	010000000001010001	PTDN	6	21	0.0019%	0	0	0	0	0	0	0	0	21	0	0
81938	010100000000010010	STEN	6	20	0.0018%	19	0	1	0	0	0	0	0	0	0	0
196609	110000000000000001	PNQ	6	17	0.0015%	0	0	0	1	0	0	0	0	16	0	0
163857	101000000000010001	PTYQ	6	15	0.0014%	0	0	0	0	0	0	0	0	15	0	0
213009	110100000000010001	PTENQ	6	14	0.0013%	0	0	0	0	0	0	0	0	14	0	0
65553	010000000000010001	PTN	6	12	0.0011%	0	0	1	8	0	3	0	0	0	0	0
81937	010100000000010001	PTEN	6	5	0.0005%	0	0	0	0	3	0	0	0	0	2	0
196753	110000000010010001	PTMNQ	6	2	0.0002%	0	0	0	0	0	0	0	0	2	0	0
32897	001000000010000001	PMY	6	2	0.0002%	0	0	0	0	0	0	0	0	0	2	0
196673	110000000001000001	PDNQ	6	2	0.0002%	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
147473	100100000000010001	PTEQ	6	2	0.0002%	0	0	0	0	0	0	0	0	2	0	0
81986	010100000001000010	SDEN	6	1	0.0001%	1	0	0	0	0	0	0	0	0	0	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.	18549(1.6951%)
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.	13070(1.1944%)
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.	55466(5.0688%)
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)	10930(0.9988%)
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.	25909(2.3677%)
+	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).	18443(1.6854%)
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.	15235(1.3923%)
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.	41150(3.7605%)
I	The protein reference used was an NCBI GenInfo Identifier (I).	13740(1.2556%)
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.	23781(2.1732%)
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	154714(14.1386%)
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.	55668(5.0873%)
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'.	41222(3.7671%)
P	The interaction record's primary (P) reference for the protein was used to make the assignment	905994(82.7948%)
S	One of the interaction record's secondary (S) references for the protein was used to make the assignment	188271(17.2052%)
Y	the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009)	16324(1.4918%)
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	54(0.0049%)

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