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From Donaldson Group

Contents 1 Summary 2 Interactions available from major taxonomies 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)

Summary

• Total distinct interactions : 369,457
• Total distinct proteins : 83,388

This page lists statistics for our internal version of iRefIndex that includes all of the data from sources used for the current build Sources_iRefIndex_4.0. This full build of the iRefIndex contains data that cannot be redistributed according to usage policies of the source databases (namely, from DIP, HPRD and MPact databases). Please contact ian.donaldson at biotek.uio.no if you would like to obtain a copy of the full iRefIndex build under an academic, collaborative agreement.

The data that are freely available at ftp://ftp.no.embnet.org/irefindex/data/current/ are a subset of the full build that we can freely redistribute according to the usage policies of the source databases. Please refer to http://irefindex.uio.no/wiki/Statistics_iRefIndex_free_4.0 for statistics that are applicable to this free dataset.

Interactions available from major taxonomies

Taxonomy	Number of interactions
562 (Escherichia coli )	1243
4932 (Saccharomyces cerevisiae )	116321
6239 (Caenorhabditis elegans)	11912
7227 (Drosophila melanogaster)	46794
9606 (Homo sapiens)	117535
10090 (Mus musculus)	10098
10116 (Rattus norvegicus)	3372

• for the full list :http://irefindex.uio.no/wikifiles//images/2/20/Interactions_by_taxonomy_beta4_full.pdf

Interactions (Corresponds to Table 6 in PMID 18823568)

BIND	62921
BioGrid	20497	163891
DIP	25914	28969	56441
HPRD	2893	1958	839	37956
INTACT	24239	25653	24807	8075	111235
MINT	21991	34654	29988	6270	45260	76607
MPACT	6904	8489	6777	0	6087	6426	13321
MPPI	385	26	41	303	89	71	0	829
OPHID	2210	1333	887	17913	7196	6396	0	183	47297
CORUM	113	18	29	390	121	66	0	9	158	1919
	BIND	BioGrid	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM
	(25903)	(111633)	(13594)	(15201)	(55807)	(15712)	(1137)	(238)	(26571)	(1403)

Interactors

BIND	40801
BioGrid	14442	27471
DIP	15395	13084	20111
HPRD	3320	2472	1249	9539
INTACT	18121	16827	15687	5792	41587
MINT	16178	15064	14987	4620	23418	28428
MPACT	4638	4560	4632	0	4859	4756	4972
MPPI	671	212	292	429	575	504	0	862
OPHID	3242	2300	1241	7357	5747	4709	1	421	9629
CORUM	1551	746	670	1845	2293	1733	0	321	1849	3581
	BIND	BioGrid	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM
	(18591)	(8169)	(1838)	(1040)	(11893)	(3241)	(17)	(45)	(1280)	(626)

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	91291(97.1625%)	62921 (68.9236%)
BioGrid	240501	240501	240197(99.8736%)	163891 (68.2319%)
dip	57675	57675	56608(98.1500%)	56441 (99.7050%)
intact	129092	128326	127893(99.6626%)	111235 (86.9750%)
mint	109412	109412	107823(98.5477%)	76607 (71.0488%)
HPRD	38037	38037	38028(99.9763%)	37956 (99.8107%)
ophid	73257	73257	72907(99.5222%)	47297 (64.8731%)
MPACT	16504	16504	16286(98.6791%)	13321 (81.7942%)
MPPI	1814	1814	1697(93.5502%)	829 (48.8509%)
CORUM	2104	2104	2104(100.0000%)	1919 (91.2072%)
ALL	862044	761587	754834(99.1133%)	369457 (48.9455%)

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

Source	Protein_Intractors	Assigned	%	Arbitrary	New	Unassigned	Unique proteins
BIND	285482	273646	95.8540	0	7942	3894	40801
CORUM	10316	10314	99.9806	0	2	0	3581
dip	20728	18513	89.3140	1261	479	475	20111
BioGrid	29318	19162	65.3592	10053	5	98	27471
HPRD	9565	9493	99.2473	53	15	4	9539
intact	97988	94387	96.3251	18	3347	236	41587
mint	76908	73745	95.8873	2	2689	472	28428
MPACT	40349	40112	99.4126	0	0	237	4972
MPPI	3628	3456	95.2591	0	39	133	862
ophid	146423	145362	99.2754	103	699	259	9629
All	720705	688190	95.4884	11490	15217	5808	83388

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	562341	78.0265%	232685	7503	0	71616	0	125715	3023	30666	91133	0
130	000000000010000010	SM	1	551	0.0765%	0	551	0	0	0	0	0	0	0	0
66	000000000001000010	SD	1	2	0.0003%	0	2	0	0	0	0	0	0	0	0
65	000000000001000001	PD	1	9533	1.3227%	8084	1446	0	3	0	0	0	0	0	0
42	000000000000101010	SVG	1	149	0.0207%	0	0	0	0	149	0	0	0	0	0
8193	000010000000000001	PI	1	48	0.0067%	0	2	0	0	0	0	0	0	46	0
8194	000010000000000010	SI	1	12395	1.7198%	12336	59	0	0	0	0	0	0	0	0
129	000000000010000001	PM	1	523	0.0726%	473	1	0	0	0	0	32	0	17	0
554	000000001000101010	SVGO	1	611	0.0848%	0	0	0	0	611	0	0	0	0	0
10	000000000000001010	SV	1	13	0.0018%	0	0	2	4	0	0	0	0	7	0
2	000000000000000010	S	1	34755	4.8224%	0	7402	17432	242	2510	0	0	6927	242	0
773	000000001100000101	PUO+	2	9	0.0012%	0	0	0	3	0	0	0	0	6	0
774	000000001100000110	SUO+	2	1	0.0001%	0	0	0	0	0	0	0	0	1	0
778	000000001100001010	SVO+	2	1	0.0001%	0	0	0	0	0	0	0	0	1	0
5	000000000000000101	PU	2	22818	3.1661%	0	0	0	264	0	19520	320	2519	195	0
6	000000000000000110	SU	2	737	0.1023%	0	659	60	4	6	0	0	0	8	0
16385	000100000000000001	PE	2	189	0.0262%	0	0	0	0	0	0	0	0	189	0
16386	000100000000000010	SE	2	5405	0.7500%	5405	0	0	0	0	0	0	0	0	0
146	000000000010010010	STM	3	1	0.0001%	0	1	0	0	0	0	0	0	0	0
145	000000000010010001	PTM	3	170	0.0236%	132	0	0	0	0	0	35	0	3	0
8209	000010000000010001	PTI	3	13	0.0018%	0	0	0	0	0	0	0	0	13	0
81	000000000001010001	PTD	3	1487	0.2063%	1486	0	0	1	0	0	0	0	0	0
26	000000000000011010	SVT	3	1	0.0001%	0	0	0	0	0	0	0	0	1	0
18	000000000000010010	ST	3	8651	1.2004%	0	1487	1015	0	6146	0	0	0	3	0
17	000000000000010001	PT	3	26398	3.6628%	11876	0	0	1604	0	122	46	0	2460	10290
8210	000010000000010010	STI	3	903	0.1253%	855	48	0	0	0	0	0	0	0	0
16401	000100000000010001	PTE	4	3	0.0004%	0	0	0	0	0	0	0	0	3	0
16402	000100000000010010	STE	4	315	0.0437%	314	0	1	0	0	0	0	0	0	0
789	000000001100010101	PUTO+	4	14	0.0019%	0	0	0	0	0	0	0	0	14	0
790	000000001100010110	SUTO+	4	1	0.0001%	0	0	0	0	1	0	0	0	0	0
22	000000000000010110	SUT	4	15	0.0021%	0	1	3	0	11	0	0	0	0	0
4373	000001000100010101	PUTL+	5	9	0.0012%	0	0	0	1	0	0	0	0	8	0
12546	000011000100000010	SLI+	5	6660	0.9241%	0	6660	0	0	0	0	0	0	0	0
810	000000001100101010	SVGO+	5	59	0.0082%	0	0	0	0	59	0	0	0	0	0
21	000000000000010101	PUT	5	33	0.0046%	0	0	0	4	0	5	0	0	0	24
131073	100000000000000001	PQ	5	2	0.0003%	0	0	0	0	0	0	0	0	2	0
131077	100000000000000101	PUQ	5	1	0.0001%	0	0	0	0	0	0	0	0	1	0
131089	100000000000010001	PTQ	5	38	0.0053%	0	0	0	0	0	0	0	0	38	0
1802	000000011100001010	SVOX+	5	4	0.0006%	0	0	0	0	0	0	0	0	4	0
4354	000001000100000010	SL+	5	4193	0.5818%	0	2984	1209	0	0	0	0	0	0	0
5378	000001010100000010	SXL+	5	1	0.0001%	0	0	0	0	0	0	0	0	1	0
4482	000001000110000010	SML+	5	409	0.0567%	0	409	0	0	0	0	0	0	0	0
4394	000001000100101010	SVGL+	5	50	0.0069%	0	0	0	0	50	0	0	0	0	0
5381	000001010100000101	PUXL+	5	27	0.0037%	0	0	0	0	0	19	0	0	8	0
5382	000001010100000110	SUXL+	5	3	0.0004%	0	0	0	0	3	0	0	0	0	0
5386	000001010100001010	SVXL+	5	2	0.0003%	0	0	0	1	0	0	0	0	1	0
4374	000001000100010110	SUTL+	5	52	0.0072%	0	0	52	0	0	0	0	0	0	0
4357	000001000100000101	PUL+	5	84	0.0117%	0	0	0	0	0	84	0	0	0	0
86274	010101000100000010	SLEN+	6	3	0.0004%	0	2	1	0	0	0	0	0	0	0
82034	010100000001110010	STGDEN	6	2	0.0003%	0	0	0	0	2	0	0	0	0	0
81938	010100000000010010	STEN	6	24	0.0033%	24	0	0	0	0	0	0	0	0	0
81937	010100000000010001	PTEN	6	5	0.0007%	3	0	0	0	0	0	2	0	0	0
81922	010100000000000010	SEN	6	5823	0.8080%	5452	3	366	2	0	0	0	0	0	0
81921	010100000000000001	PEN	6	2869	0.3981%	2462	0	0	49	0	98	37	0	221	2
65601	010000000001000001	PDN	6	1	0.0001%	1	0	0	0	0	0	0	0	0	0
65553	010000000000010001	PTN	6	26	0.0036%	0	0	0	0	0	0	0	0	26	0
65537	010000000000000001	PN	6	6463	0.8968%	0	0	112	2638	13	601	0	0	3099	0
196625	110000000000010001	PTNQ	6	1	0.0001%	0	0	0	0	0	0	0	0	1	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.	11025(1.5422%)
E	The protein reference was a retired NCBI Identifier. NCBI's eUtils (E) were used to retrieve the current accession and/or sequence.	14638(2.0476%)
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.	871(0.1218%)
L	More than one possible assignment is possible (see + above). The assignment with the largest (L) SEGUID is arbitrarily chosen (see Methods)	11493(1.6076%)
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.	1654(0.2314%)
+	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).	11582(1.6201%)
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.	15217(2.1286%)
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.	700(0.0979%)
I	The protein reference used was an NCBI GenInfo Identifier (I).	20019(2.8003%)
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.	23804(3.3297%)
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	38162(5.3381%)
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.	890(0.1245%)
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(0.0059%)
P	The interaction record's primary (P) reference for the protein was used to make the assignment	633105(88.5589%)
S	One of the interaction record's secondary (S) references for the protein was used to make the assignment	81792(11.4411%)
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	37(0.0052%)