Statistics iRefIndex 5.0

Summary

• Total interactions : 871,172
• Total distinct interactions (based on RIGID): 357,156
• Total distinct proteins (based on ROGID) : 83,938

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

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

NCBI taxonomy identifier	Name	Number of interactions
4932	Saccharomyces cerevisiae	115570
9606	Homo sapiens	103700
7227	Drosophila melanogaster	46240
40674	Mammalia	35023
197	Campylobacter jejuni	11998
6239	Caenorhabditis elegans	11793
284812	Schizosaccharomyces pombe 972h-	11556
10090	Mus musculus	9964
562	Escherichia coli	8512
3702	Arabidopsis thaliana	5348
160	Treponema pallidum	3646
83333	Escherichia coli K-12	3490
10116	Rattus norvegicus	3477
1142	Synechocystis	3057
36329	Plasmodium falciparum 3D7	2731

• for the full list :http://irefindex.uio.no/wikifiles//images/9/90/Interactions_by_taxonomy_beta5_full.pdf

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

4932	Saccharomyces cerevisiae	115562
9606	Homo sapiens	114618
7227	Drosophila melanogaster	46244
197	Campylobacter jejuni	11998
4896	Schizosaccharomyces pombe	11831
6239	Caenorhabditis elegans	11793
10090	Mus musculus	8569
83333	Escherichia coli K-12	7482
3702	Arabidopsis thaliana	5354
155864	Escherichia coli O157:H7 EDL933	4928
160	Treponema pallidum	3646
1148	Synechocystis sp. PCC 6803	3166
36329	Plasmodium falciparum 3D7	2731
10116	Rattus norvegicus	2650
85962	Helicobacter pylori 26695	1598

• for the full list corrected :http://irefindex.uio.no/wikifiles//images/4/4e/Interactions_by_taxonomy_beta5_full_cor.pdf

Interactions (Corresponds to Table 6 in PMID 18823568)

BIND	62896
BIOGRID	20564	164770
DIP	25930	29004	56430
HPRD	2947	2016	858	39966
INTACT	24400	26946	25008	8442	113877
MINT	22066	34683	30052	6563	45338	76602
MPACT	6938	8489	6793	0	6132	6426	13321
MPPI	385	27	41	304	89	71	0	826
OPHID	2226	1357	899	18063	7248	6396	0	183	47297
CORUM	116	18	29	403	122	66	0	9	158	1919
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM
	(25793)	(111301)	(13496)	(16472)	(56805)	(15495)	(1132)	(235)	(26461)	(1398)

Interactors

BIND	40783
BIOGRID	14503	27694
DIP	15398	13106	20108
HPRD	3357	2522	1251	9750
INTACT	18205	16989	15721	5967	42061
MINT	16198	15112	14999	4669	23460	28424
MPACT	4651	4560	4639	0	4874	4756	4972
MPPI	674	219	294	430	579	505	0	861
OPHID	3253	2325	1242	7426	5809	4708	1	422	9626
CORUM	1561	756	671	1867	2312	1733	0	322	1849	3581
	BIND	BIOGRID	DIP	HPRD	INTACT	MINT	MPACT	MPPI	OPHID	CORUM
	(18529)	(8247)	(1834)	(1094)	(12125)	(3228)	(16)	(42)	(1257)	(620)

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	91265(97.1349%)	62896(68.9158%)
grid	242126	242126	241823(99.8749%)	164770(68.1366%)
dip	57675	57675	56597(98.1309%)	56430(99.7049%)
intact	133302	132525	132077(99.6620%)	113877(86.2202%)
mint	109398	109398	107808(98.5466%)	76602(71.0541%)
HPRD	40075	40075	40075(100.0000%)	39966(99.7280%)
ophid	73257	73257	72907(99.5222%)	47297(64.8731%)
MPACT	16504	16504	16286(98.6791%)	13321(81.7942%)
MPPI	1814	1814	1688(93.0540%)	826(48.9336%)
CORUM	2104	2104	2104(100.0000%)	1919(91.2072%)
ALL	869903	769435	762630(99.1156%)	372649(48.8637%)

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

Source	Protein_Intractors	Assigned	%	Arbitrary	New	Unassigned	Unique proteins
bind	285482	273658	95.8582	0	7887	3937	40783
CORUM	10316	10314	99.9806	0	2	0	3581
dip	20728	18527	89.3815	1246	477	478	20108
grid	29599	19354	65.3873	10141	6	98	27694
HPRD	9773	9676	99.0075	55	42	0	9750
intact	100752	97166	96.4408	19	3323	244	42061
mint	76898	73745	95.8998	2	2678	473	28424
MPACT	40349	40112	99.4126	0	0	237	4972
MPPI	3628	3457	95.2867	0	30	141	861
ophid	146423	145362	99.2754	103	699	259	9626
All	723948	691371	95.5001	11566	15144	5867	83809

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	565134	78.0628%	232690	7520	0	71606	0	125715	3023	30666	93914	0
554	000000001000101010	SVGO	1	624	0.0862%	0	0	0	0	624	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	9581	1.3234%	8084	1494	0	3	0	0	0	0	0	0
42	000000000000101010	SVG	1	163	0.0225%	0	0	0	0	163	0	0	0	0	0
8193	000010000000000001	PI	1	49	0.0068%	0	2	0	0	0	0	0	0	47	0
129	000000000010000001	PM	1	523	0.0722%	473	1	0	0	0	0	32	0	17	0
8194	000010000000000010	SI	1	12399	1.7127%	12336	63	0	0	0	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	35124	4.8517%	0	7473	17447	252	2772	0	0	6927	253	0
130	000000000010000010	SM	1	570	0.0787%	0	570	0	0	0	0	0	0	0	0
778	000000001100001010	SVO+	2	1	0.0001%	0	0	0	0	0	0	0	0	1	0
774	000000001100000110	SUO+	2	1	0.0001%	0	0	0	0	0	0	0	0	1	0
16385	000100000000000001	PE	2	184	0.0254%	0	0	0	0	0	0	0	0	184	0
16386	000100000000000010	SE	2	5414	0.7478%	5414	0	0	0	0	0	0	0	0	0
773	000000001100000101	PUO+	2	12	0.0017%	0	0	0	3	0	1	0	0	8	0
5	000000000000000101	PU	2	22812	3.1511%	0	0	0	264	0	19519	320	2519	190	0
6	000000000000000110	SU	2	767	0.1059%	0	690	60	4	5	0	0	0	8	0
145	000000000010010001	PTM	3	170	0.0235%	132	0	0	0	0	0	35	0	3	0
8210	000010000000010010	STI	3	905	0.1250%	855	50	0	0	0	0	0	0	0	0
8209	000010000000010001	PTI	3	12	0.0017%	0	0	0	0	0	0	0	0	12	0
17	000000000000010001	PT	3	26392	3.6456%	11873	0	0	1604	0	122	47	0	2456	10290
18	000000000000010010	ST	3	8547	1.1806%	0	1487	1015	0	6042	0	0	0	3	0
26	000000000000011010	SVT	3	1	0.0001%	0	0	0	0	0	0	0	0	1	0
81	000000000001010001	PTD	3	1487	0.2054%	1486	0	0	1	0	0	0	0	0	0
146	000000000010010010	STM	3	1	0.0001%	0	1	0	0	0	0	0	0	0	0
790	000000001100010110	SUTO+	4	1	0.0001%	0	0	0	0	1	0	0	0	0	0
16401	000100000000010001	PTE	4	3	0.0004%	0	0	0	0	0	0	0	0	3	0
789	000000001100010101	PUTO+	4	14	0.0019%	0	0	0	0	0	0	0	0	14	0
16402	000100000000010010	STE	4	315	0.0435%	315	0	0	0	0	0	0	0	0	0
22	000000000000010110	SUT	4	18	0.0025%	0	1	3	0	14	0	0	0	0	0
131073	100000000000000001	PQ	5	2	0.0003%	0	0	0	0	0	0	0	0	2	0
21	000000000000010101	PUT	5	33	0.0046%	0	0	0	4	0	5	0	0	0	24
12546	000011000100000010	SLI+	5	6716	0.9277%	0	6716	0	0	0	0	0	0	0	0
131077	100000000000000101	PUQ	5	1	0.0001%	0	0	0	0	0	0	0	0	1	0
131089	100000000000010001	PTQ	5	38	0.0052%	0	0	0	0	0	0	0	0	38	0
4373	000001000100010101	PUTL+	5	9	0.0012%	0	0	0	1	0	0	0	0	8	0
4354	000001000100000010	SL+	5	4208	0.5813%	0	3014	1194	0	0	0	0	0	0	0
1802	000000011100001010	SVOX+	5	3	0.0004%	0	0	0	0	0	0	0	0	3	0
810	000000001100101010	SVGO+	5	55	0.0076%	0	0	0	0	55	0	0	0	0	0
4357	000001000100000101	PUL+	5	84	0.0116%	0	0	0	0	0	84	0	0	0	0
4374	000001000100010110	SUTL+	5	52	0.0072%	0	0	52	0	0	0	0	0	0	0
4394	000001000100101010	SVGL+	5	52	0.0072%	0	0	0	0	52	0	0	0	0	0
4482	000001000110000010	SML+	5	411	0.0568%	0	411	0	0	0	0	0	0	0	0
5381	000001010100000101	PUXL+	5	29	0.0040%	0	0	0	0	0	19	0	0	10	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
86274	010101000100000010	SLEN+	6	3	0.0004%	0	2	1	0	0	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	3	0.0004%	3	0	0	0	0	0	0	0	0	0
81922	010100000000000010	SEN	6	5766	0.7965%	5397	4	364	1	0	0	0	0	0	0
81921	010100000000000001	PEN	6	2858	0.3948%	2462	0	0	49	0	98	30	0	217	2
65601	010000000001000001	PDN	6	1	0.0001%	1	0	0	0	0	0	0	0	0	0
65553	010000000000010001	PTN	6	10	0.0014%	0	0	0	0	0	0	0	0	10	0
65537	010000000000000001	PN	6	6478	0.8948%	0	0	112	2628	42	601	0	0	3095	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.	11071(1.5417%)
E	The protein reference was a retired NCBI Identifier. NCBI's eUtils (E) were used to retrieve the current accession and/or sequence.	14570(2.029%)
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.	894(0.1245%)
L	More than one possible assignment is possible (see + above). The assignment with the largest (L) SEGUID is arbitrarily chosen (see Methods)	11569(1.6111%)
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.	1675(0.2333%)
+	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).	11656(1.6232%)
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.	15144(2.109%)
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.	711(0.099%)
I	The protein reference used was an NCBI GenInfo Identifier (I).	20081(2.7965%)
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.	23836(3.3194%)
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	38036(5.2969%)
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.	914(0.1273%)
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(0.0058%)
P	The interaction record's primary (P) reference for the protein was used to make the assignment	635920(88.5583%)
S	One of the interaction record's secondary (S) references for the protein was used to make the assignment	82161(11.4417%)
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%)