Statistics iRefIndex 13.0

Interactions available from major taxonomies (corrected)

NCBI taxonomy identifier	Scientific name	Number of interactions
9606	Homo sapiens	259634
559292	Saccharomyces cerevisiae S288c	117420
7227	Drosophila melanogaster	58383
10090	Mus musculus	31434
3702	Arabidopsis thaliana	23376
6239	Caenorhabditis elegans	17514
83333	Escherichia coli K-12	15118
192222	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	11974
284812	Schizosaccharomyces pombe 972h-	8629
10116	Rattus norvegicus	8545
632	Yersinia pestis	3958
243276	Treponema pallidum subsp. pallidum str. Nichols	3642
1111708	Synechocystis sp. PCC 6803 substr. Kazusa	3231
1392	Bacillus anthracis	3042

Interactions

	BIND	BIND_TRANSLATION	BIOGRID	CORUM	DIP	HPRD	INNATEDB	INTACT	MATRIXDB	MPACT	MPI-IMEX	MPI-LIT	MPPI	OPHID
BIND	62978	52195	22636	221	25228	1957	168	26435	4	6318	6	25	353	2159
BIND_TRANSLATION		60774	24740	195	25245	2684	236	26936	4	6284	6	21	362	2757
BIOGRID			286455	149	30154	10285	618	53317	6	4219		1	114	6619
CORUM				2607	146	154	30	361					15	239
DIP					72351	518	218	30454	3	6704	42	186	54	1160
HPRD						40536	439	5299	17				111	7327
INNATEDB							5495	686	3				18	677
INTACT								200788	16	6747	292	164	159	9901
MATRIXDB									229				1	25
MPACT										13338
MPI-IMEX											468
MPI-LIT												738
MPPI													778	181
OPHID														47497
(Exclusive to source)	8940	4364	208329	1934	26422	24895	3916	124327	186	5337	166	452	224	30445

Interactors

	BIND	BIND_TRANSLATION	BIOGRID	CORUM	DIP	HPRD	INNATEDB	INTACT	MATRIXDB	MPACT	MPI-IMEX	MPI-LIT	MPPI	OPHID
BIND	37513	30347	17198	2035	15852	2751	1355	20028	99	4360	32	85	660	3088
BIND_TRANSLATION		36160	17915	2003	16038	3095	1476	20286	117	4003	30	94	662	3342
BIOGRID			49568	2500	15195	6439	2103	30814	115	4514		2	480	5776
CORUM				4363	1581	1544	938	3735	51				408	2248
DIP					24567	1621	1211	20312	77	4553	127	387	404	2325
HPRD						9839	1377	5873	102				268	5153
INNATEDB							3776	2998	85				275	1993
INTACT								68510	191	4948	382	553	727	8039
MATRIXDB									249				15	145
MPACT										4982				1
MPI-IMEX											470	81
MPI-LIT												922
MPPI													835	418
OPHID														9525
(Exclusive to source)	5661	3529	14570	353	2352	1908	385	26107	33	18	79	307	19	652

Summary of mapping interaction records to RIGs (Table 5)

Source	Total records	Protein-related interactions	PPI assigned to RIGID	%	Unique RIGIDs	%
BIND	157736	91309	91096	99.77	62978	69.13
BIND_TRANSLATION	192923	84138	82034	97.50	60774	74.08
BIOGRID	722541	433702	431705	99.54	286455	66.35
CORUM	2844	2844	2844	100.00	2607	91.67
DIP	76271	74759	74728	99.96	72351	96.82
HPRD	83022	83022	82983	99.95	40536	48.85
INNATEDB	19531	19531	8059	41.26	5495	68.18
INTACT	281793	269273	269148	99.95	200788	74.60
MATRIXDB	1065	392	392	100.00	229	58.42
MPACT	16504	16504	16308	98.81	13338	81.79
MPI-IMEX	473	473	468	98.94	468	100.00
MPI-LIT	745	745	741	99.46	738	99.60
MPPI	1814	1758	1583	90.05	778	49.15
OPHID	73257	73257	73257	100.00	47497	64.84
(All)	1630519	1151707	1135346	98.58	566670	49.91

Assignment of protein interactors to ROGs (Table 3)

Source	Protein interactors	Assigned	%	Arbitrary	Matching sequence	New or obsolete sequence	Unassigned	Unique proteins
BIND	252251	251999	99.90	0	0	40561	252	37513
BIND_TRANSLATION	257681	252213	97.88	20799	0	23960	5468	36160
BIOGRID	50562	49780	98.45	10270	0	347	782	49568
CORUM	12916	12916	100.00	7	0	0	0	4363
DIP	25335	25320	99.94	600	0	1290	15	24567
HPRD	123812	123812	100.00	13701	96018	217	0	9839
INNATEDB	41975	26539	63.23	0	0	0	15436	3776
INTACT	223699	223586	99.95	108	35	469	113	68510
MATRIXDB	1274	1274	100.00	0	0	0	0	249
MPACT	40349	40134	99.47	0	0	3	215	4982
MPI-IMEX	946	940	99.37	2	0	0	6	470
MPI-LIT	1460	1455	99.66	7	0	0	5	922
MPPI	3568	3366	94.34	16	0	5	202	835
OPHID	146514	146514	100.00	405	12	1014	0	9525
(All)	1182342	1159848	98.10	45915	96065	67866	22494	113221

ROG summary

	BIND	BIND_TRANSLATION	BIOGRID	CORUM	DIP	HPRD	INNATEDB	INTACT	MATRIXDB	MPACT	MPI-IMEX	MPI-LIT	MPPI	OPHID
P		185575	33846	12877			26539	222535			616	1044
P+IN								2
P+LY		160	2
P+N								9
PD	124746								1271				2996	124455
PD+IN								1
PD+LQ		10194
PD+LYQ		67
PD+N														22
PD+XQ		26
PDIQ		219
PDIYQ		513
PDQ		15769
PDY	4628												5	992
PDYQ		15454
PGD		623	2050					1
PGD+L		6290	10243					7
PGD+X			12
PI								10
PIY								409
PT		2664	2538					1		30579	320	400
PTD	86577							1	3				44	114
PTD+LQ		4025
PTD+LYQ		12
PTDIYQ		13
PTDQ		2162
PTDY	218
PTDYQ		138
PTGD		23	1
PTGD+L		15	2
PTI								14
PTY			1
PU		16		32				387				2
PU+L		17		7				71				7
PU+O								19
PU+X		610						2				1
PUD	7												143	16979
PUD+L													13	265
PUD+O														12
PUD+X	82												162	3526
PUT		4						15		2527	2	1
PUT+L		19						29			2
PUT+O								16
PUTD	4													9
PUTD+L													3	140
PV								9
PV+LY								1
PVY								8
PY		7603	293					34
S		2	735		11965	84
S+L			6		190	545
S+LY			17		66	6
S+N								2
S+O						306
S+X					86
S+XY					176
SD					4061	3107
SD+L					225	378
SD+LY					29
SD+N						128
SD+O						11135
SD+OY						14
SD+X					1117
SD+XY					3
SDY					232
SGD						627
SGD+L						2094
SGD+O						15516
SI	17
SIY	32240
ST					4796	88				7025
ST+L					25	3755
ST+LY						61
ST+O						876
STD					670	8457
STD+L					4	919
STD+O						28238
STD+OY						6
STDY					2	2
STGD						1600
STGD+L						5928
STGD+O						39794
STI	5
STIY	3475
STY					2			2		3
SUD					46
SUD+L					34	8
SUD+O						2
SUD+X					773
SUTD					11
SUTD+L					27	7
SUTD+O						131
SY			34		780			1

Scores definitions (Table 2)

Character	Description of feature (when the value is 1)	align="center" style="background:#f0f0f0;"
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.
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.
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.
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)
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.
+	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).
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.
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.
I	The protein reference used was an NCBI GenInfo Identifier (I).
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.
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
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.
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'.
P	The interaction record's primary (P) reference for the protein was used to make the assignment
S	One of the interaction record's secondary (S) references for the protein was used to make the assignment
Y	the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009)
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