Statistics iRefIndex 19.0

Interactions available from major taxonomies (corrected)

Taxons of the protein interactors have been corrected to correspond to the taxon provided in the protein sequence record regardless of the taxon listed in the interaction record. See PMID 18823568 for details.

NCBI taxonomy identifier	Scientific name	Number of interactions
9606	Homo sapiens	1096914
559292	Saccharomyces cerevisiae S288C	155935
10090	Mus musculus	104631
3702	Arabidopsis thaliana	87766
7227	Drosophila melanogaster	86357
6239	Caenorhabditis elegans	41801
2697049	Severe acute respiratory syndrome coronavirus 2	22047
83333	Escherichia coli K-12	16903
10116	Rattus norvegicus	15952
4896	Schizosaccharomyces pombe	13816
316407	Escherichia coli str. K-12 substr. W3110	12822
192222	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	11931
381518	Influenza A virus (A/Wilson-Smith/1933(H1N1))	5101
632	Yersinia pestis	4147

Summary of mapping interaction records to RIGs (redundant interaction groups)

Source: Interaction data source. Total records: Total number of interaction records found in source. Protein-only interactors:Total number of interactions involving only protein interactors. PPI assigned to RIGID: Number of interactions where all protein interactors were assigned to a ROG. Percentage of column 3 is shown. Unique RIGIDs (interactions): Number of unique protein interactions and complexes (RIGID's) found in the data source (also expressed as a percentage of column 4). For a description of the term RIGs, see README_MITAB2.6_for_iRefIndex#Understanding_the_iRefIndex_MITAB_format and the original paper PMID 18823568.

Source	Total records	Protein-related interactions	PPI assigned to RIGID	%	Unique RIGIDs	%
BAR	9641	9637	9631	99.94	9511	98.75
BHF_UCL	2341	2325	2325	100.00	1512	65.03
BIND	157736	91309	68064	74.54	49511	72.74
BIND_TRANSLATION	192923	84138	82342	97.87	60892	73.95
BIOGRID	2381483	1468878	1461287	99.48	1104937	75.61
CORUM	4274	4274	4270	99.91	4018	94.10
DIP	81731	80134	79876	99.68	77466	96.98
HPIDB	3019	2847	2847	100.00	1562	54.86
HPRD	83022	83022	83022	100.00	40551	48.84
HURI	171545	168756	168750	100.00	51482	30.51
IMEX	604755	584805	584779	100.00	298580	51.06
INNATEDB	18408	18408	6888	37.42	4802	69.72
INTACT	740851	679738	679615	99.98	378244	55.66
INTCOMPLEX	3795	3061	3061	100.00	3009	98.30
MATRIXDB	1776	1775	1775	100.00	1419	79.94
MBINFO	542	522	522	100.00	331	63.41
MINT	86801	86192	86177	99.98	49603	57.56
MPACT	16504	16504	16373	99.21	13398	81.83
MPIDB	1497	1461	1461	100.00	923	63.18
MPPI	1814	1758	1578	89.76	776	49.18
QUICKGO	60413	51679	51139	98.96	24350	47.62
REACTOME	141996	141996	141844	99.89	126328	89.06
UNIPROTPP	16297	16197	16197	100.00	9431	58.23
VIRUSHOST	55115	55115	55115	100.00	47015	85.30
(All)	4838279	3654531	3608938	98.75	1647374	45.65

Assignment of protein interactors to ROGs (redundant object group)

Source: Interaction data source (see methods). Protein interactors: Total number of interactors found in all interaction records. Assigned: Number of proteins assigned unambiguously to a ROG. Assignments listed in columns 5 and 6 are not included here. %: Column 3 expressed as a percentage of column 2. Arbitrary: Total number of ROG assignments that were ambiguous and resolved with an arbitrary method (see ROG scores with 'L'). Matching sequence: Total number of assignments made where a sequence in the interaction record matched a known sequence. Unassigned:Total number of protein interactors that could not be assigned to a ROG. Unique: Total number of unique proteins (ROG's). For a description of the term ROGs, see README_MITAB2.6_for_iRefIndex#Understanding_the_iRefIndex_MITAB_format and the original paper PMID 18823568.

Source	Protein interactors	Assigned	%	Arbitrary	Matching sequence	New or obsolete sequence	Unassigned	Unique proteins
BAR	19431	19425	99.97	0	0	0	6	2299
BHF_UCL	6182	6182	100.00	0	0	0	0	1789
BIND	252251	215207	85.31	17	0	11394	37044	30232
BIND_TRANSLATION	257681	254342	98.70	20013	0	15555	3339	36932
BIOGRID	80211	78910	98.38	4099	0	10506	1301	78394
CORUM	17317	17313	99.98	2	0	62	4	6124
DIP	28066	27914	99.46	648	0	2415	152	27155
HPIDB	7724	7724	100.00	0	0	0	0	2482
HPRD	123812	123812	100.00	16461	94894	153	0	9837
HURI	340295	340289	100.00	39	0	2135	6	8181
IMEX	1564289	1564257	100.00	447	0	76	32	89051
INNATEDB	42658	25463	59.69	0	0	2	17195	3727
INTACT	625577	625397	99.97	168	63	442	180	100324
INTCOMPLEX	13645	13645	100.00	0	9	0	0	7530
MATRIXDB	66584	66584	100.00	0	0	57	0	14886
MBINFO	1136	1136	100.00	0	0	0	0	274
MINT	219108	219091	99.99	122	0	10	17	27488
MPACT	40349	40199	99.63	0	0	0	150	4995
MPIDB	3157	3157	100.00	0	0	2	0	967
MPPI	3568	3361	94.20	16	0	0	207	833
QUICKGO	112092	111515	99.49	0	0	0	577	20142
REACTOME	283992	283839	99.95	704	0	0	153	5860
UNIPROTPP	47779	47779	100.00	1	0	0	0	10600
VIRUSHOST	110230	110230	100.00	0	0	867	0	10590
(All)	4267134	4206771	98.59	42737	94966	43676	60363	160932

Mapping score summary

See below for definitions of the mapping score codes.

	BAR	BHF_UCL	BIND	BIND_TRANSLATION	BIOGRID	CORUM	DIP	HPIDB	HPRD	HURI	IMEX	INNATEDB	INTACT	INTCOMPLEX	MATRIXDB	MBINFO	MINT	MPACT	MPIDB	MPPI	QUICKGO	REACTOME	UNIPROTPP	VIRUSHOST
P	19270	6173		174608	50530	17216		7720		337140	1562392	25459	624153	13622	66472	1136	218609		3155		111515	266602	47710	109363
PD			123093		7998								3							2994
PD+LQ				9459
PD+LYQ				39
PDQ				31177
PD+XQ				26
PD+XYQ				50
PDY			9815		2
PDYQ				12
PE					417
PGD				627	1966								3
PGD+L				6287	4076								4
PGD+X					2
P+IN													385
P+N													15
PT				8779	3318	19					4		3				2	30579
PTD			80564		2								2							44
PTD+LQ				4163
PTDQ				2854
PTDY			1579
PTDYQ				6
PTGD				14
PTGD+L				23	2
PTM													3
PTY				250	16	3
PU	155	9		118		14		4		975	1324	2	532	14	55		335					16533	68
PUD			81		12															145
PUD+L			7		11															13
PUD+X			54																	162
PU+L				11		2				39	438		156				115					704	1
PU+O													49	9
PUT				4							2		12				4	2527
PUTD			4
PUTD+L			10																	3
PUT+L				31							9		8				7
PUT+O													14
PU+X				604							3		1
PV											9		9				9
PY				15198	10477	59				2135	76	2	30		57		10		2					867
S				2	62		12010		79				3
SD							5348		2567
SD+L							229		442
SD+LY							3
SD+N									121
SD+O									11679
SD+OY									2
SD+X							1283
SDY							15
SE					1
SGD									698
SGD+L									2684
SGD+O									14727
S+IN													1
S+L					7		210		757
S+LY					3		88
S+N													4
S+O									309
ST							4686		100									7093
STD							752		7270
STD+L							11		996
STD+O									30211
STD+OY									27
STDY									3
STGD									1615
STGD+L									7572
STGD+O									36908
ST+L							22		3962
ST+LY							5
ST+O									865
STY							43
SUD							79		2
SUD+L							44		25
SUD+O									7
SUD+X							569
SUTD							24		2
SUTD+L							36		23
SUTD+O									159
S+X							196
S+XY							233
SY					8		2028						7

Mapping score code definitions

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