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
7227	Drosophila melanogaster	86357
3702	Arabidopsis thaliana	87766
6239	Caenorhabditis elegans	41801
10116	Rattus norvegicus	15952
316407	Escherichia coli str. K-12 substr. W3110	12822
4896	Schizosaccharomyces pombe	13816
192222	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	11931
83333	Escherichia coli K-12	16903
381518	Influenza A virus (A/Wilson-Smith/1933(H1N1))	5104
632	Yersinia pestis	4147
2697049	Severe acute respiratory syndrome coronavirus	22047

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	23432	23432	23420	99.95	23414	99.97
BHF_UCL	2341	2326	2326	100.00	1513	65.05
BIND	157736	153063	73206	47.83	54156	73.98
BIND_TRANSLATION	192923	84138	74093	88.06	56577	76.36
BIOGRID	1855067	967393	963176	99.56	727908	75.57
CORUM	4274	4274	4270	99.91	4018	94.10
DIP	76796	0	0	\N	0	\N
HPIDB	3019	2845	2845	100.00	1560	54.83
HPRD	83022	83022	83022	100.00	40548	48.84
HURI	171545	168756	168750	100.00	51482	30.51
I2D_IMEX	596071	575676	575479	99.97	292694	50.86
INNATEDB	18408	18408	6895	37.46	4809	69.75
INTACT	731876	671221	671089	99.98	372746	55.54
INTCOMPLEX	3287	2658	2658	100.00	2611	98.23
MATRIXDB	1776	1775	1775	100.00	1419	79.94
MBINFO	542	522	522	100.00	331	63.41
MINT	85784	85180	85165	99.98	48860	57.37
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	58761	50321	49835	99.03	23889	47.94
REACTOME	141996	141996	141844	99.89	126328	89.06
SPIKE	29686	29686	28329	95.43	27830	98.24
UNIPROTPP	15042	14950	14950	100.00	8692	58.14
VIRUSHOST	40005	40005	40004	100.00	35076	87.68
(All)	4313204	3141370	3033065	96.55	1269053	41.84

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	46864	46852	99.97	1	0	0	12	4649
BHF_UCL	6184	6184	100.00	0	0	0	0	1791
BIND	322722	226129	70.07	17	0	41	96593	30475
BIND_TRANSLATION	257681	235695	91.47	20505	0	56	21986	33559
BIOGRID	73125	71929	98.36	3158	0	1	1196	71603
CORUM	17317	17313	99.98	2	0	7	4	6124
HPIDB	7724	7724	100.00	0	0	0	0	2481
HPRD	123812	123812	100.00	16529	87317	162	0	9838
HURI	340295	340289	100.00	39	0	941	6	8181
I2D_IMEX	1496885	1496674	99.99	445	0	8	211	86702
INNATEDB	42658	25490	59.75	0	0	2	17168	3739
INTACT	601576	601387	99.97	170	62	512	189	99546
INTCOMPLEX	11807	11807	100.00	0	0	0	0	6645
MATRIXDB	66584	66584	100.00	0	0	22	0	14891
MBINFO	1136	1136	100.00	0	0	0	0	274
MINT	229166	229149	99.99	141	0	0	17	28458
MPACT	40349	40199	99.63	0	0	0	150	4995
MPIDB	3157	3157	100.00	0	0	0	0	967
MPPI	3568	3361	94.20	16	0	0	207	833
QUICKGO	109082	108565	99.53	0	0	0	517	20082
REACTOME	283992	283839	99.95	704	0	0	153	5860
SPIKE	65934	64567	97.93	888	0	19	1367	8810
UNIPROTPP	42085	42085	100.00	1	0	0	0	9468
VIRUSHOST	80010	80009	100.00	0	0	0	1	9892
(All)	4273713	4133936	96.73	42616	87379	1771	139777	153059

Mapping score summary

See below for definitions of the mapping score codes.

	BAR	BHF_UCL	BIND	BIND_TRANSLATION	BIOGRID	CORUM	HPIDB	HPRD	HURI	I2D_IMEX	INNATEDB	INTACT	INTCOMPLEX	MATRIXDB	MBINFO	MINT	MPACT	MPIDB	MPPI	QUICKGO	REACTOME	SPIKE	UNIPROTPP	VIRUSHOST
P	46456	6175		187409	56273	17271	7720		338595	1494943	25486	600045	11790	66522	1136	228607		3157		108565	266602	54963	42029	80009
P+IN												385
P+N												116
PD			133916		7424														2994
PD+LQ				9895
PD+LYQ				39
PD+XQ				26
PDQ				15743
PDY			33		1
PDYQ				11
PGD				675	1888																	400
PGD+L				6236	3108							4										875
PGD+X					1
PT				8417	3112	19				1		2					30579						2
PTD			92006		2							1							44
PTD+LQ				4274
PTDQ				2156
PTDY			8
PTDYQ				6
PTGD				18	1
PTGD+L				19	2
PTM												3
PTY						3
PU	395	9		118		14	4		714	1264	2	560	17	40		388					16533	8297	53
PU+L	1			17		2			39	436		158				134					704	13	1
PU+O												48
PU+X				604						3		1
PUD			81		9														145
PUD+L			7		10														13
PUD+X			54																162
PUT				4						1		11				4	2527
PUT+L				25						9		8				7
PUT+O												14
PUTD			14
PUTD+L			10																3
PV										9		9				9
PY						4			941	8	2	6		22								19
S				3	60			147				11
S+IN												1
S+L					38			737
S+N												4
S+O								243
SD								4279
SD+L								607
SD+N								133
SD+O								10176
SD+OY								2
SGD								1012
SGD+L								2227
SGD+O								14252
ST								136									7093
ST+L								4787
ST+O								829
STD								11722
STD+L								1181
STD+O								26255
STD+OY								27
STGD								2537
STGD+L								6940
STGD+O								35367
SUD+L								27
SUD+O								7
SUTD+L								23
SUTD+O								159

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