Statistics iRefIndex 12.0

Data source information

Source	Release date	Release URL	Download files	Version
BIND	2013-06-03		20060525*.txt
BIND_TRANSLATION	2013-06-03		BINDTranslation_v1_xml_AllSpecies.tar.gz
BIOGRID	2013-05-31	http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.2.101/	BIOGRID-ALL-3.2.101.psi25.zip
CORUM	2009-12-02	http://mips.gsf.de/genre/export/sites/default/corum/	allComplexes.psimi.zip
DIG	2013-06-03		morbidmap14062010.txt
DIP	2013-01-31	http://dip.doe-mbi.ucla.edu/dip/Download.cgi?SM=3
FLY	2013-05-29	http://www.uniprot.org/docs/	fly.txt	2013_06
GENE	2013-06-02	ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/	gene2refseq.gz gene_info.gz gene2go.gz gene_history.gz
INNATEDB	2013-06-02	http://www.innatedb.com/download/interactions/	innatedb_all.mitab.gz
INTACT	2013-05-02	ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/	pmidMIF25.zip
IPI	2013-06-03		*.fasta.gz
MATRIXDB	2012-08-03	http://matrixdb.ibcp.fr/cgi-bin/download%3C../../	MatrixDB_20120801.xml.zip
MINT	2013-06-03		*.psi25.zip
MMDB	2013-05-31	ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/	table
MPACT	2013-06-03		mpact-complete.psi25.xml.gz
MPIDB	2013-06-03	http://www.jcvi.org/mpidb/download.php?dbsource=	MPI-IMEX MPI-LIT
MPPI	2013-06-03		mppi.gz
OPHID	2013-06-03		ophid*.xml
PDB	2013-06-01	ftp://ftp.ncbi.nih.gov/blast/db/FASTA/	pdbaa.gz
PSI_MI	2013-06-03	http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mi/rel25/data/	psi-mi25.obo
REFSEQ	2013-05-01	ftp://ftp.ncbi.nih.gov/refseq/release//complete/	complete*.protein.gpff.gz
TAXONOMY	2013-06-02	ftp://ftp.ncbi.nih.gov/pub/taxonomy/	taxdump.tar.gz
UNIPROT	2013-05-29	ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/	uniprot_sprot.dat.gz uniprot_trembl.dat.gz uniprot_sprot_varsplic.fasta.gz reldate.txt	2013_06
YEAST	2013-05-29	http://www.uniprot.org/docs/	yeast.txt	2013_06

Interactions available from major taxonomies

NCBI taxonomy identifier	Scientific name	Number of interactions
9606	Homo sapiens	238350
559292	Saccharomyces cerevisiae S288c	100970
7227	Drosophila melanogaster	59275
4932	Saccharomyces cerevisiae	46791
40674	Mammalia	36341
10090	Mus musculus	31510
3702	Arabidopsis thaliana	21077
83333	Escherichia coli K-12	15198
6239	Caenorhabditis elegans	15188
192222	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	11970
10116	Rattus norvegicus	9238
562	Escherichia coli	5370
4896	Schizosaccharomyces pombe	4972
632	Yersinia pestis	3954

Interactions available from major taxonomies (corrected)

NCBI taxonomy identifier	Scientific name	Number of interactions
9606	Homo sapiens	248233
559292	Saccharomyces cerevisiae S288c	114846
7227	Drosophila melanogaster	59278
10090	Mus musculus	28245
3702	Arabidopsis thaliana	21077
83333	Escherichia coli K-12	17234
6239	Caenorhabditis elegans	15188
192222	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	12000
10116	Rattus norvegicus	7755
284812	Schizosaccharomyces pombe 972h-	5189
632	Yersinia pestis	3954
243276	Treponema pallidum subsp. pallidum str. Nichols	3643
1111708	Synechocystis sp. PCC 6803 substr. Kazusa	3229
1392	Bacillus anthracis	3041

Interactions

	BIND	BIND_TRANSLATION	BIOGRID	CORUM	DIP	HPRD	INNATEDB	INTACT	MATRIXDB	MINT	MPACT	MPI-IMEX	MPI-LIT	MPPI	OPHID
BIND	62980	52196	22669	221	25157	1981	171	23748	4	22196	6318	6	27	357	2160
BIND_TRANSLATION		60766	24787	195	25164	2741	241	24211	4	23050	6284	6	23	365	2779
BIOGRID			265695	156	29930	11040	660	40539	6	40327	4212		1	122	7387
CORUM				2607	132	160	30	286		128				15	239
DIP					70253	525	212	26612	3	33102	6755	43	192	57	1174
HPRD						40531	472	4496	17	3443				120	7449
INNATEDB							5331	446	3	323				18	694
INTACT								166524	14	44965	6251	290	166	103	7905
MATRIXDB									229	2				1	25
MINT										88926	6484	15	37	90	7220
MPACT											13338
MPI-IMEX												468	30
MPI-LIT													742
MPPI														778	181
OPHID															47499
(Exclusive to source)	8911	4314	187038	1951	23006	24264	3780	98060	186	21088	5343	163	434	221	30013

Interactors

	BIND	BIND_TRANSLATION	BIOGRID	CORUM	DIP	HPRD	INNATEDB	INTACT	MATRIXDB	MINT	MPACT	MPI-IMEX	MPI-LIT	MPPI	OPHID
BIND	37516	30353	17223	2036	15589	2782	1298	18476	99	16890	4360	32	88	663	3095
BIND_TRANSLATION		36143	17918	2010	15757	3146	1428	18783	116	17005	4003	30	97	666	3365
BIOGRID			46054	2557	14793	6704	2016	27864	117	19241	4483		2	494	6003
CORUM				4363	1428	1559	899	3427	51	2676				408	2248
DIP					23368	1470	1047	18530	75	17312	4550	127	385	384	2083
HPRD						9836	1329	5568	103	4102				275	5209
INNATEDB							3487	2534	85	1868				270	1899
INTACT								59229	167	26157	4932	378	529	662	7576
MATRIXDB									249	118				15	145
MINT										32869	4804	69	243	567	5691
MPACT											4982				1
MPI-IMEX												470	91
MPI-LIT													934
MPPI														835	418
OPHID															9533
(Exclusive to source)	5670	3553	12614	388	1898	1735	395	18948	35	3674	18	80	314	23	650

Summary of mapping interaction records to RIGs (Table 5)

Source	Total records	Protein-related interactions	PPI assigned to RIGID	%	Unique RIGIDs	%
BIND	157736	91767	91094	99.27	62980	69.14
BIND_TRANSLATION	192923	84138	82037	97.50	60766	74.07
BIOGRID	684996	404834	402886	99.52	265695	65.95
CORUM	2844	2844	2844	100.00	2607	91.67
DIP	74086	72661	72630	99.96	70253	96.73
HPRD	83022	83022	82983	99.95	40531	48.84
INNATEDB	18676	18676	7853	42.05	5331	67.88
INTACT	204708	198018	197976	99.98	166524	84.11
MATRIXDB	1065	392	392	100.00	229	58.42
MINT	127577	127022	126718	99.76	88926	70.18
MPACT	16504	16504	16308	98.81	13338	81.79
MPI-IMEX	473	473	468	98.94	468	100.00
MPI-LIT	745	745	742	99.60	742	100.00
MPPI	1814	1758	1583	90.05	778	49.15
OPHID	73257	73257	73257	100.00	47499	64.84
(All)	1640426	1176111	1159771	98.61	826667	71.28

Assignment of protein interactors to ROGs (Table 3)

Source	Protein interactors	Assigned	%	Arbitrary	Matching sequence	New or obsolete sequence	Unassigned	Unique proteins
BIND	253014	251997	99.60	0	0	40366	1017	37516
BIND_TRANSLATION	257683	252224	97.88	20770	0	23766	5459	36143
BIOGRID	47011	46247	98.37	9960	0	312	764	46054
CORUM	12916	12916	100.00	7	0	0	0	4363
DIP	24142	24127	99.94	570	0	1272	15	23368
HPRD	123812	123812	100.00	13685	85465	213	0	9836
INNATEDB	39725	25384	63.90	0	0	0	14341	3487
INTACT	169815	169749	99.96	69	29	395	66	59229
MATRIXDB	1274	1274	100.00	0	0	0	0	249
MINT	91829	91589	99.74	570	11	4031	240	32869
MPACT	40349	40134	99.47	0	0	3	215	4982
MPI-IMEX	946	940	99.37	2	0	0	6	470
MPI-LIT	1490	1487	99.80	7	0	0	3	934
MPPI	3568	3366	94.34	16	0	5	202	835
OPHID	146514	146514	100.00	405	12	1014	0	9533
(All)	1214088	1191760	98.16	46061	85517	71377	22328	108227

ROG summary

	BIND	BIND_TRANSLATION	BIOGRID	CORUM	DIP	HPRD	INNATEDB	INTACT	MATRIXDB	MINT	MPACT	MPI-IMEX	MPI-LIT	MPPI	OPHID
P		185770	31422	12877			25384	168920		51762		616	1071
P+IN								2
P+LY		160	2
P+N								9		223
PD	124956								1271	2				2996	124479
PD+IN								1
PD+LQ		10230
PD+LYQ		67
PD+N															22
PD+XQ		26
PDIQ		219
PDIYQ		513
PDQ		15773
PDY	4437									1				5	992
PDYQ		15454
PGD		657	2163							308
PGD+L		6256	9933							493
PGD+X			13
PI								2		17
PIY								373		49
PT		2671	1851							34333	30579	320	405
PTD	86561								3	2				44	114
PTD+LQ		3992
PTD+LYQ		12
PTDIYQ		13
PTDQ		2159
PTDY	220
PTDYQ		138
PTGD		21	1
PTGD+L		17	3
PTI								11
PTIY										1
PTY			1
PU		15		32				306		366			2
PU+L		17		7				42		39			7
PU+O								14		3
PU+X		610						2		15			1
PUD	6													143	16955
PUD+L														13	265
PUD+O															12
PUD+X	82													162	3526
PUT		4						14		170	2527	2	1
PUT+L		19						27		37		2
PUT+O								15		8
PUTD	4														9
PUTD+L														3	140
PV										3
PV+LY										1
PVY										7
PY		7409	269					8		3747
S		2	543		11535	168		1
S+L			6		167	752
S+LY			16		66	6
S+N								2
S+O						223
S+X					88
S+XY					175
SD					3418	5709
SD+L					220	465
SD+LY					29
SD+N						124
SD+O						8626
SD+OY						14
SD+X					1112
SD+XY					3
SDY					233
SGD						1126
SGD+L						1669
SGD+O						14940
SI	17
SIY	32240
ST					4768	216					7025
ST+L					25	4628
ST+LY						61
ST+O						748
STD					627	14013
STD+L					4	1162
STD+O						22808
STD+OY						6
STDY					2	2
STGD						3296
STGD+L						4927
STGD+O						37967
STI	5
STIY	3469
STY					2						3
SUD					44
SUD+L					32	8
SUD+O						2
SUD+X					777
SUTD					11	8
SUTD+L					27	7
SUTD+O						131
SY			24		762					2