Statistics iRefIndex 11.0

Data source information

Source	Release date	Release URL	Download files	Version
BIND	2013-05-16		20060525*.txt
BIND_TRANSLATION	2010-12-15	http://download.baderlab.org/BINDTranslation/release1_0/	BINDTranslation_v1_xml_AllSpecies.tar.gz
BIOGRID	2013-05-01	http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.2.100/	BIOGRID-ALL-3.2.100.psi25.zip
CORUM	2009-12-02	http://mips.gsf.de/genre/export/sites/default/corum/	allComplexes.psimi.zip
DIG	2013-05-16		morbidmap14062010.txt
DIP	2013-01-31	http://dip.doe-mbi.ucla.edu/dip/Download.cgi?SM=3
FLY	2013-05-01	http://www.uniprot.org/docs/	fly.txt	2013_05
GENE	2013-05-16	ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/	gene2refseq.gz gene_info.gz gene2go.gz gene_history.gz
HPRD	2010-04-13	http://www.hprd.org/RELEASE9/	HPRD_PSIMI_041310.tar.gz	Release 9
INNATEDB	2013-05-12	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	2012-07-19	ftp://ftp.ebi.ac.uk/pub/databases/IPI/last_release/current/	*.fasta.gz
MATRIXDB	2012-08-03	http://matrixdb.ibcp.fr/cgi-bin/download%3C../../	MatrixDB_20120801.xml.zip
MINT	2011-12-04	ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmids/	*.psi25.zip
MMDB	2013-05-09	ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/	table
MPACT	2013-05-17	ftp://ftpmips.gsf.de/yeast/PPI/	mpact-complete.psi25.xml.gz
MPIDB	2013-05-16	http://www.jcvi.org/mpidb/download.php?dbsource=	MPI-IMEX MPI-LIT
MPPI	2004-06-01	http://mips.gsf.de/proj/ppi/data/	mppi.gz
OPHID	2013-05-16		ophid*.xml
PDB	2013-05-15	ftp://ftp.ncbi.nih.gov/blast/db/FASTA/	pdbaa.gz
PSI_MI	2013-05-16	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	2013-05-16	ftp://ftp.ncbi.nih.gov/pub/taxonomy/	taxdump.tar.gz
UNIPROT	2013-05-01	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_05
YEAST	2013-05-01	http://www.uniprot.org/docs/	yeast.txt	2013_05

Interactions available from major taxonomies

NCBI taxonomy identifier	Scientific name	Number of interactions
9606	Homo sapiens	237377
559292	Saccharomyces cerevisiae S288c	100777
7227	Drosophila melanogaster	59262
4932	Saccharomyces cerevisiae	46791
40674	Mammalia	36341
10090	Mus musculus	31453
3702	Arabidopsis thaliana	21070
83333	Escherichia coli K-12	15198
6239	Caenorhabditis elegans	15187
192222	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	11970
10116	Rattus norvegicus	9207
562	Escherichia coli	5370
4896	Schizosaccharomyces pombe	4965
632	Yersinia pestis	3954

Interactions available from major taxonomies (corrected)

NCBI taxonomy identifier	Scientific name	Number of interactions
9606	Homo sapiens	247270
559292	Saccharomyces cerevisiae S288c	114658
7227	Drosophila melanogaster	59265
10090	Mus musculus	28188
3702	Arabidopsis thaliana	21070
83333	Escherichia coli K-12	17234
6239	Caenorhabditis elegans	15187
192222	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	12000
10116	Rattus norvegicus	7724
284812	Schizosaccharomyces pombe 972h-	5182
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	52155	22656	221	25157	1981	171	23748	4	22196	6318	6	27	357	2160
BIND_TRANSLATION		60761	24749	195	25164	2741	241	24211	4	23050	6284	6	23	365	2779
BIOGRID			264292	156	29918	10990	654	40459	6	40312	4211		1	122	7380
CORUM				2607	132	160	30	286		128				15	239
DIP					70253	525	212	26612	3	33102	6755	43	192	57	1174
HPRD						40531	472	4494	17	3440				120	7449
INNATEDB							5305	446	3	323				18	694
INTACT								166525	14	44965	6251	290	166	103	7905
MATRIXDB									229	2				1	25
MINT										88927	6484	15	37	90	7220
MPACT											13338
MPI-IMEX												468	30
MPI-LIT													742
MPPI														778	181
OPHID															47499
(Exclusive to source)	8950	4361	185799	1951	23016	24292	3757	98129	186	21105	5344	163	434	221	30014

Interactors

	BIND	BIND_TRANSLATION	BIOGRID	CORUM	DIP	HPRD	INNATEDB	INTACT	MATRIXDB	MINT	MPACT	MPI-IMEX	MPI-LIT	MPPI	OPHID
BIND	37516	30340	17216	2036	15589	2782	1295	18476	99	16890	4360	32	88	664	3095
BIND_TRANSLATION		36139	17909	2010	15758	3146	1423	18782	116	17005	4003	30	97	666	3365
BIOGRID			45950	2556	14791	6697	2001	27842	117	19231	4483		2	494	5997
CORUM				4363	1428	1559	893	3427	51	2676				408	2248
DIP					23368	1470	1045	18530	75	17312	4550	127	385	384	2083
HPRD						9836	1320	5567	103	4101				275	5208
INNATEDB							3475	2522	84	1856				270	1888
INTACT								59230	167	26156	4932	378	529	661	7576
MATRIXDB									249	118				15	145
MINT										32870	4804	69	243	567	5691
MPACT											4982				1
MPI-IMEX												470	91
MPI-LIT													934
MPPI														835	418
OPHID															9533
(Exclusive to source)	5682	3562	12551	388	1897	1738	397	18967	35	3679	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	91309	91094	99.76	62980	69.14
BIND_TRANSLATION	192923	84138	82037	97.50	60761	74.07
BIOGRID	681783	402335	400421	99.52	264292	66.00
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	18625	18625	7827	42.02	5305	67.78
INTACT	204708	198018	197976	99.98	166525	84.11
MATRIXDB	1065	392	392	100.00	229	58.42
MINT	127577	127022	126719	99.76	88927	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)	1637162	1173103	1157281	98.65	825235	71.31

Assignment of protein interactors to ROGs (Table 3)

Source	Protein interactors	Assigned	%	Arbitrary	Matching sequence	New or obsolete sequence	Unassigned	Unique proteins
BIND	252251	251997	99.90	0	0	40387	254	37516
BIND_TRANSLATION	257681	252224	97.88	21358	0	23766	5457	36139
BIOGRID	46903	46144	98.38	9953	0	307	759	45950
CORUM	12916	12916	100.00	7	0	0	0	4363
DIP	24142	24127	99.94	573	0	1272	15	23368
HPRD	123812	123812	100.00	13672	85462	213	0	9836
INNATEDB	39572	25280	63.88	0	0	0	14292	3475
INTACT	169815	169749	99.96	69	29	395	66	59230
MATRIXDB	1274	1274	100.00	0	0	0	0	249
MINT	91829	91590	99.74	570	11	4017	239	32870
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)	1213062	1191554	98.23	46632	85514	71379	21508	108177

ROG summary

	BIND	BIND_TRANSLATION	BIOGRID	CORUM	DIP	HPRD	INNATEDB	INTACT	MATRIXDB	MINT	MPACT	MPI-IMEX	MPI-LIT	MPPI	OPHID
P		185184	31341	12877			25280	168921		51769		616	1071
P+IN								2
P+L		586								1
P+LY		160	2
P+N								9		223
PD	124481								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	2159							308
PGD+L		6256	9928							493
PGD+X			10
PI								2		17
PIY								373		49
PT		2669	1848							34333	30579	320	405
PT+L		2
PTD	86506								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				305		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										10
PVY										1
PY		7409	266					8		3740
S		2	541		11532	168		1
S+L			6		170	752
S+LY			14		66	6
S+N								2
S+O						223
S+X					88
S+XY					175
SD					3419	5713
SD+L					220	465
SD+LY					29
SD+N						124
SD+O						8622
SD+OY						14
SD+X					1112
SD+XY					3
SDY					233
SGD						1119
SGD+L						1660
SGD+O						14956
SI	492
SIY	32240
ST					4768	216					7025
ST+L					25	4628
ST+LY						61
ST+O						748
STD					627	14020
STD+L					4	1162
STD+O						22801
STD+OY						6
STDY					2	2
STGD						3308
STGD+L						4923
STGD+O						37959
STI	39
STIY	3490
STY					2						3
SUD					43
SUD+L					32	8
SUD+O						2
SUD+X					777
SUTD					11	8
SUTD+L					27	7
SUTD+O						131
SY			24		762					2