Difference between revisions of "Statistics iRefIndex 11.0"

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== Data source information ==
 
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{| cellspacing="0" cellpadding="5"
 
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| align="center" style="background:#f0f0f0;"|'''Source''' ||align="center" style="background:#f0f0f0;"|'''Release date''' ||align="center" style="background:#f0f0f0;"|'''Release URL''' ||align="center" style="background:#f0f0f0;"|'''Download files''' ||align="center" style="background:#f0f0f0;"|'''Version'''
 
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| BIND ||2013-05-16 ||  ||20060525*.txt ||
 
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| BIND_TRANSLATION ||2010-12-15 ||http://download.baderlab.org/BINDTranslation/release1_0/ ||BINDTranslation_v1_xml_AllSpecies.tar.gz ||
 
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| BIOGRID ||2013-05-01 ||http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.2.100/ ||BIOGRID-ALL-3.2.100.psi25.zip ||
 
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| CORUM ||2009-12-02 ||http://mips.gsf.de/genre/export/sites/default/corum/ ||allComplexes.psimi.zip ||
 
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| DIG ||2013-05-16 ||  ||morbidmap14062010.txt ||
 
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| DIP ||2013-01-31 ||http://dip.doe-mbi.ucla.edu/dip/Download.cgi?SM=3 ||  ||
 
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| FLY ||2013-05-01 ||http://www.uniprot.org/docs/ ||fly.txt ||2013_05
 
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| GENE ||2013-05-16 ||ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ ||gene2refseq.gz gene_info.gz gene2go.gz gene_history.gz ||
 
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| HPRD ||2010-04-13 ||http://www.hprd.org/RELEASE9/ ||HPRD_PSIMI_041310.tar.gz ||Release 9
 
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| INNATEDB ||2013-05-12 ||http://www.innatedb.com/download/interactions/ ||innatedb_all.mitab.gz ||
 
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| INTACT ||2013-05-02 ||ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/ ||pmidMIF25.zip ||
 
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| IPI ||2012-07-19 ||ftp://ftp.ebi.ac.uk/pub/databases/IPI/last_release/current/ ||*.fasta.gz ||
 
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| MATRIXDB ||2012-08-03 ||http://matrixdb.ibcp.fr/cgi-bin/download%3C../../ ||MatrixDB_20120801.xml.zip ||
 
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| MINT ||2011-12-04 ||ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/pmids/ ||*.psi25.zip ||
 
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| MMDB ||2013-05-09 ||ftp://ftp.ncbi.nih.gov/mmdb/pdbeast/ ||table ||
 
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| MPACT ||2013-05-17 ||ftp://ftpmips.gsf.de/yeast/PPI/ ||mpact-complete.psi25.xml.gz ||
 
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| MPIDB ||2013-05-16 ||http://www.jcvi.org/mpidb/download.php?dbsource= ||MPI-IMEX MPI-LIT ||
 
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| MPPI ||2004-06-01 ||http://mips.gsf.de/proj/ppi/data/ ||mppi.gz ||
 
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| OPHID ||2013-05-16 ||  ||ophid*.xml ||
 
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| PDB ||2013-05-15 ||ftp://ftp.ncbi.nih.gov/blast/db/FASTA/ ||pdbaa.gz ||
 
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| PSI_MI ||2013-05-16 ||http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mi/rel25/data/ ||psi-mi25.obo ||
 
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| REFSEQ ||2013-05-01 ||ftp://ftp.ncbi.nih.gov/refseq/release//complete/ ||complete*.protein.gpff.gz ||
 
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| TAXONOMY ||2013-05-16 ||ftp://ftp.ncbi.nih.gov/pub/taxonomy/ ||taxdump.tar.gz ||
 
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| 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
 
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| YEAST ||2013-05-01 ||http://www.uniprot.org/docs/ ||yeast.txt ||2013_05
 
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|}
 
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== Interactions available from major taxonomies ==
 
== Interactions available from major taxonomies ==
  

Revision as of 10:51, 27 May 2013

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
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