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Statistics iRefIndex 6.0

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Summary

Last updated : 24 September 2009

  • Total interactions : 760,703
  • Total distinct interactions (based on RIGID):359,694 ( 47% of total interactions)
  • Total distinct proteins (based on ROGID)  : 79,741

This page lists statistics for our internal version of iRefIndex that includes all of the data from sources used for the current build Sources_iRefIndex_6.0. This full build of the iRefIndex contains data that cannot be redistributed according to usage policies of the source databases (namely, from DIP, HPRD, CORUM and MPact databases). Please contact ian.donaldson at biotek.uio.no if you would like to obtain a copy of the full iRefIndex build under an academic, collaborative agreement.

The data that are freely available at ftp://ftp.no.embnet.org/irefindex/data/archive/release_6.0/ are a subset of the full build that we can freely redistribute according to the usage policies of the source databases. Please refer to http://irefindex.uio.no/wiki/Statistics_iRefIndex_free_6.0 for statistics that are applicable to this free dataset.

Interactions available from major taxonomies

Top 15 uncorrected taxonomy groups in iRefIndex (Taxonomy identifiers as they appear in original source)

NCBI taxonomy identifier Scientific_name Number_of_interactions
4932 Saccharomyces cerevisiae 116015
9606 Homo sapiens 100234
7227 Drosophila melanogaster 45998
40674 Mammalia 35023
562 Escherichia coli 12091
197 Campylobacter jejuni 12025
4896 Schizosaccharomyces pombe 11856
10090 Mus musculus 11516
6239 Caenorhabditis elegans 11097
3702 Arabidopsis thaliana 5233
10116 Rattus norvegicus 4239
160 Treponema pallidum 3647
83333 Escherichia coli K-12 3504
1142 Synechocystis 3057
36329 Plasmodium falciparum 3D7 2758
  • Full list [[1]]

Top 15 corrected taxonomy groups in iRefIndex (Taxonomy identifiers corrected using sequence database information)

NCBI taxonomy identifier Scientific_name Number_of_interactions
4932 Saccharomyces cerevisiae 116003
9606 Homo sapiens 109541
7227 Drosophila melanogaster 46002
197 Campylobacter jejuni 12025
4896 Schizosaccharomyces pombe 11876
6239 Caenorhabditis elegans 11097
83333 Escherichia coli K-12 10981
10090 Mus musculus 10130
3702 Arabidopsis thaliana 5239
155864 Escherichia coli O157:H7 EDL933 4928
160 Treponema pallidum 3647
10116 Rattus norvegicus 3411
1148 Synechocystis sp. PCC 6803 3168
36329 Plasmodium falciparum 3D7 2758
83334 Escherichia coli O157:H7 2560
  • Full list [[2]]

Interactions (Corresponds to Table 6 in PMID 18823568)

BIND 62894
BIOGRID 22554 163090
DIP 26180 32544 56450
HPRD 2946 11290 830 39966
INTACT 24453 31801 24981 8556 113849
MINT 22359 37493 30238 6699 45779 77950
MPACT 6938 8226 6748 0 6132 6427 13321
MPPI 388 135 40 304 90 73 0 827
OPHID 2226 8074 876 18079 7283 6444 0 183 47531
CORUM 116 109 28 403 125 69 0 9 158 1919
I2D 0 0 0 0 0 0 0 0 0 0 0
BIND BIOGRID DIP HPRD INTACT MINT MPACT MPPI OPHID CORUM I2D
(25944) (97557) (12371) (14444) (55889) (16770) (1291) (240) (26499) (1392) (0)


Interactors

BIND 40781
BIOGRID 16909 27409
DIP 15500 14298 20118
HPRD 3359 5743 1215 9750
INTACT 18207 19351 15620 5981 41944
MINT 16451 17009 15020 4792 23622 28908
MPACT 4651 4445 4609 0 4874 4756 4972
MPPI 674 418 284 429 579 511 0 861
OPHID 3253 5167 1206 7445 5813 4805 1 421 9646
CORUM 1561 1580 643 1870 2313 1771 0 321 1849 3581
I2D 0 0 0 0 0 0 0 0 0 0 0
BIND BIOGRID DIP HPRD INTACT MINT MPACT MPPI OPHID CORUM I2D
(18075) (4175) (1755) (887) (12041) (3398) (18) (45) (1287) (613) (0)

Summary of mapping interaction records to RIGs (Corresponds to Table 5 in PMID 18823568)

Source Total records Protein-only interactors PPI Assigned to RIGID Unique RIGIDs
bind 193648 93957 91264(97.1338%) 62894(68.9144%)
grid 239485 238211 237796(99.8258%) 163090(68.5840%)
dip 57675 57675 56613(98.1586%) 56450(99.7121%)
intact 133302 132525 132076(99.6612%) 113849(86.1996%)
mint 110788 110788 109639(98.9629%) 77950(71.0970%)
HPRD 40075 40075 40075(100.0000%) 39966(99.7280%)
ophid 73257 73257 73160(99.8676%) 47531(64.9686%)
MPACT 16504 16504 16286(98.6791%) 13321(81.7942%)
MPPI 1814 1814 1690(93.1643%) 827(48.9349%)
CORUM 2104 2104 2104(100.0000%) 1919(91.2072%)
ALL 868652 766910 760703(99.1906%) 359694(47.2844%)


Assignment of protein interactors to ROGs (Corresponds to Table 3 in PMID 18823568)

Source Protein_Intractors Assigned % Arbitrary New Unassigned Unique proteins
bind 285482 273657 95.8579 0 7887 3938 40781
CORUM 10316 10314 99.9806 0 2 0 3581
dip 20728 18533 89.4105 1246 484 465 20118
grid 27629 22369 80.9620 5126 1 133 27409
HPRD 9773 9676 99.0075 55 42 0 9750
intact 100752 97752 97.0224 19 2738 239 41944
mint 77936 74979 96.2059 2 2721 228 28908
MPACT 40349 40112 99.4126 0 0 237 4972
MPPI 3628 3457 95.2867 0 32 139 861
ophid 146423 145362 99.2754 103 952 6 9646
All 723016 696221 96.2940 6551 14859 5385 79741


ROG summary (Corresponds to Table 4 in PMID 18823568)

Decimal_score Binary_flag String_score Score_class Proteins Percentage BIND BioGrid DIP MINT HPRD OPHID MPPI MPACT IntAct CORUM
1 000000000000000001 P 1 577648 79.8942% 232419 19992 0 72231 0 125686 3023 30666 93631 0
2 000000000000000010 S 1 27580 3.8146% 0 1 17413 231 2772 0 0 6927 236 0
8194 000010000000000010 SI 1 12336 1.7062% 12336 0 0 0 0 0 0 0 0 0
65 000000000001000001 PD 1 8086 1.1184% 8083 0 0 3 0 0 0 0 0 0
41 000000000000101001 PVG 1 2362 0.3267% 0 2362 0 0 0 0 0 0 0 0
129 000000000010000001 PM 1 522 0.0722% 473 0 0 0 0 0 32 0 17 0
554 000000001000101010 SVGO 1 480 0.0664% 0 0 0 0 480 0 0 0 0 0
10 000000000000001010 SV 1 245 0.0339% 0 0 5 9 0 0 0 0 231 0
42 000000000000101010 SVG 1 163 0.0225% 0 0 0 0 163 0 0 0 0 0
8193 000010000000000001 PI 1 48 0.0066% 0 0 0 0 0 0 0 0 48 0
5 000000000000000101 PU 2 22841 3.1591% 0 0 0 293 0 19519 320 2519 190 0
16386 000100000000000010 SE 2 5419 0.7495% 5413 0 6 0 0 0 0 0 0 0
16385 000100000000000001 PE 2 884 0.1223% 0 0 0 199 0 0 0 0 685 0
16449 000100000001000001 PDE 2 116 0.0160% 0 0 0 34 0 0 0 0 82 0
6 000000000000000110 SU 2 77 0.0106% 0 0 60 4 5 0 0 0 8 0
773 000000001100000101 PUO+ 2 12 0.0017% 0 0 0 3 0 1 0 0 8 0
774 000000001100000110 SUO+ 2 1 0.0001% 0 0 0 0 0 0 0 0 1 0
778 000000001100001010 SVO+ 2 1 0.0001% 0 0 0 0 0 0 0 0 1 0
17 000000000000010001 PT 3 26406 3.6522% 11871 0 0 1620 0 122 47 0 2456 10290
18 000000000000010010 ST 3 7060 0.9765% 0 0 1015 0 6042 0 0 0 3 0
81 000000000001010001 PTD 3 1487 0.2057% 1486 0 0 1 0 0 0 0 0 0
8210 000010000000010010 STI 3 855 0.1183% 855 0 0 0 0 0 0 0 0 0
145 000000000010010001 PTM 3 170 0.0235% 132 0 0 0 0 0 35 0 3 0
8209 000010000000010001 PTI 3 12 0.0017% 0 0 0 0 0 0 0 0 12 0
26 000000000000011010 SVT 3 1 0.0001% 0 0 0 0 0 0 0 0 1 0
16402 000100000000010010 STE 4 315 0.0436% 315 0 0 0 0 0 0 0 0 0
22 000000000000010110 SUT 4 17 0.0024% 0 0 3 0 14 0 0 0 0 0
789 000000001100010101 PUTO+ 4 14 0.0019% 0 0 0 0 0 0 0 0 14 0
16401 000100000000010001 PTE 4 4 0.0006% 0 0 0 0 0 0 0 0 4 0
790 000000001100010110 SUTO+ 4 1 0.0001% 0 0 0 0 1 0 0 0 0 0
4393 000001000100101001 PVGL+ 5 5117 0.7077% 0 5117 0 0 0 0 0 0 0 0
4354 000001000100000010 SL+ 5 1203 0.1664% 0 9 1194 0 0 0 0 0 0 0
810 000000001100101010 SVGO+ 5 199 0.0275% 0 0 0 0 199 0 0 0 0 0
4357 000001000100000101 PUL+ 5 84 0.0116% 0 0 0 0 0 84 0 0 0 0
4394 000001000100101010 SVGL+ 5 52 0.0072% 0 0 0 0 52 0 0 0 0 0
4374 000001000100010110 SUTL+ 5 52 0.0072% 0 0 52 0 0 0 0 0 0 0
131089 100000000000010001 PTQ 5 38 0.0053% 0 0 0 0 0 0 0 0 38 0
21 000000000000010101 PUT 5 31 0.0043% 0 0 0 2 0 5 0 0 0 24
5381 000001010100000101 PUXL+ 5 29 0.0040% 0 0 0 0 0 19 0 0 10 0
4373 000001000100010101 PUTL+ 5 9 0.0012% 0 0 0 1 0 0 0 0 8 0
5382 000001010100000110 SUXL+ 5 3 0.0004% 0 0 0 0 3 0 0 0 0 0
1802 000000011100001010 SVOX+ 5 3 0.0004% 0 0 0 0 0 0 0 0 3 0
5386 000001010100001010 SVXL+ 5 2 0.0003% 0 0 0 1 0 0 0 0 1 0
131077 100000000000000101 PUQ 5 1 0.0001% 0 0 0 0 0 0 0 0 1 0
131073 100000000000000001 PQ 5 1 0.0001% 0 0 0 0 0 0 0 0 1 0
65537 010000000000000001 PN 6 7448 1.0301% 1673 0 112 2437 42 668 5 0 2511 0
81922 010100000000000010 SEN 6 5574 0.7709% 5200 0 372 2 0 0 0 0 0 0
65601 010000000001000001 PDN 6 1081 0.1495% 668 0 0 161 0 250 0 0 2 0
32769 001000000000000001 PY 6 696 0.0963% 271 14 0 326 0 29 0 0 56 0
81921 010100000000000001 PEN 6 499 0.0690% 319 0 0 121 0 34 23 0 0 2
32770 001000000000000010 SY 6 73 0.0101% 0 0 30 23 0 0 0 0 20 0
81938 010100000000010010 STEN 6 19 0.0026% 19 0 0 0 0 0 0 0 0 0
65553 010000000000010001 PTN 6 17 0.0024% 7 0 0 0 0 0 0 0 10 0
81937 010100000000010001 PTEN 6 3 0.0004% 1 0 0 0 0 0 2 0 0 0
65665 010000000010000001 PMN 6 2 0.0003% 0 0 0 0 0 0 2 0 0 0
32785 001000000000010001 PTY 6 2 0.0003% 2 0 0 0 0 0 0 0 0 0
147473 100100000000010001 PTEQ 6 1 0.0001% 0 0 0 0 0 0 0 0 1 0
82034 010100000001110010 STGDEN 6 1 0.0001% 0 1 0 0 0 0 0 0 0 0
32833 001000000001000001 PDY 6 1 0.0001% 1 0 0 0 0 0 0 0 0 0
32786 001000000000010010 STY 6 1 0.0001% 0 0 1 0 0 0 0 0 0 0
163841 101000000000000001 PYQ 6 1 0.0001% 0 0 0 0 0 0 0 0 1 0
73729 010010000000000001 PIN 6 215 0.0297% 0 0 0 0 0 0 0 0 215 0

Scores (Corresponds to Table 2 in PMID 18823568)

Character Description of feature (when the value is 1) Frequency
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. 10772(1.5011%)
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, seeunce information obtained form UniProt. 12835(1.7885%)
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. 8374(1.1669%)
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) 6551(0.9129%)
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. 694(0.0967%)
+ 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). 6782(0.9451%)
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. 14859(2.0706%)
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. 711(0.0991%)
I The protein reference used was an NCBI GenInfo Identifier (I). 13466(1.8765%)
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. 23172(3.229%)
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 36516(5.0885%)
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. 8625(1.2019%)
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'. 42(0.0059%)
P The interaction record's primary (P) reference for the protein was used to make the assignment 655888(91.3975%)
S One of the interaction record's secondary (S) references for the protein was used to make the assignment 61733(8.6025%)
Y the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009) 774(0.1079%)
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 37(0.0052%)


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