Difference between revisions of "Statistics iRefIndex 5.0"

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== Summary ==
 
== Summary ==
  
−
*Total interactions : 871,172
+
*Total interactions : 764,017
−
*Total distinct interactions (based on RIGID): 357,170
+
*Total distinct interactions (based on RIGID): 373,488 (48.88 % of total interactions)
−
*Total distinct proteins (based on ROGID)    :  83.940
+
*Total distinct proteins (based on ROGID)    :  83,953
  
−
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_5.0]].  This full build of the iRefIndex contains data that cannot be redistributed according to usage policies of the source databases (namely, from DIP, HPRD 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.
+
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_5.0]].  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/current/ 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_5.0 for statistics that are applicable to this free dataset.
+
The data that are freely available at ftp://ftp.no.embnet.org/irefindex/data/archive/release_5.0/ 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_5.0 for statistics that are applicable to this free dataset.
  
 
== Interactions available from major taxonomies ==
 
== Interactions available from major taxonomies ==
 
=== Top 15 uncorrected taxonomy groups in iRefIndex (Taxonomy identifiers as they appear in original source)===
 
=== Top 15 uncorrected taxonomy groups in iRefIndex (Taxonomy identifiers as they appear in original source)===
 +
 
{| {{table}}
 
{| {{table}}
 
| align="center" style="background:#f0f0f0;"|'''NCBI taxonomy identifier'''
 
| align="center" style="background:#f0f0f0;"|'''NCBI taxonomy identifier'''
Line 48: Line 49:
 
|  
 
|  
 
|}
 
|}
−
* Full list [[http://irefindex.uio.no/wikifiles//images/9/90/Interactions_by_taxonomy_beta5_full.pdf]]
+
* Full list [[http://irefindex.uio.no/wikifiles//images/0/0d/Interactions_by_taxonomy_beta5_complete.pdf]]
  
 
===Top 15 corrected taxonomy groups in iRefIndex (Taxonomy identifiers corrected using sequence database information)===  
 
===Top 15 corrected taxonomy groups in iRefIndex (Taxonomy identifiers corrected using sequence database information)===  
−
 
+
{| {{table}}
−
 
+
| align="center" style="background:#f0f0f0;"|'''NCBI taxonomy identifier'''
−
* Full list [[http://irefindex.uio.no/wikifiles//images/9/90/Interactions_by_taxonomy_beta5_full.pdf]]
+
| align="center" style="background:#f0f0f0;"|''' Name'''
 +
| align="center" style="background:#f0f0f0;"|'''Number of interactions'''
 +
| align="center" style="background:#f0f0f0;"|''''''
 +
|-
 +
| 9606|| Homo sapiens                    ||120548||
 +
|-
 +
| 4932|| Saccharomyces cerevisiae        ||116702||
 +
|-
 +
| 7227|| Drosophila melanogaster        ||46702||
 +
|-
 +
| 6239|| Caenorhabditis elegans          ||12188||
 +
|-
 +
| 197|| Campylobacter jejuni            ||12025||
 +
|-
 +
| 4896|| Schizosaccharomyces pombe      ||11878||
 +
|-
 +
| 83333|| Escherichia coli K-12          ||10996||
 +
|-
 +
| 10090|| Mus musculus                    ||10241||
 +
|-
 +
| 3702|| Arabidopsis thaliana            ||5416||
 +
|-
 +
| 155864|| Escherichia coli O157:H7 EDL933 ||4928||
 +
|-
 +
| 160|| Treponema pallidum              ||3647||
 +
|-
 +
| 10116|| Rattus norvegicus              ||3435||
 +
|-
 +
| 1148|| Synechocystis sp. PCC 6803      ||3168||
 +
|-
 +
| 36329|| Plasmodium falciparum 3D7      ||2758||
 +
|-
 +
| 83334|| Escherichia coli O157:H7        ||2560||
 +
|-
 +
|
 +
|}
 +
* Full list [[http://irefindex.uio.no/wikifiles//images/0/0d/Interactions_by_taxonomy_beta5_complete.pdf]]
  
 
== Interactions  (Corresponds to Table 6 in PMID 18823568)==
 
== Interactions  (Corresponds to Table 6 in PMID 18823568)==

Latest revision as of 17:07, 10 August 2009

Summary

  • Total interactions : 764,017
  • Total distinct interactions (based on RIGID): 373,488 (48.88 % of total interactions)
  • Total distinct proteins (based on ROGID) : 83,953

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_5.0. 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_5.0/ 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_5.0 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 Name Number of interactions
4932 Saccharomyces cerevisiae 116710
9606 Homo sapiens 110039
7227 Drosophila melanogaster 46698
40674 Mammalia 35023
6239 Caenorhabditis elegans 12188
562 Escherichia coli 12090
197 Campylobacter jejuni 12025
10090 Mus musculus 11636
284812 Schizosaccharomyces pombe 972h- 11556
3702 Arabidopsis thaliana 5410
10116 Rattus norvegicus 4265
160 Treponema pallidum 3647
83333 Escherichia coli K-12 3505
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 Name Number of interactions '
9606 Homo sapiens 120548
4932 Saccharomyces cerevisiae 116702
7227 Drosophila melanogaster 46702
6239 Caenorhabditis elegans 12188
197 Campylobacter jejuni 12025
4896 Schizosaccharomyces pombe 11878
83333 Escherichia coli K-12 10996
10090 Mus musculus 10241
3702 Arabidopsis thaliana 5416
155864 Escherichia coli O157:H7 EDL933 4928
160 Treponema pallidum 3647
10116 Rattus norvegicus 3435
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 62895
BIOGRID 20557 164770
DIP 25930 28958 56429
HPRD 2947 2016 862 39966
INTACT 24398 26968 25004 8442 113878
MINT 22090 34777 30077 6612 45434 77540
MPACT 6938 8489 6793 0 6132 6427 13321
MPPI 385 27 41 304 89 73 0 826
OPHID 2226 1357 902 18063 7248 6417 0 183 47297
CORUM 116 18 29 403 122 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
(25790) (111300) (13529) (16454) (56806) (16318) (1132) (235) (26466) (1398) (0)

Interactors

BIND 40782
BIOGRID 14505 27694
DIP 15397 13105 20107
HPRD 3357 2522 1251 9750
INTACT 18203 16989 15718 5967 42060
MINT 16368 15163 15029 4777 23565 28854
MPACT 4651 4560 4639 0 4874 4756 4972
MPPI 674 219 294 430 579 511 0 861
OPHID 3253 2324 1242 7426 5809 4794 1 422 9626
CORUM 1561 756 671 1867 2312 1770 0 322 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
(18427) (8245) (1835) (1078) (12120) (3369) (16) (42) (1248) (614) (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%) 62895(68.9155%)
grid 242126 242126 241823(99.8749%) 164770(68.1366%)
dip 57675 57675 56597(98.1309%) 56429(99.7032%)
intact 133302 132525 132078(99.6627%) 113878(86.2203%)
mint 110788 110788 109195(98.5621%) 77540(71.0106%)
HPRD 40075 40075 40075(100.0000%) 39966(99.7280%)
ophid 73257 73257 72907(99.5222%) 47297(64.8731%)
MPACT 16504 16504 16286(98.6791%) 13321(81.7942%)
MPPI 1814 1814 1688(93.0540%) 826(48.9336%)
CORUM 2104 2104 2104(100.0000%) 1919(91.2072%)
ALL 871293 770825 764017(99.1168%) 373488(48.8848%)

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 40782
CORUM 10316 10314 99.9806 0 2 0 3581
dip 20728 18527 89.3815 1246 477 478 20107
grid 29599 19351 65.3772 10144 6 98 27694
HPRD 9773 9676 99.0075 55 42 0 9750
intact 100752 97167 96.4418 19 3323 243 42060
mint 77936 74746 95.9069 2 2711 477 28854
MPACT 40349 40112 99.4126 0 0 237 4972
MPPI 3628 3457 95.2867 0 30 141 861
ophid 146423 145362 99.2754 103 699 259 9626
All 724986 692369 95.5010 11569 15177 5871 83953

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 565158 77.9543% 232419 7502 0 72231 0 125686 3023 30666 93631 0
8194 000010000000000010 SI 1 12412 1.7120% 12336 76 0 0 0 0 0 0 0 0
554 000000001000101010 SVGO 1 624 0.0861% 0 0 0 0 624 0 0 0 0 0
130 000000000010000010 SM 1 577 0.0796% 0 577 0 0 0 0 0 0 0 0
66 000000000001000010 SD 1 2 0.0003% 0 2 0 0 0 0 0 0 0 0
65 000000000001000001 PD 1 9580 1.3214% 8083 1494 0 3 0 0 0 0 0 0
42 000000000000101010 SVG 1 163 0.0225% 0 0 0 0 163 0 0 0 0 0
129 000000000010000001 PM 1 523 0.0721% 473 1 0 0 0 0 32 0 17 0
8193 000010000000000001 PI 1 50 0.0069% 0 2 0 0 0 0 0 0 48 0
2 000000000000000010 S 1 35046 4.8340% 0 7464 17416 231 2772 0 0 6927 236 0
10 000000000000001010 SV 1 242 0.0334% 0 0 2 9 0 0 0 0 231 0
16385 000100000000000001 PE 2 184 0.0254% 0 0 0 0 0 0 0 0 184 0
16386 000100000000000010 SE 2 5413 0.7466% 5413 0 0 0 0 0 0 0 0 0
6 000000000000000110 SU 2 771 0.1063% 0 694 60 4 5 0 0 0 8 0
778 000000001100001010 SVO+ 2 1 0.0001% 0 0 0 0 0 0 0 0 1 0
774 000000001100000110 SUO+ 2 1 0.0001% 0 0 0 0 0 0 0 0 1 0
5 000000000000000101 PU 2 22841 3.1505% 0 0 0 293 0 19519 320 2519 190 0
773 000000001100000101 PUO+ 2 12 0.0017% 0 0 0 3 0 1 0 0 8 0
8210 000010000000010010 STI 3 905 0.1248% 855 50 0 0 0 0 0 0 0 0
8209 000010000000010001 PTI 3 12 0.0017% 0 0 0 0 0 0 0 0 12 0
146 000000000010010010 STM 3 1 0.0001% 0 1 0 0 0 0 0 0 0 0
145 000000000010010001 PTM 3 170 0.0234% 132 0 0 0 0 0 35 0 3 0
81 000000000001010001 PTD 3 1487 0.2051% 1486 0 0 1 0 0 0 0 0 0
17 000000000000010001 PT 3 26406 3.6423% 11871 0 0 1620 0 122 47 0 2456 10290
18 000000000000010010 ST 3 8547 1.1789% 0 1487 1015 0 6042 0 0 0 3 0
26 000000000000011010 SVT 3 1 0.0001% 0 0 0 0 0 0 0 0 1 0
16401 000100000000010001 PTE 4 3 0.0004% 0 0 0 0 0 0 0 0 3 0
16402 000100000000010010 STE 4 315 0.0434% 315 0 0 0 0 0 0 0 0 0
790 000000001100010110 SUTO+ 4 1 0.0001% 0 0 0 0 1 0 0 0 0 0
789 000000001100010101 PUTO+ 4 14 0.0019% 0 0 0 0 0 0 0 0 14 0
22 000000000000010110 SUT 4 18 0.0025% 0 1 3 0 14 0 0 0 0 0
131073 100000000000000001 PQ 5 1 0.0001% 0 0 0 0 0 0 0 0 1 0
131077 100000000000000101 PUQ 5 1 0.0001% 0 0 0 0 0 0 0 0 1 0
12546 000011000100000010 SLI+ 5 6735 0.9290% 0 6735 0 0 0 0 0 0 0 0
810 000000001100101010 SVGO+ 5 55 0.0076% 0 0 0 0 55 0 0 0 0 0
131089 100000000000010001 PTQ 5 38 0.0052% 0 0 0 0 0 0 0 0 38 0
5386 000001010100001010 SVXL+ 5 2 0.0003% 0 0 0 1 0 0 0 0 1 0
4354 000001000100000010 SL+ 5 4191 0.5781% 0 2997 1194 0 0 0 0 0 0 0
1802 000000011100001010 SVOX+ 5 3 0.0004% 0 0 0 0 0 0 0 0 3 0
21 000000000000010101 PUT 5 31 0.0043% 0 0 0 2 0 5 0 0 0 24
4357 000001000100000101 PUL+ 5 84 0.0116% 0 0 0 0 0 84 0 0 0 0
4373 000001000100010101 PUTL+ 5 9 0.0012% 0 0 0 1 0 0 0 0 8 0
4374 000001000100010110 SUTL+ 5 52 0.0072% 0 0 52 0 0 0 0 0 0 0
4394 000001000100101010 SVGL+ 5 52 0.0072% 0 0 0 0 52 0 0 0 0 0
4482 000001000110000010 SML+ 5 412 0.0568% 0 412 0 0 0 0 0 0 0 0
5381 000001010100000101 PUXL+ 5 29 0.0040% 0 0 0 0 0 19 0 0 10 0
5382 000001010100000110 SUXL+ 5 3 0.0004% 0 0 0 0 3 0 0 0 0 0
81937 010100000000010001 PTEN 6 3 0.0004% 3 0 0 0 0 0 0 0 0 0
81938 010100000000010010 STEN 6 24 0.0033% 24 0 0 0 0 0 0 0 0 0
86274 010101000100000010 SLEN+ 6 3 0.0004% 0 2 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
81922 010100000000000010 SEN 6 5767 0.7955% 5397 4 364 2 0 0 0 0 0 0
81921 010100000000000001 PEN 6 2859 0.3944% 2462 0 0 50 0 98 30 0 217 2
65601 010000000001000001 PDN 6 1 0.0001% 1 0 0 0 0 0 0 0 0 0
65553 010000000000010001 PTN 6 10 0.0014% 0 0 0 0 0 0 0 0 10 0
65537 010000000000000001 PN 6 6509 0.8978% 0 0 112 2659 42 601 0 0 3095 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
32785 001000000000010001 PTY 6 2 0.0003% 2 0 0 0 0 0 0 0 0 0
32770 001000000000000010 SY 6 73 0.0101% 0 0 30 23 0 0 0 0 20 0
32769 001000000000000001 PY 6 682 0.0941% 271 0 0 326 0 29 0 0 56 0
196625 110000000000010001 PTNQ 6 1 0.0001% 0 0 0 0 0 0 0 0 1 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. 11071(1.5395%)
E The protein reference was a retired NCBI Identifier. NCBI's eUtils (E) were used to retrieve the current accession and/or sequence. 14571(2.0262%)
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. 894(0.1243%)
L More than one possible assignment is possible (see + above). The assignment with the largest (L) SEGUID is arbitrarily chosen (see Methods) 11572(1.6092%)
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. 1683(0.234%)
+ 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). 11659(1.6213%)
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. 15177(2.1105%)
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(0.0989%)
I The protein reference used was an NCBI GenInfo Identifier (I). 20114(2.797%)
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. 23867(3.3189%)
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 38051(5.2914%)
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. 1143(0.1589%)
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(0.0058%)
P The interaction record's primary (P) reference for the protein was used to make the assignment 636702(88.5397%)
S One of the interaction record's secondary (S) references for the protein was used to make the assignment 82413(11.4603%)
Y The accession was referring an accession which was removed (deleted) from RefSeq or UniProt 760(0.1057%)
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(0.0051%)
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