Difference between revisions of "Statistics iRefIndex 7.0"

From irefindex
(New page: == Summary == Last updated : 28 February, 2010 *Total interactions : 1,121,724 *Total distinct interactions (based on RIGID):320,687 ( 29% of total interactions) *Total distinct proteins (...)
 
Line 1: Line 1:
 
== Summary ==
 
== Summary ==
 
Last updated : 28 February, 2010
 
Last updated : 28 February, 2010
*Total interactions : 1,121,724
+
*Total interactions : 760,696
*Total distinct interactions (based on RIGID):320,687 ( 29% of total interactions)
+
*Total distinct interactions (based on RIGID):320,687 ( 42% of total interactions)
 
*Total distinct proteins (based on ROGID)    :  81,880  
 
*Total distinct proteins (based on ROGID)    :  81,880  
  

Revision as of 16:59, 28 February 2010

Summary

Last updated : 28 February, 2010

  • Total interactions : 760,696
  • Total distinct interactions (based on RIGID):320,687 ( 42% of total interactions)
  • Total distinct proteins (based on ROGID) : 81,880

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_7.0. 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_7.0/ 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_7.0 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)

  • Full list [[1]]

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

  • Full list [[2]]

Interactions (Corresponds to Table 6 in PMID 18823568)

BIND 62903
BIOGRID 23005 108790
DIP 26433 32715 61680
HPRD 3029 11604 843 39966
INTACT 24208 32250 25053 8652 117840
MINT 22100 37845 30107 6758 46680 79710
MPACT 6953 4026 6847 0 6147 6430 13321
MPPI 376 141 41 304 92 76 0 830
OPHID 2295 8351 882 18093 7330 6482 0 183 47530
CORUM 232 165 64 549 220 107 0 15 236 2607
I2D 0 0 0 0 0 0 0 0 0 0 0
BIND_TRANSLATION 42739 22374 18370 3980 19401 17755 2145 369 2928 193 0 48765
BIND BIOGRID DIP HPRD INTACT MINT MPACT MPPI OPHID CORUM I2D BIND_TRANSLATION
(10383) (45051) (17043) (13963) (58423) (16973) (5454) (240) (26312) (1837) (0) (2639)


Interactors

BIND 40790
BIOGRID 16988 27072
DIP 15526 14196 20171
HPRD 3407 6000 1236 9750
INTACT 18310 19951 15628 6189 44616
MINT 16422 16981 15000 4935 23979 29217
MPACT 4655 4326 4646 0 4877 4761 4972
MPPI 675 435 289 429 592 520 0 865
OPHID 3307 5439 1226 7453 6036 4918 1 421 9645
CORUM 2028 2064 842 2293 2908 2225 0 415 2245 4365
I2D 0 0 0 0 0 0 0 0 0 0 0
BIND BIOGRID DIP HPRD INTACT MINT MPACT MPPI OPHID CORUM I2D
(17969) (3251) (1749) (833) (13827) (3413) (24) (48) (1222) (699) (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 91276(97.1466%) 62903(68.9152%)
grid 336097 164163 163768(99.7594%) 108790(66.4293%)
dip 62903 62903 61843(98.3149%) 61680(99.7364%)
intact 140723 139787 139310(99.6588%) 117840(84.5883%)
mint 113258 113258 112159(99.0296%) 79710(71.0688%)
HPRD 40075 40075 40075(100.0000%) 39966(99.7280%)
ophid 73257 73257 73160(99.8676%) 47530(64.9672%)
MPACT 16504 16504 16286(98.6791%) 13321(81.7942%)
MPPI 1814 1814 1701(93.7707%) 830(48.7948%)
CORUM 2844 2844 2844(100.0000%) 2607(91.6667%)
BIND_Translation 140601 61585 58274(94.6237%) 48765(83.6823%)
ALL 1121724 770147 760696(98.7728%) 320687(42.1571%)


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

Source Protein_Intractors Assigned % Arbitrary New Unassigned Unique proteins
bind 285482 276808 96.9616 0 4764 3905 40790
BIND_Translation 187563 173355 92.4249 9625 454 4129 26792
CORUM 12916 12916 100.0000 0 0 0 4365
dip 20785 18942 91.1330 1255 121 467 20171
grid 29171 23394 80.1961 5583 2 192 27072
HPRD 9773 9663 98.8745 64 46 0 9750
intact 108593 107842 99.3084 19 468 264 44616
mint 79057 78553 99.3625 2 276 226 29217
MPACT 40349 40112 99.4126 0 0 237 4972
MPPI 3628 3461 95.3969 0 40 125 865
ophid 146423 146061 99.7528 103 253 6 9645
All 923740 891114 96.4681 16651 6424 9551 81880

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 BIND_Translation
1 000000000000000001 P 1 600844 65.0447% 232081 21836 0 73314 0 125683 3023 30666 101306 12916 19
8193 000010000000000001 PI 1 152094 16.4650% 0 0 0 1 0 0 0 0 48 0 152045
2 000000000000000010 S 1 43093 4.6651% 0 37 17426 244 2772 0 0 6927 255 0 15432
8194 000010000000000010 SI 1 12336 1.3354% 12336 0 0 0 0 0 0 0 0 0 0
65 000000000001000001 PD 1 8076 0.8743% 8073 0 0 3 0 0 0 0 0 0 0
41 000000000000101001 PVG 1 1511 0.1636% 0 1511 0 0 0 0 0 0 0 0 0
10 000000000000001010 SV 1 1293 0.1400% 0 0 5 14 0 0 0 0 237 0 1037
129 000000000010000001 PM 1 528 0.0572% 473 0 0 0 0 0 32 0 23 0 0
554 000000001000101010 SVGO 1 477 0.0516% 0 0 0 0 477 0 0 0 0 0 0
42 000000000000101010 SVG 1 171 0.0185% 0 0 12 0 159 0 0 0 0 0 0
66 000000000001000010 SD 1 99 0.0107% 0 4 9 0 0 0 0 0 0 0 86
5 000000000000000101 PU 2 22826 2.4710% 0 0 0 289 0 19519 320 2519 179 0 0
16386 000100000000000010 SE 2 5429 0.5877% 5423 0 6 0 0 0 0 0 0 0 0
16385 000100000000000001 PE 2 1532 0.1658% 0 0 0 202 0 0 0 0 720 0 610
6 000000000000000110 SU 2 816 0.0883% 0 2 58 4 5 0 0 0 10 0 737
16449 000100000001000001 PDE 2 120 0.0130% 0 0 0 34 0 0 0 0 86 0 0
773 000000001100000101 PUO+ 2 13 0.0014% 0 0 0 3 0 1 0 0 9 0 0
774 000000001100000110 SUO+ 2 1 0.0001% 0 0 0 0 0 0 0 0 1 0 0
778 000000001100001010 SVO+ 2 1 0.0001% 0 0 0 0 0 0 0 0 1 0 0
17 000000000000010001 PT 3 16060 1.7386% 11785 0 0 1632 0 122 46 0 2475 0 0
18 000000000000010010 ST 3 8104 0.8773% 0 0 1016 0 6042 0 0 0 3 0 1043
8209 000010000000010001 PTI 3 2052 0.2221% 0 0 0 0 0 0 0 0 13 0 2039
81 000000000001010001 PTD 3 1497 0.1621% 1496 0 0 1 0 0 0 0 0 0 0
8210 000010000000010010 STI 3 855 0.0926% 855 0 0 0 0 0 0 0 0 0 0
145 000000000010010001 PTM 3 184 0.0199% 132 0 0 0 0 0 35 0 17 0 0
26 000000000000011010 SVT 3 1 0.0001% 0 0 0 0 0 0 0 0 1 0 0
16402 000100000000010010 STE 4 317 0.0343% 316 0 1 0 0 0 0 0 0 0 0
16401 000100000000010001 PTE 4 269 0.0291% 0 0 0 0 0 0 0 0 4 0 265
22 000000000000010110 SUT 4 17 0.0018% 0 0 3 0 14 0 0 0 0 0 0
789 000000001100010101 PUTO+ 4 14 0.0015% 0 0 0 0 0 0 0 0 14 0 0
790 000000001100010110 SUTO+ 4 1 0.0001% 0 0 0 0 1 0 0 0 0 0 0
4393 000001000100101001 PVGL+ 5 5566 0.6026% 0 5566 0 0 0 0 0 0 0 0 0
4362 000001000100001010 SVL+ 5 5498 0.5952% 0 0 0 0 0 0 0 0 0 0 5498
4354 000001000100000010 SL+ 5 5337 0.5778% 0 15 1195 0 0 0 0 0 0 0 4127
810 000000001100101010 SVGO+ 5 193 0.0209% 0 0 0 0 193 0 0 0 0 0 0
4357 000001000100000101 PUL+ 5 84 0.0091% 0 0 0 0 0 84 0 0 0 0 0
4394 000001000100101010 SVGL+ 5 71 0.0077% 0 2 8 0 61 0 0 0 0 0 0
4374 000001000100010110 SUTL+ 5 52 0.0056% 0 0 52 0 0 0 0 0 0 0 0
131089 100000000000010001 PTQ 5 39 0.0042% 0 0 0 0 0 0 0 0 39 0 0
5381 000001010100000101 PUXL+ 5 29 0.0031% 0 0 0 0 0 19 0 0 10 0 0
4373 000001000100010101 PUTL+ 5 9 0.0010% 0 0 0 1 0 0 0 0 8 0 0
21 000000000000010101 PUT 5 7 0.0008% 0 0 0 2 0 5 0 0 0 0 0
1802 000000011100001010 SVOX+ 5 4 0.0004% 0 0 0 0 0 0 0 0 4 0 0
5382 000001010100000110 SUXL+ 5 3 0.0003% 0 0 0 0 3 0 0 0 0 0 0
5386 000001010100001010 SVXL+ 5 2 0.0002% 0 0 0 1 0 0 0 0 1 0 0
131073 100000000000000001 PQ 5 1 0.0001% 0 0 0 0 0 0 0 0 1 0 0
131077 100000000000000101 PUQ 5 1 0.0001% 0 0 0 0 0 0 0 0 1 0 0
32769 001000000000000001 PY 6 8873 0.9606% 3051 4 0 2785 0 731 5 0 2297 0 0
81922 010100000000000010 SEN 6 4667 0.5052% 4658 0 9 0 0 0 0 0 0 0 0
32833 001000000001000001 PDY 6 755 0.0817% 755 0 0 0 0 0 0 0 0 0 0
32770 001000000000000010 SY 6 567 0.0614% 0 0 405 25 0 0 0 0 95 0 42
65601 010000000001000001 PDN 6 557 0.0603% 52 0 0 248 0 253 2 0 2 0 0
65537 010000000000000001 PN 6 456 0.0494% 35 0 112 25 46 0 5 0 233 0 0
81921 010100000000000001 PEN 6 430 0.0465% 0 2 0 3 0 0 31 0 2 0 392
73729 010010000000000001 PIN 6 223 0.0241% 0 0 0 0 0 0 0 0 223 0 0
81937 010100000000010001 PTEN 6 64 0.0069% 0 0 0 0 0 0 2 0 0 0 62
32785 001000000000010001 PTY 6 32 0.0035% 32 0 0 0 0 0 0 0 0 0 0
81938 010100000000010010 STEN 6 19 0.0021% 19 0 0 0 0 0 0 0 0 0 0
65553 010000000000010001 PTN 6 8 0.0009% 0 0 0 0 0 0 0 0 8 0 0
147473 100100000000010001 PTEQ 6 1 0.0001% 0 0 0 0 0 0 0 0 1 0 0
40961 001010000000000001 PIY 6 1 0.0001% 0 0 0 0 0 0 0 0 1 0 0
32786 001000000000010010 STY 6 1 0.0001% 0 0 1 0 0 0 0 0 0 0 0
163841 101000000000000001 PYQ 6 1 0.0001% 0 0 0 0 0 0 0 0 1 0 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%)