Difference between revisions of "Statistics iRefIndex free 5.0"

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== Interactions  (Corresponds to Table 6 in PMID 18823568)==
 
== Interactions  (Corresponds to Table 6 in PMID 18823568)==
 
{|
 
{|
−
| BIND||62895
+
|BIND||62895
 
|-
 
|-
 
| BIOGRID||20557  || 164770
 
| BIOGRID||20557  || 164770
Line 259: Line 259:
 
| S||One of the interaction record's secondary (S) references for the protein was used to make the assignment||45617(7.1426%)
 
| S||One of the interaction record's secondary (S) references for the protein was used to make the assignment||45617(7.1426%)
 
|-
 
|-
−
| Y|| the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009)||729(0.1141%)
+
| Y|| the accession was referring an accession which was removed from RefSeq or UniProt ||729(0.1141%)
 
|-
 
|-
 
| 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||34(0.0053%)
 
| 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||34(0.0053%)

Latest revision as of 14:35, 16 August 2009

Summary

  • Total interactions : 648,955
  • Total distinct interactions (based on RIGID): 340,674 (52.50 % of total interactions)
  • Total distinct proteins (based on ROGID) : 80,354


Interactions (Corresponds to Table 6 in PMID 18823568)

BIND 62895
BIOGRID 20557 164770
DIP 0 0 0
HPRD 0 0 0 0
INTACT 24393 26965 0 0 113878
MINT 22085 34774 0 0 45434 77540
MPACT 0 0 0 0 0 0 0
MPPI 387 27 0 0 89 73 0 826
OPHID 2226 1357 0 0 7248 6417 0 183 47297
CORUM 0 0 0 0 0 0 0 0 0 0
I2D 0 0 0 0 0 0 0 0 0 0 0
BIND BIOGRID DIP HPRD INTACT MINT MPACT MPPI OPHID CORUM I2D
(31051) (120578) (0) (0) (58846) (17573) (0) (312) (36276) (0) (0)

Interactors

BIND 40782
BIOGRID 14505 27694
DIP 0 0 0
HPRD 0 0 0 0
INTACT 18200 16988 0 0 42060
MINT 16365 15162 0 0 23565 28854
MPACT 0 0 0 0 0 0 0
MPPI 672 218 0 0 578 510 0 859
OPHID 3253 2324 0 0 5809 4794 0 421 9626
CORUM 0 0 0 0 0 0 0 0 0 0
I2D 0 0 0 0 0 0 0 0 0 0 0
BIND BIOGRID DIP HPRD INTACT MINT MPACT MPPI OPHID CORUM I2D
(20064) (8662) (0) (0) (13198) (3631) (0) (49) (2256) (0) (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%)
intact 133302 132525 132078(99.6627%) 113878(86.2203%)
mint 110788 110788 109195(98.5621%) 77540(71.0106%)
ophid 73257 73257 72907(99.5222%) 47297(64.8731%)
MPPI 1814 1814 1688(93.0540%) 826(48.9336%)
ALL 754935 654467 648955(99.1578%) 340674(52.4958%)


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
grid 29599 19351 65.3772 10144 6 98 27694
intact 100752 97167 96.4418 19 3323 243 42060
mint 77936 74746 95.9069 2 2711 477 28854
MPPI 3628 3456 95.2591 0 30 142 859
ophid 146423 145362 99.2754 103 699 259 9626
All 643820 613739 95.3277 10268 14656 5157 80354


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 534492 83.0189% 232419 7502 0 72231 0 125686 3023 0 93631 0
66 000000000001000010 SD 1 2 0.0003% 0 2 0 0 0 0 0 0 0 0
8193 000010000000000001 PI 1 50 0.0078% 0 2 0 0 0 0 0 0 48 0
8194 000010000000000010 SI 1 12412 1.9279% 12336 76 0 0 0 0 0 0 0 0
129 000000000010000001 PM 1 523 0.0812% 473 1 0 0 0 0 32 0 17 0
10 000000000000001010 SV 1 240 0.0373% 0 0 0 9 0 0 0 0 231 0
130 000000000010000010 SM 1 577 0.0896% 0 577 0 0 0 0 0 0 0 0
2 000000000000000010 S 1 7931 1.2319% 0 7464 0 231 0 0 0 0 236 0
65 000000000001000001 PD 1 9580 1.4880% 8083 1494 0 3 0 0 0 0 0 0
774 000000001100000110 SUO+ 2 1 0.0002% 0 0 0 0 0 0 0 0 1 0
778 000000001100001010 SVO+ 2 1 0.0002% 0 0 0 0 0 0 0 0 1 0
16385 000100000000000001 PE 2 184 0.0286% 0 0 0 0 0 0 0 0 184 0
16386 000100000000000010 SE 2 5413 0.8408% 5413 0 0 0 0 0 0 0 0 0
6 000000000000000110 SU 2 706 0.1097% 0 694 0 4 0 0 0 0 8 0
5 000000000000000101 PU 2 20322 3.1565% 0 0 0 293 0 19519 320 0 190 0
773 000000001100000101 PUO+ 2 12 0.0019% 0 0 0 3 0 1 0 0 8 0
8209 000010000000010001 PTI 3 12 0.0019% 0 0 0 0 0 0 0 0 12 0
146 000000000010010010 STM 3 1 0.0002% 0 1 0 0 0 0 0 0 0 0
17 000000000000010001 PT 3 16115 2.5030% 11871 0 0 1620 0 122 46 0 2456 0
18 000000000000010010 ST 3 1490 0.2314% 0 1487 0 0 0 0 0 0 3 0
8210 000010000000010010 STI 3 905 0.1406% 855 50 0 0 0 0 0 0 0 0
26 000000000000011010 SVT 3 1 0.0002% 0 0 0 0 0 0 0 0 1 0
145 000000000010010001 PTM 3 170 0.0264% 132 0 0 0 0 0 35 0 3 0
81 000000000001010001 PTD 3 1487 0.2310% 1486 0 0 1 0 0 0 0 0 0
16402 000100000000010010 STE 4 315 0.0489% 315 0 0 0 0 0 0 0 0 0
789 000000001100010101 PUTO+ 4 14 0.0022% 0 0 0 0 0 0 0 0 14 0
16401 000100000000010001 PTE 4 3 0.0005% 0 0 0 0 0 0 0 0 3 0
22 000000000000010110 SUT 4 1 0.0002% 0 1 0 0 0 0 0 0 0 0
131089 100000000000010001 PTQ 5 38 0.0059% 0 0 0 0 0 0 0 0 38 0
1802 000000011100001010 SVOX+ 5 3 0.0005% 0 0 0 0 0 0 0 0 3 0
131073 100000000000000001 PQ 5 1 0.0002% 0 0 0 0 0 0 0 0 1 0
131077 100000000000000101 PUQ 5 1 0.0002% 0 0 0 0 0 0 0 0 1 0
12546 000011000100000010 SLI+ 5 6735 1.0461% 0 6735 0 0 0 0 0 0 0 0
5386 000001010100001010 SVXL+ 5 2 0.0003% 0 0 0 1 0 0 0 0 1 0
4357 000001000100000101 PUL+ 5 84 0.0130% 0 0 0 0 0 84 0 0 0 0
4354 000001000100000010 SL+ 5 2997 0.4655% 0 2997 0 0 0 0 0 0 0 0
21 000000000000010101 PUT 5 7 0.0011% 0 0 0 2 0 5 0 0 0 0
4373 000001000100010101 PUTL+ 5 9 0.0014% 0 0 0 1 0 0 0 0 8 0
4482 000001000110000010 SML+ 5 412 0.0640% 0 412 0 0 0 0 0 0 0 0
5381 000001010100000101 PUXL+ 5 29 0.0045% 0 0 0 0 0 19 0 0 10 0
163841 101000000000000001 PYQ 6 1 0.0002% 0 0 0 0 0 0 0 0 1 0
86274 010101000100000010 SLEN+ 6 2 0.0003% 0 2 0 0 0 0 0 0 0 0
81938 010100000000010010 STEN 6 24 0.0037% 24 0 0 0 0 0 0 0 0 0
81937 010100000000010001 PTEN 6 5 0.0008% 3 0 0 0 0 0 2 0 0 0
81922 010100000000000010 SEN 6 5403 0.8392% 5397 4 0 2 0 0 0 0 0 0
81921 010100000000000001 PEN 6 2845 0.4419% 2462 0 0 44 0 98 28 0 213 0
65601 010000000001000001 PDN 6 1 0.0002% 1 0 0 0 0 0 0 0 0 0
65553 010000000000010001 PTN 6 10 0.0016% 0 0 0 0 0 0 0 0 10 0
65537 010000000000000001 PN 6 6365 0.9886% 0 0 0 2665 0 601 0 0 3099 0
32833 001000000001000001 PDY 6 1 0.0002% 1 0 0 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 43 0.0067% 0 0 0 23 0 0 0 0 20 0
32769 001000000000000001 PY 6 682 0.1059% 271 0 0 326 0 29 0 0 56 0
196625 110000000000010001 PTNQ 6 1 0.0002% 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(1.7335%)
E The protein reference was a retired NCBI Identifier. NCBI's eUtils (E) were used to retrieve the current accession and/or sequence. 14194(2.2225%)
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. 0(0.0%)
L More than one possible assignment is possible (see + above). The assignment with the largest (L) SEGUID is arbitrarily chosen (see Methods) 10270(1.608%)
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(0.2635%)
+ 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). 10301(1.6129%)
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. 14656(2.2948%)
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. 31(0.0049%)
I The protein reference used was an NCBI GenInfo Identifier (I). 20114(3.1494%)
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. 21186(3.3172%)
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 20610(3.2271%)
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. 247(0.0387%)
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(0.0066%)
P The interaction record's primary (P) reference for the protein was used to make the assignment 593046(92.8574%)
S One of the interaction record's secondary (S) references for the protein was used to make the assignment 45617(7.1426%)
Y the accession was referring an accession which was removed from RefSeq or UniProt 729(0.1141%)
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 34(0.0053%)
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