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iRefIndex/PBR

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Contents

Interactions

BIND 11001
BIOGRID 0 0
DIP 0 0 0
HPRD 0 0 0 0
INTACT 0 0 0 0 0
MINT 0 0 0 0 0 0
MPACT 0 0 0 0 0 0 0
MPPI 0 0 0 0 0 0 0 0
OPHID 0 0 0 0 0 0 0 0 0
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
(11001) (0) (0) (0) (0) (0) (0) (0) (0) (0) (0)

Interactors

BIND 6491
BIOGRID 0 0
DIP 0 0 0
HPRD 0 0 0 0
INTACT 0 0 0 0 0
MINT 0 0 0 0 0 0
MPACT 0 0 0 0 0 0 0
MPPI 0 0 0 0 0 0 0 0
OPHID 0 0 0 0 0 0 0 0 0
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
(6491) (0) (0) (0) (0) (0) (0) (0) (0) (0) (0)

Summary of mapping interaction records to RIGs (Table 5)

Source Total records Protein-only interactors PPI Assigned to RIGID Unique RIGIDs
bind 15496 15496 14991(96.7411%) 11001(73.3840%)
ALL 15496 15496 14991(96.7411%) 11001(73.3840%)

Assignment of protein interactors to ROGs (Table 3)

Source Protein_Intractors Assigned % Arbitrary New Unassigned Unique proteins
bind 30992 28269 91.2139 1692 414 617 6491
All 30992 28269 91.2139 1692 414 617 6491

ROG summary

Decimal_score Binary_flag String_score Score_class Proteins Percentage BIND BioGrid DIP MINT HPRD OPHID MPPI MPACT IntAct CORUM
139265 100010000000000001 PIQ -1 23300 75.1807% 23300 0 0 0 0 0 0 0 0 0
139281 100010000000010001 PTIQ -1 947 3.0556% 947 0 0 0 0 0 0 0 0 0
147457 100100000000000001 PEQ -1 106 0.3420% 106 0 0 0 0 0 0 0 0 0
172033 101010000000000001 PIYQ -1 3 0.0097% 3 0 0 0 0 0 0 0 0 0
212993 110100000000000001 PENQ -1 414 1.3358% 414 0 0 0 0 0 0 0 0 0
2 000000000000000010 S 1 3867 12.4774% 3867 0 0 0 0 0 0 0 0 0
6 000000000000000110 SU 2 28 0.0903% 28 0 0 0 0 0 0 0 0 0
18 000000000000010010 ST 3 18 0.0581% 18 0 0 0 0 0 0 0 0 0
4354 000001000100000010 SL+ 5 1692 5.4595% 1692 0 0 0 0 0 0 0 0 0

Scores (Table 2)

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. 0(0.0%)
E The protein reference was a retired NCBI Identifier. NCBI's eUtils (E) were used to retrieve the current accession and/or sequence. 520(1.7119%)
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) 1692(5.5704%)
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. 0(0.0%)
+ 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). 1692(5.5704%)
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. 414(1.363%)
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. 0(0.0%)
I The protein reference used was an NCBI GenInfo Identifier (I). 24250(79.8354%)
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. 28(0.0922%)
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 965(3.177%)
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. 0(0.0%)
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'. 24770(81.5473%)
P The interaction record's primary (P) reference for the protein was used to make the assignment 24770(81.5473%)
S One of the interaction record's secondary (S) references for the protein was used to make the assignment 5605(18.4527%)
Y the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009) 3(0.0099%)
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 0(0.0%)