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Contents

Interactions

BIND 62903
BIOGRID 23140 226496
DIP 0 0 0
HPRD 0 0 0 0
INTACT 24214 32627 0 0 117840
MINT 22100 37903 0 0 46689 79710
MPACT 0 0 0 0 0 0 0
MPPI 376 141 0 0 92 76 0 830
OPHID 2295 8356 0 0 7330 6482 0 183 47530
CORUM 0 0 0 0 0 0 0 0 0 0
(30160) (171076) (0) (0) (59998) (18149) (0) (315) (32861) (0) (0) (0)

Interactors

BIND 40790
BIOGRID 17313 29090
DIP 0 0 0
HPRD 0 0 0 0
INTACT 18310 20511 0 0 44616
MINT 16422 17286 0 0 23979 29217
MPACT 0 0 0 0 0 0 0
MPPI 675 435 0 0 592 520 0 865
OPHID 3307 5444 0 0 6036 4918 0 421 9645
CORUM 0 0 0 0 0 0 0 0 0 0
BIND BIOGRID DIP HPRD INTACT MINT MPACT MPPI OPHID CORUM I2D BIND_TRANSLATION
(19341) (5327) (0) (0) (14646) (3665) (0) (55) (1841) (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 193648 93957 91276(97.1466%) 62903(68.9152%)
grid 333977 329642 329185(99.8614%) 226496(68.8051%)
intact 140723 139787 139310(99.6588%) 117840(84.5883%)
mint 113258 113258 112159(99.0296%) 79710(71.0688%)
ophid 73257 73257 73160(99.8676%) 47530(64.9672%)
MPPI 1814 1814 1701(93.7707%) 830(48.7948%)
ALL 856677 751715 746791(99.3450%) 396249(53.0602%)

Assignment of protein interactors to ROGs (Table 3)

Source Protein_Intractors Assigned % Arbitrary New Unassigned Unique proteins
bind 285482 276808 96.9616 0 4764 3905 40790
grid 36333 30259 83.2824 5869 1 204 29090
intact 108593 107842 99.3084 19 468 264 44616
mint 79057 78553 99.3625 2 276 226 29217
MPPI 3628 3461 95.3969 0 40 125 865
ophid 146423 146061 99.7528 103 253 6 9645
All 659516 642991 97.4944 5993 5802 4730 79283

ROG summary

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 564030 85.5218% 232081 28623 0 73314 0 125683 3023 0 101306 0 0
8194 000010000000000010 SI 1 12336 1.8705% 12336 0 0 0 0 0 0 0 0 0 0
65 000000000001000001 PD 1 8076 1.2245% 8073 0 0 3 0 0 0 0 0 0 0
41 000000000000101001 PVG 1 1583 0.2400% 0 1583 0 0 0 0 0 0 0 0 0
2 000000000000000010 S 1 543 0.0823% 0 44 0 244 0 0 0 0 255 0 0
129 000000000010000001 PM 1 528 0.0801% 473 0 0 0 0 0 32 0 23 0 0
10 000000000000001010 SV 1 251 0.0381% 0 0 0 14 0 0 0 0 237 0 0
8193 000010000000000001 PI 1 49 0.0074% 0 0 0 1 0 0 0 0 48 0 0
66 000000000001000010 SD 1 4 0.0006% 0 4 0 0 0 0 0 0 0 0 0
5 000000000000000101 PU 2 20307 3.0791% 0 0 0 289 0 19519 320 0 179 0 0
16386 000100000000000010 SE 2 5423 0.8223% 5423 0 0 0 0 0 0 0 0 0 0
16385 000100000000000001 PE 2 922 0.1398% 0 0 0 202 0 0 0 0 720 0 0
16449 000100000001000001 PDE 2 120 0.0182% 0 0 0 34 0 0 0 0 86 0 0
6 000000000000000110 SU 2 15 0.0023% 0 1 0 4 0 0 0 0 10 0 0
773 000000001100000101 PUO+ 2 13 0.0020% 0 0 0 3 0 1 0 0 9 0 0
774 000000001100000110 SUO+ 2 1 0.0002% 0 0 0 0 0 0 0 0 1 0 0
778 000000001100001010 SVO+ 2 1 0.0002% 0 0 0 0 0 0 0 0 1 0 0
17 000000000000010001 PT 3 16060 2.4351% 11785 0 0 1632 0 122 46 0 2475 0 0
81 000000000001010001 PTD 3 1497 0.2270% 1496 0 0 1 0 0 0 0 0 0 0
8210 000010000000010010 STI 3 855 0.1296% 855 0 0 0 0 0 0 0 0 0 0
145 000000000010010001 PTM 3 184 0.0279% 132 0 0 0 0 0 35 0 17 0 0
8209 000010000000010001 PTI 3 13 0.0020% 0 0 0 0 0 0 0 0 13 0 0
18 000000000000010010 ST 3 3 0.0005% 0 0 0 0 0 0 0 0 3 0 0
26 000000000000011010 SVT 3 1 0.0002% 0 0 0 0 0 0 0 0 1 0 0
16402 000100000000010010 STE 4 316 0.0479% 316 0 0 0 0 0 0 0 0 0 0
789 000000001100010101 PUTO+ 4 14 0.0021% 0 0 0 0 0 0 0 0 14 0 0
16401 000100000000010001 PTE 4 4 0.0006% 0 0 0 0 0 0 0 0 4 0 0
4393 000001000100101001 PVGL+ 5 5854 0.8876% 0 5854 0 0 0 0 0 0 0 0 0
4357 000001000100000101 PUL+ 5 84 0.0127% 0 0 0 0 0 84 0 0 0 0 0
131089 100000000000010001 PTQ 5 39 0.0059% 0 0 0 0 0 0 0 0 39 0 0
5381 000001010100000101 PUXL+ 5 29 0.0044% 0 0 0 0 0 19 0 0 10 0 0
4354 000001000100000010 SL+ 5 14 0.0021% 0 14 0 0 0 0 0 0 0 0 0
4373 000001000100010101 PUTL+ 5 9 0.0014% 0 0 0 1 0 0 0 0 8 0 0
21 000000000000010101 PUT 5 7 0.0011% 0 0 0 2 0 5 0 0 0 0 0
1802 000000011100001010 SVOX+ 5 4 0.0006% 0 0 0 0 0 0 0 0 4 0 0
5386 000001010100001010 SVXL+ 5 2 0.0003% 0 0 0 1 0 0 0 0 1 0 0
131077 100000000000000101 PUQ 5 1 0.0002% 0 0 0 0 0 0 0 0 1 0 0
131073 100000000000000001 PQ 5 1 0.0002% 0 0 0 0 0 0 0 0 1 0 0
4394 000001000100101010 SVGL+ 5 1 0.0002% 0 1 0 0 0 0 0 0 0 0 0
32769 001000000000000001 PY 6 8873 1.3454% 3051 4 0 2785 0 731 5 0 2297 0 0
81922 010100000000000010 SEN 6 4515 0.6846% 4515 0 0 0 0 0 0 0 0 0 0
32833 001000000001000001 PDY 6 755 0.1145% 755 0 0 0 0 0 0 0 0 0 0
65601 010000000001000001 PDN 6 559 0.0848% 52 0 0 247 0 253 5 0 2 0 0
65537 010000000000000001 PN 6 450 0.0682% 178 1 0 26 0 0 11 0 234 0 0
73729 010010000000000001 PIN 6 223 0.0338% 0 0 0 0 0 0 0 0 223 0 0
32770 001000000000000010 SY 6 120 0.0182% 0 0 0 25 0 0 0 0 95 0 0
32785 001000000000010001 PTY 6 32 0.0049% 32 0 0 0 0 0 0 0 0 0 0
81921 010100000000000001 PEN 6 26 0.0039% 0 0 0 3 0 0 22 0 1 0 0
81938 010100000000010010 STEN 6 19 0.0029% 19 0 0 0 0 0 0 0 0 0 0
65553 010000000000010001 PTN 6 8 0.0012% 0 0 0 0 0 0 0 0 8 0 0
81937 010100000000010001 PTEN 6 2 0.0003% 0 0 0 0 0 0 2 0 0 0 0
147473 100100000000010001 PTEQ 6 1 0.0002% 0 0 0 0 0 0 0 0 1 0 0
40961 001010000000000001 PIY 6 1 0.0002% 0 0 0 0 0 0 0 0 1 0 0
163841 101000000000000001 PYQ 6 1 0.0002% 0 0 0 0 0 0 0 0 1 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. 11011(1.6816%)
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. 11348(1.7331%)
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. 7438(1.136%)
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) 5993(0.9153%)
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. 712(0.1087%)
+ 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). 6026(0.9203%)
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. 5802(0.8861%)
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. 33(0.0050%)
I The protein reference used was an NCBI GenInfo Identifier (I). 13477(2.0583%)
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. 20480(3.1278%)
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 19064(2.9115%)
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. 7697(1.1755%)
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'. 43(0.0066%)
P The interaction record's primary (P) reference for the protein was used to make the assignment 630355(96.2699%)
S One of the interaction record's secondary (S) references for the protein was used to make the assignment 24424(3.7301%)
Y the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009) 9782(1.4939%)
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 35(0.0053%)

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