Statistics iRefIndex 9.0

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Interactions

BIND 62901
GRID 24424 263295
DIP 25910 38242 89716
INTACT 25434 37330 39017 155235
MINT 22278 40367 36677 47248 85758
HPRD 1955 8695 1125 5667 4489 40460
OPHID 2418 9274 1462 7537 6911 10267 47479
MPACT 6714 7768 6992 6210 6464 0 0 13311
MPPI 387 153 63 98 93 160 187 0 830
CORUM 248 193 115 244 119 248 237 0 15 2607
BIND_TRANSLATION 56114 24426 25078 24832 22203 2206 2725 6542 344 186 60212
INNATEDB 339 1273 403 789 654 1045 1221 0 52 82 399 7000
MATRIXDB 4 11 2 15 2 14 24 0 2 0 4 5 201
MPILIT 24 0 85 108 32 0 0 0 0 0 24 0 0 744
MPIIMEX 7 0 25 33 14 0 0 0 0 0 7 0 0 30 473
BIND GRID DIP INTACT MINT HPRD OPHID MPACT MPPI CORUM BIND_TRANSLATION INNATEDB MATRIXDB MPILIT MPIIMEX
(5184) (188537) (27825) (83340) (19066) (24359) (28562) (1588) (248) (1932) (3054) (4297) (156) (540) (398)

Interactors

BIND 40790
GRID 17983 33559
DIP 17562 18347 29969
INTACT 19129 23211 24531 52751
MINT 16844 18434 19654 25479 31621
HPRD 2926 5803 3484 6005 4536 9824
OPHID 3400 5928 4220 6976 5398 6218 9577
MPACT 4585 4477 4730 4932 4795 0 1 4976
MPPI 682 476 470 636 564 316 424 0 864
CORUM 2072 2344 2212 3217 2532 1858 2248 0 417 4365
BIND_TRANSLATION 35081 17444 16970 18582 16279 2960 3333 4189 660 1932 37155
INNATEDB 1620 2076 1791 2564 2136 1707 2112 0 359 1148 1622 3403
MATRIXDB 112 111 87 138 116 111 144 0 18 52 111 89 221
MPILIT 92 0 332 440 227 0 0 0 0 0 92 0 0 936
MPIIMEX 33 0 111 128 65 0 0 0 0 0 31 0 0 92 473
BIND GRID DIP INTACT MINT HPRD OPHID MPACT MPPI CORUM BIND_TRANSLATION INNATEDB MATRIXDB MPILIT MPIIMEX
(4337) (6423) (2236) (15606) (4032) (1718) (943) (11) (35) (521) (1398) (269) (35) (366) (282)

Summary of mapping interaction records to RIGs (Table 5)

Source Total records Protein-only interactors PPI Assigned to RIGID Unique RIGIDs
bind 193648 93957 91268(97.1381%) 62901(68.9190%)
grid 392218 386984 386462(99.8651%) 263295(68.1296%)
dip 90994 90994 89910(98.8087%) 89716(99.7842%)
intact 183079 181384 180718(99.6328%) 155235(85.8990%)
mint 122775 122775 122269(99.5879%) 85758(70.1388%)
HPRD 83022 83022 83022(100.0000%) 40460(48.7341%)
ophid 73257 73257 73160(99.8676%) 47479(64.8975%)
MPACT 16504 16504 16273(98.6003%) 13311(81.7981%)
MPPI 1814 1814 1699(93.6604%) 830(48.8523%)
CORUM 2844 2844 2844(100.0000%) 2607(91.6667%)
BIND_Translation 192923 87081 83349(95.7143%) 60212(72.2408%)
InnateDB 14729 11476 11248(98.0132%) 7000(62.2333%)
MatrixDB 846 349 321(91.9771%) 201(62.6168%)
mpilit 745 745 745(100.0000%) 744(99.8658%)
mpiimex 473 473 473(100.0000%) 473(100.0000%)
ALL 1369871 1153659 1143761(99.1420%) 532634(46.5686%)

Assignment of protein interactors to ROGs (Table 3)

Source Protein_Intractors Assigned % Arbitrary N_and_Y Unassigned Unique proteins
bind 285482 272483 95.4466 0 9075 3924 40790
BIND_Translation 264346 239988 90.7856 73 15383 8902 37155
CORUM 12916 12909 99.9458 7 0 0 4365
dip 30978 29401 94.9093 640 454 483 29969
grid 41420 34125 82.3877 7065 7 223 33559
HPRD 123812 103372 83.4911 20209 231 0 9824
InnateDB 27209 26914 98.9158 0 0 295 3403
intact 150972 148103 98.0996 34 2433 402 52751
MatrixDB 1123 1077 95.9038 0 0 46 221
mint 87509 83389 95.2919 48 3927 145 31621
MPACT 40349 40098 99.3779 0 1 250 4976
mpiimex 946 946 100.0000 0 0 0 473
mpilit 1490 1486 99.7315 3 1 0 936
MPPI 3628 3456 95.2591 0 42 130 864
ophid 146423 145149 99.1299 265 1003 6 9577
All 1218603 1142896 93.7874 28344 32557 14806 96059

ROG summary

Decimal_score Binary_flag String_score Score_class Proteins Percentage bind grid dip intact mint mpiimex mpilit HPRD ophid InnateDB MatrixDB MPACT BIND_Translation MPPI CORUM
786 000000001100010010 STO+ -1 8850 0.7262% 0 0 0 0 0 0 0 8850 0 0 0 0 0 0 0
898 000000001110000010 SMO+ -1 20 0.0016% 0 0 0 16 0 0 0 4 0 0 0 0 0 0 0
1794 000000011100000010 SOX+ -1 8 0.0007% 0 0 0 6 2 0 0 0 0 0 0 0 0 0 0
131093 100000000000010101 PUTQ -1 5 0.0004% 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0
163905 101000000001000001 PDYQ -1 2 0.0002% 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0
914 000000001110010010 STMO+ -1 2 0.0002% 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0
1922 000000011110000010 SMOX+ -1 2 0.0002% 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0
218370 110101010100000010 SXLENQ+ -1 1 0.0001% 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
163921 101000000001010001 PTDYQ -1 1 0.0001% 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
1 000000000000000001 P 1 809581 66.4352% 229929 21809 0 147356 81034 934 1472 0 124771 26914 828 30649 127973 3021 12891
2 000000000000000010 S 1 51662 4.2394% 0 41 28210 15 294 0 0 13141 0 0 0 9375 586 0 0
131201 100000000010000001 PMQ 1 23587 1.9356% 0 0 0 0 0 0 0 0 0 0 0 0 23587 0 0
554 000000001000101010 SVGO 1 17263 1.4166% 0 0 0 0 0 0 0 17263 0 0 0 0 0 0 0
8194 000010000000000010 SI 1 12336 1.0123% 12336 0 0 0 0 0 0 0 0 0 0 0 0 0 0
65 000000000001000001 PD 1 8057 0.6612% 8055 0 0 0 2 0 0 0 0 0 0 0 0 0 0
130 000000000010000010 SM 1 6594 0.5411% 0 0 0 0 0 0 0 6594 0 0 0 0 0 0 0
41 000000000000101001 PVG 1 1936 0.1589% 0 1936 0 0 0 0 0 0 0 0 0 0 0 0 0
42 000000000000101010 SVG 1 1123 0.0922% 0 0 122 0 0 0 0 1001 0 0 0 0 0 0 0
129 000000000010000001 PM 1 688 0.0565% 470 0 0 49 0 0 0 0 0 0 137 0 0 32 0
139265 100010000000000001 PIQ 1 337 0.0277% 0 0 0 0 0 0 0 0 0 0 0 0 337 0 0
10 000000000000001010 SV 1 84 0.0069% 0 0 5 44 35 0 0 0 0 0 0 0 0 0 0
8193 000010000000000001 PI 1 37 0.0030% 0 0 0 29 8 0 0 0 0 0 0 0 0 0 0
66 000000000001000010 SD 1 35 0.0029% 0 4 0 0 13 0 0 0 0 0 18 0 0 0 0
9 000000000000001001 PV 1 5 0.0004% 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0
5 000000000000000101 PU 2 21571 1.7701% 0 0 0 61 234 9 2 0 20246 0 0 0 679 322 18
16386 000100000000000010 SE 2 5377 0.4412% 5377 0 0 0 0 0 0 0 0 0 0 0 0 0 0
770 000000001100000010 SO+ 2 3486 0.2861% 0 0 0 4 0 0 0 3482 0 0 0 0 0 0 0
147458 100100000000000010 SEQ 2 1985 0.1629% 0 0 0 4 0 0 0 0 0 0 0 0 1981 0 0
6 000000000000000110 SU 2 173 0.0142% 0 0 128 26 5 0 0 13 0 0 0 0 1 0 0
16385 000100000000000001 PE 2 153 0.0126% 0 0 0 144 9 0 0 0 0 0 0 0 0 0 0
147457 100100000000000001 PEQ 2 53 0.0043% 0 0 0 0 0 0 0 0 0 0 0 0 53 0 0
773 000000001100000101 PUO+ 2 17 0.0014% 0 0 0 7 1 0 0 0 9 0 0 0 0 0 0
1797 000000011100000101 PUOX+ 2 4 0.0003% 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0
16514 000100000010000010 SME 2 3 0.0002% 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0
774 000000001100000110 SUO+ 2 1 0.0001% 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
17 000000000000010001 PT 3 87494 7.1799% 13466 10310 0 176 1706 3 12 0 118 0 2 7 61647 47 0
18 000000000000010010 ST 3 33709 2.7662% 0 25 931 1 0 0 0 32752 0 0 0 0 0 0 0
146 000000000010010010 STM 3 16663 1.3674% 0 0 0 0 0 0 0 16663 0 0 0 0 0 0 0
131217 100000000010010001 PTMQ 3 5300 0.4349% 0 0 0 0 0 0 0 0 0 0 0 0 5300 0 0
81 000000000001010001 PTD 3 1591 0.1306% 1500 0 0 0 0 0 0 0 0 0 91 0 0 0 0
8210 000010000000010010 STI 3 855 0.0702% 855 0 0 0 0 0 0 0 0 0 0 0 0 0 0
145 000000000010010001 PTM 3 190 0.0156% 135 0 0 21 0 0 0 0 0 0 0 0 0 34 0
163985 101000000010010001 PTMYQ 3 57 0.0047% 0 0 0 0 0 0 0 0 0 0 0 0 57 0 0
139281 100010000000010001 PTIQ 3 42 0.0034% 0 0 0 0 0 0 0 0 0 0 0 0 42 0 0
8209 000010000000010001 PTI 3 15 0.0012% 0 0 0 15 0 0 0 0 0 0 0 0 0 0 0
16530 000100000010010010 STME 3 13 0.0011% 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0
26 000000000000011010 SVT 3 1 0.0001% 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
82 000000000001010010 STD 3 1 0.0001% 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
147474 100100000000010010 STEQ 4 668 0.0548% 0 0 0 2 0 0 0 0 0 0 0 0 666 0 0
16402 000100000000010010 STE 4 345 0.0283% 344 0 1 0 0 0 0 0 0 0 0 0 0 0 0
22 000000000000010110 SUT 4 138 0.0113% 0 0 4 0 0 0 0 134 0 0 0 0 0 0 0
790 000000001100010110 SUTO+ 4 48 0.0039% 0 0 0 19 27 0 0 2 0 0 0 0 0 0 0
789 000000001100010101 PUTO+ 4 19 0.0016% 0 0 0 18 1 0 0 0 0 0 0 0 0 0 0
16401 000100000000010001 PTE 4 3 0.0002% 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0
5378 000001010100000010 SXL+ 5 18701 1.5346% 0 0 0 11 1 0 0 18689 0 0 0 0 0 0 0
131073 100000000000000001 PQ 5 16324 1.3396% 0 0 0 6 0 0 0 0 0 0 0 0 16318 0 0
4393 000001000100101001 PVGL+ 5 7049 0.5784% 0 7049 0 0 0 0 0 0 0 0 0 0 0 0 0
810 000000001100101010 SVGO+ 5 3471 0.2848% 0 0 0 0 0 0 0 3471 0 0 0 0 0 0 0
4394 000001000100101010 SVGL+ 5 1621 0.1330% 0 0 112 0 0 0 0 1509 0 0 0 0 0 0 0
131089 100000000000010001 PTQ 5 860 0.0706% 0 0 0 48 0 0 0 0 0 0 0 0 812 0 0
4354 000001000100000010 SL+ 5 528 0.0433% 0 16 510 2 0 0 0 0 0 0 0 0 0 0 0
4357 000001000100000101 PUL+ 5 241 0.0198% 0 0 0 0 0 0 3 0 222 0 0 0 9 0 7
21 000000000000010101 PUT 5 108 0.0089% 0 0 0 20 12 0 0 0 5 0 0 67 4 0 0
4373 000001000100010101 PUTL+ 5 70 0.0057% 0 0 0 8 0 0 0 0 4 0 0 0 58 0 0
5381 000001010100000101 PUXL+ 5 56 0.0046% 0 0 0 12 5 0 0 0 39 0 0 0 0 0 0
5386 000001010100001010 SVXL+ 5 43 0.0035% 0 0 0 1 42 0 0 0 0 0 0 0 0 0 0
4374 000001000100010110 SUTL+ 5 25 0.0021% 0 0 12 0 0 0 0 7 0 0 0 0 6 0 0
4358 000001000100000110 SUL+ 5 6 0.0005% 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0
5382 000001010100000110 SUXL+ 5 4 0.0003% 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0
1802 000000011100001010 SVOX+ 5 1 0.0001% 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
32769 001000000000000001 PY 6 15999 1.3129% 3696 5 0 1873 3389 0 1 0 750 0 0 0 6280 5 0
65601 010000000001000001 PDN 6 8727 0.7161% 52 0 0 2 247 0 0 0 253 0 0 0 8168 5 0
81922 010100000000000010 SEN 6 4417 0.3625% 4417 0 0 0 0 0 0 0 0 0 0 0 0 0 0
65537 010000000000000001 PN 6 969 0.0795% 35 0 189 263 256 0 0 215 0 0 0 0 0 11 0
32833 001000000001000001 PDY 6 769 0.0631% 769 0 0 0 0 0 0 0 0 0 0 0 0 0 0
32770 001000000000000010 SY 6 424 0.0348% 0 2 262 88 25 0 0 0 0 0 0 1 46 0 0
163969 101000000010000001 PMYQ 6 401 0.0329% 0 0 0 0 0 0 0 0 0 0 0 0 401 0 0
212993 110100000000000001 PENQ 6 279 0.0229% 0 0 0 0 0 0 0 0 0 0 0 0 279 0 0
73729 010010000000000001 PIN 6 198 0.0162% 0 0 0 198 0 0 0 0 0 0 0 0 0 0 0
32785 001000000000010001 PTY 6 147 0.0121% 86 0 0 2 0 0 0 0 0 0 0 0 59 0 0
196609 110000000000000001 PNQ 6 31 0.0025% 0 0 0 0 0 0 0 0 0 0 0 0 31 0 0
81921 010100000000000001 PEN 6 27 0.0022% 0 0 0 1 10 0 0 0 0 0 0 0 0 16 0
65617 010000000001010001 PTDN 6 23 0.0019% 0 0 0 0 0 0 0 0 0 0 0 0 23 0 0
196625 110000000000010001 PTNQ 6 22 0.0018% 0 0 0 0 0 0 0 0 0 0 0 0 22 0 0
65553 010000000000010001 PTN 6 21 0.0017% 0 0 1 4 0 0 0 16 0 0 0 0 0 0 0
81938 010100000000010010 STEN 6 19 0.0016% 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0
213009 110100000000010001 PTENQ 6 14 0.0011% 0 0 0 0 0 0 0 0 0 0 0 0 14 0 0
32897 001000000010000001 PMY 6 2 0.0002% 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0
32786 001000000000010010 STY 6 2 0.0002% 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0
81937 010100000000010001 PTEN 6 2 0.0002% 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0
147473 100100000000010001 PTEQ 6 2 0.0002% 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0
163857 101000000000010001 PTYQ 6 1 0.0001% 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
81986 010100000001000010 SDEN 6 1 0.0001% 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
32913 001000000010010001 PTMY 6 1 0.0001% 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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. 19207(1.5955%)
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, sequence information obtained from UniProt. 13362(1.11%)
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. 32463(2.6967%)
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) 28345(2.3546%)
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. 53523(4.4462%)
+ 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). 44274(3.6779%)
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. 14751(1.2254%)
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. 33192(2.7573%)
I The protein reference used was an NCBI GenInfo Identifier (I). 13820(1.148%)
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. 22486(1.8679%)
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 157327(13.0692%)
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. 32597(2.7078%)
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'. 49972(4.1512%)
P The interaction record's primary (P) reference for the protein was used to make the assignment 1013088(84.1577%)
S One of the interaction record's secondary (S) references for the protein was used to make the assignment 190709(15.8423%)
Y the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009) 17806(1.4792%)
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 18820(1.5634%)