Difference between revisions of "Statistics iRefIndex 2.0"

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| align="center" style="background:#f0f0f0;"|'''Unique RIGIDs'''
 
| align="center" style="background:#f0f0f0;"|'''Unique RIGIDs'''
 
|-
 
|-
−
| bind||193648||93957||91234(97.1019%)||62859(68.8987%)
+
| bind||193648||93957||91234 (97.1019%)||62859 (68.8987%)
 
|-
 
|-
−
| grid||225470||225470||225208(99.8838%)||150619 (66.8022%)
+
| grid||225470||225470||225208 (99.8838%)||150619 (66.8022%)
 
|-
 
|-
−
| intact||111572||111008||110598(99.6307%)||97012(87.7159%)
+
| intact||111572||111008||110598 (99.6307%)||97012 (87.7159%)
 
|-
 
|-
−
| mint||104847||104847||103522(98.7363%)||73733(71.2245%)
+
| mint||104847||104847||103522 (98.7363%)||73733 (71.2245%)
 
|-
 
|-
−
| ophid||73257||73257||72907(99.5222%)||47318(64.9019%)
+
| ophid||73257||73257||72907 (99.5222%)||47318 (64.9019%)
 
|-
 
|-
−
| MPPI||1814||1814||1695(93.4399%)||827(48.7906%)
+
| MPPI||1814||1814||1695 (93.4399%)||827 (48.7906%)
 
|-
 
|-
−
| ALL||710608||610353||605164(99.1498%)||310665(51.3357%)
+
| ALL||710608||610353||605164 (99.1498%)||310665 (51.3357%)
 
|-
 
|-
 
|  
 
|  
 
|}
 
|}
  
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<!--
+
[[Category:iRefIndex]]
−
== Features of the ROG assignment score and their corresponding character representation ==
 
−
 
 
−
{| {{table}}
 
−
| align="center" style="background:#f0f0f0;"|'''Character'''
 
−
| align="center" style="background:#f0f0f0;"|'''Description of feature (when the value is 1)'''
 
−
| align="center" style="background:#f0f0f0;"|'''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.||12719(2.0243%)
 
−
|-
 
−
| E||The protein reference was a retired NCBI Identifier. NCBI\'s eUtils (E) were used to retrieve the current accession and/or sequence.||10909(1.7363%)
 
−
|-
 
−
| 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)||9150(1.4563%)
 
−
|-
 
−
| 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.||1882(0.2995%)
 
−
|-
 
−
| +||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).||9172(1.4598%)
 
−
|-
 
−
| 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.||14485(2.3054%)
 
−
|-
 
−
| 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.||22(0.0035%)
 
−
|-
 
−
| I||The protein reference used was an NCBI GenInfo Identifier (I).||13495(2.1479%)
 
−
|-
 
−
| 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.||20644(3.2857%)
 
−
|-
 
−
| 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||24056(3.8287%)
 
−
|-
 
−
| 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\'.||27(0.0043%)
 
−
|-
 
−
| P||The interaction record\'s primary (P) reference for the protein was used to make the assignment||584548(93.0362%)
 
−
|-
 
−
| S||One of the interaction record\'s secondary (S) references for the protein was used to make the assignment||43754(6.9638%)
 
−
|-
 
−
| 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(0.0056%)
 
−
|-
 
−
|
 
−
|}
 
−
 
 
−
 
 
−
 
 
−
 
 
−
== Number of protein references successfully assigned to ROG's and broken down by assignment score ==
 
−
 
 
−
{| {{table}}
 
−
| align="center" style="background:#f0f0f0;"|'''Binary_flag'''
 
−
| align="center" style="background:#f0f0f0;"|'''String_score'''
 
−
| align="center" style="background:#f0f0f0;"|'''Score_class'''
 
−
| align="center" style="background:#f0f0f0;"|'''Proteins'''
 
−
| align="center" style="background:#f0f0f0;"|'''Percentage'''
 
−
| align="center" style="background:#f0f0f0;"|'''BIND'''
 
−
| align="center" style="background:#f0f0f0;"|'''BioGrid'''
 
−
| align="center" style="background:#f0f0f0;"|'''DIP'''
 
−
| align="center" style="background:#f0f0f0;"|'''MINT'''
 
−
| align="center" style="background:#f0f0f0;"|'''HPRD'''
 
−
| align="center" style="background:#f0f0f0;"|'''OPHID'''
 
−
| align="center" style="background:#f0f0f0;"|'''MIIP'''
 
−
| align="center" style="background:#f0f0f0;"|'''MPACT'''
 
−
|-
 
−
| 010101000100000010||SLEN+||-1||1||0.0002%||0||1||0||0||0||0||0||0
 
−
|-
 
−
| 010100000000010001||PTEN||-1||18||0.0028%||0||0||0||0||0||0||18||0
 
−
|-
 
−
| 010000000010010001||PTMN||-1||2||0.0003%||0||0||0||0||0||0||2||0
 
−
|-
 
−
| 000001010100000010||SXL+||-1||1||0.0002%||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 100000000000000101||PUQ||-1||1||0.0002%||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 000000000010010010||STM||-1||3||0.0005%||0||3||0||0||0||0||0||0
 
−
|-
 
−
| 000000001100010101||PUTO+||-1||15||0.0024%||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 000000000000000001||P||1||523340||82.6130%||232755||7313||0||74939||0||126446||0||0
 
−
|-
 
−
| 000010000000000001||PI||1||19||0.0030%||0||2||0||0||0||0||0||0
 
−
|-
 
−
| 000010000001000010||SDI||1||1066||0.1683%||1044||22||0||0||0||0||0||0
 
−
|-
 
−
| 000010000001000001||PDI||1||40||0.0063%||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 000010000000000010||SI||1||11457||1.8086%||11287||170||0||0||0||0||0||0
 
−
|-
 
−
| 000000000010000010||SM||1||1190||0.1879%||0||1190||0||0||0||0||0||0
 
−
|-
 
−
| 000000000001000010||SD||1||6||0.0009%||0||6||0||0||0||0||0||0
 
−
|-
 
−
| 000000000000000010||S||1||8209||1.2958%||0||7754||0||236||0||0||0||0
 
−
|-
 
−
| 000000000001000001||PD||1||9244||1.4592%||8091||1134||0||19||0||0||0||0
 
−
|-
 
−
| 000000000010000001||PM||1||488||0.0770%||473||1||0||0||0||0||0||0
 
−
|-
 
−
| 000000000000000101||PU||2||19850||3.1335%||0||0||0||346||0||18835||0||0
 
−
|-
 
−
| 000000000000000110||SU||2||286||0.0451%||0||275||0||5||0||0||0||0
 
−
|-
 
−
| 000100000000000001||PE||2||246||0.0388%||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 000000001100000110||SUO+||2||1||0.0002%||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 000000001100000101||PUO+||2||6||0.0009%||0||0||0||1||0||0||0||0
 
−
|-
 
−
| 000100000000000010||SE||2||5434||0.8578%||5434||0||0||0||0||0||0||0
 
−
|-
 
−
| 000010000001010010||STDI||3||66||0.0104%||29||37||0||0||0||0||0||0
 
−
|-
 
−
| 000010000000010010||STI||3||834||0.1317%||826||8||0||0||0||0||0||0
 
−
|-
 
−
| 000010000001010001||PTDI||3||13||0.0021%||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 000000000001010001||PTD||3||1483||0.2341%||1483||0||0||0||0||0||0||0
 
−
|-
 
−
| 000000000000010010||ST||3||1383||0.2183%||0||1380||0||0||0||0||0||0
 
−
|-
 
−
| 000000000000010001||PT||3||19265||3.0411%||11825||0||0||1742||0||122||3072||0
 
−
|-
 
−
| 000000000010010001||PTM||3||199||0.0314%||132||0||0||0||0||0||67||0
 
−
|-
 
−
| 000100000000010010||STE||4||316||0.0499%||316||0||0||0||0||0||0||0
 
−
|-
 
−
| 000100000000010001||PTE||4||2||0.0003%||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 000001000100000101||PUL+||5||84||0.0133%||0||0||0||0||0||84||0||0
 
−
|-
 
−
| 000001000100010101||PUTL+||5||187||0.0295%||0||0||0||1||0||0||178||0
 
−
|-
 
−
| 000001000100000010||SL+||5||8843||1.3959%||0||8843||0||0||0||0||0||0
 
−
|-
 
−
| 100000000000000001||PQ||5||2||0.0003%||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 000001010100000101||PUXL+||5||34||0.0054%||0||0||0||5||0||19||0||0
 
−
|-
 
−
| 000000000000010101||PUT||5||180||0.0284%||0||0||0||6||0||5||142||0
 
−
|-
 
−
| 100000000000010001||PTQ||5||24||0.0038%||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 010100000000010010||STEN||6||22||0.0035%||22||0||0||0||0||0||0||0
 
−
|-
 
−
| 010100000000000010||SEN||6||4636||0.7318%||4635||0||0||1||0||0||0||0
 
−
|-
 
−
| 010100000000000001||PEN||6||234||0.0369%||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 010000000001000001||PDN||6||801||0.1264%||799||2||0||0||0||0||0||0
 
−
|-
 
−
| 010000000000000001||PN||6||8727||1.3776%||2322||0||0||2763||0||653||11||0
 
−
|-
 
−
| 010000000000010001||PTN||6||44||0.0069%||4||0||0||0||0||0||2||0
 
−
|-
 
−
|
 
−
|}
 
−
 
 
−
 
 
−
== Redundancy between pairs of interaction datasets processed in this study ==
 
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−
{| {{table}}
 
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| align="center" style="background:#f0f0f0;"|'''BIND'''
 
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| align="center" style="background:#f0f0f0;"|'''40766'''
 
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| align="center" style="background:#f0f0f0;"|''''''
 
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| align="center" style="background:#f0f0f0;"|''''''
 
−
| align="center" style="background:#f0f0f0;"|''''''
 
−
| align="center" style="background:#f0f0f0;"|''''''
 
−
| align="center" style="background:#f0f0f0;"|''''''
 
−
| align="center" style="background:#f0f0f0;"|''''''
 
−
| align="center" style="background:#f0f0f0;"|''''''
 
−
| align="center" style="background:#f0f0f0;"|''''''
 
−
|-
 
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| BIOGRID||14613||26945|| ||||||||||||
 
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|-
 
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| DIP||0||0||0|| ||||||||||
 
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|-
 
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| HPRD||0||0||0||0|| ||||||||
 
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|-
 
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| INTACT||18047||16580||0||0||39678|| ||||||
 
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|-
 
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| MINT||16465||15288||0||0||22659||28055|| ||||
 
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|-
 
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| MPACT||0||0||0||0||0||0||0|| ||
 
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|-
 
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| MPPI||647||181||0||0||548||539||0||857||
 
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|-
 
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| OPHID||3172||2732||0||0||5549||4796||0||404||9663
 
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|-
 
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| ||BIND||BIOGRID||DIP||HPRD||INTACT||MINT||MPACT||MPPI||OPHID
 
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|-
 
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| ||20177||0||2301||3476||8162||0||0||53||12338
 
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|-
 
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|
 
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|}
 
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foo-->
 

Latest revision as of 17:30, 4 March 2009

Assignment of protein interactors to ROG's

Source Intractors Assigned % Arbitrary New Unassigned Unique proteins
bind 285482 273695 95.87 0 7782 4005 40766
grid 28218 19295 68.38 8843 3 77 26945
intact 89190 85695 96.08 19 3250 226 39678
mint 80543 77294 95.97 6 2764 479 28055
MPPI 3628 3281 90.44 178 33 136 857
ophid 146423 145408 99.31 103 653 259 9663
All 633484 604668 95.45 9149 14485 5182 77745


Summary of mapping interaction records to RIG's.

Source Total records Protein-only interactors PPI Assigned to RIGID Unique RIGIDs
bind 193648 93957 91234 (97.1019%) 62859 (68.8987%)
grid 225470 225470 225208 (99.8838%) 150619 (66.8022%)
intact 111572 111008 110598 (99.6307%) 97012 (87.7159%)
mint 104847 104847 103522 (98.7363%) 73733 (71.2245%)
ophid 73257 73257 72907 (99.5222%) 47318 (64.9019%)
MPPI 1814 1814 1695 (93.4399%) 827 (48.7906%)
ALL 710608 610353 605164 (99.1498%) 310665 (51.3357%)
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