Difference between revisions of "Statistics iRefIndex 3.0"

From irefindex
(New page: == Interactions == {| | BIND||62831 |- | BIOGRID||20701 || 155527 |- | DIP||0 || 0 || 0 |- | HPRD||0 || 0 || 0 || 0 |- | INTACT||24372 || 25772 || 0 || 0 || 110545 |- | MINT||22...)
 
 
(12 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
== Interactions ==
+
== Summary ==
 +
 
 +
*Total distinct interactions : 358, 599
 +
*Total distinct proteins :  77,821
 +
 
 +
The present collection includes 105,342 distinct human interactions and complexes involving 20,289 distinct human proteins.
 +
 
 +
== Interactions (Corresponds to Table 6 in PMID 18823568)==
  
 
{|
 
{|
Line 6: Line 13:
 
| BIOGRID||20701  || 155527
 
| BIOGRID||20701  || 155527
 
|-
 
|-
−
| DIP||0 || 0 || 0
+
| DIP||25938 || 29041 || 55126
 
|-
 
|-
−
| HPRD||0 || 0 || 0 || 0
+
| HPRD||2882 || 1903 || 753 || 37956
 
|-
 
|-
−
| INTACT||24372 || 25772 || 0 || 0 || 110545
+
| INTACT||24375 || 25775 || 24853 || 8021 || 110545
 
|-
 
|-
−
| MINT||22406 || 32690 || 0 || 0 || 42208  || 73729
+
| MINT||22409 || 32693 || 30271 || 6927 || 42208  || 73729
 
|-
 
|-
−
| MPACT||0 || 0 || 0 || 0  || 0 || 0 || 0
+
| MPACT||6904 || 8427 || 6777 || 0  || 6079 || 6458 || 13320
 
|-
 
|-
−
| MPPI||385  || 26  || 0 || 0 || 88  || 106  || 0  || 825
+
| MPPI||385  || 26  || 31 || 305 || 88  || 106  || 0  || 825
 
|-
 
|-
−
| OPHID||2201  || 1309  || 0 || 0 || 7177  || 7141  || 0  || 183  || 47303
+
| OPHID||2201  || 1309  || 809 || 17895 || 7177  || 7141  || 0  || 183  || 47303
 
|-
 
|-
−
| CORUM||0 || 0 || 0 || 0 || 0 || 0 || 0  || 0 || 0 || 0
+
| CORUM||112 || 19 || 22 || 386 || 120 || 65 || 0  || 9 || 158 || 1917
 
|-
 
|-
 
| ||BIND||BIOGRID||DIP||HPRD||INTACT||MINT||MPACT||MPPI||OPHID||CORUM
 
| ||BIND||BIOGRID||DIP||HPRD||INTACT||MINT||MPACT||MPPI||OPHID||CORUM
 
|-
 
|-
−
| ||(30966)||(112572)||(0)||(0)||(57940)||(16196)||(0)||(298)||(35791)||(0)
+
| ||(25768)||(103361)||(12549)||(15276)||(56308)||(15199)||(1136)||(227)||(26529)||(1409)
 
|}
 
|}
  
Line 34: Line 41:
 
| BIOGRID||14397  || 27164
 
| BIOGRID||14397  || 27164
 
|-
 
|-
−
| DIP||0 || 0 || 0
+
| DIP||15136 || 12915 || 19263
 
|-
 
|-
−
| HPRD||0 || 0 || 0 || 0
+
| HPRD||3281 || 2419 || 1026 || 9539
 
|-
 
|-
−
| INTACT||18077 || 16676 || 0 || 0 || 41370
+
| INTACT||18079 || 16677 || 15356 || 5749 || 41370
 
|-
 
|-
−
| MINT||16294 || 14898 || 0 || 0 || 22877  || 28043
+
| MINT||16296 || 14899 || 14788 || 4695 || 22877  || 28043
 
|-
 
|-
−
| MPACT||0 || 0 || 0 || 0  || 0 || 0 || 0
+
| MPACT||4638 || 4494 || 4630 || 0  || 4857 || 4728 || 4972
 
|-
 
|-
−
| MPPI||669  || 209  || 0 || 0 || 575  || 551  || 0  || 858
+
| MPPI||669  || 209  || 252 || 430 || 575  || 551  || 0  || 858
 
|-
 
|-
−
| OPHID||3210  || 2261  || 0 || 0 || 5720  || 4807  || 0 || 422  || 9631
+
| OPHID||3210  || 2261  || 1027 || 7339 || 5720  || 4807  || 1 || 422  || 9631
 
|-
 
|-
−
| CORUM||0 || 0 || 0 || 0 || 0 || 0 || 0  || 0 || 0 || 0
+
| CORUM||1536 || 736 || 528 || 1843 || 2289 || 1750 || 0  || 321 || 1849 || 3579
 
|-
 
|-
 
| ||BIND||BIOGRID||DIP||HPRD||INTACT||MINT||MPACT||MPPI||OPHID||CORUM
 
| ||BIND||BIOGRID||DIP||HPRD||INTACT||MINT||MPACT||MPPI||OPHID||CORUM
 
|-
 
|-
−
| ||(20125)||(8457)||(0)||(0)||(13240)||(3410)||(0)||(43)||(2301)||(0)
+
| ||(18505)||(8050)||(1498)||(1078)||(12260)||(3191)||(17)||(38)||(1293)||(626)
 
|}
 
|}
  
−
== Summary of mapping interaction records to RIGs (Table 5) ==
+
== Summary of mapping interaction records to RIGs (Corresponds to Table 5 in PMID 18823568) ==
  
 
{|
 
{|
Line 63: Line 70:
 
|-
 
|-
 
| grid||229399||229399||229101(99.8701%)||155527(67.8858%)
 
| grid||229399||229399||229101(99.8701%)||155527(67.8858%)
 +
|-
 +
| dip||56638||56638||55275(97.5935%)||55126(99.7304%)
 
|-
 
|-
 
| intact||127880||127179||126757(99.6682%)||110545(87.2102%)
 
| intact||127880||127179||126757(99.6682%)||110545(87.2102%)
 
|-
 
|-
 
| mint||104847||104847||103520(98.7343%)||73729(71.2220%)
 
| mint||104847||104847||103520(98.7343%)||73729(71.2220%)
 +
|-
 +
| HPRD||38037||38037||38026(99.9711%)||37956(99.8159%)
 
|-
 
|-
 
| ophid||73257||73257||72907(99.5222%)||47303(64.8813%)
 
| ophid||73257||73257||72907(99.5222%)||47303(64.8813%)
 +
|-
 +
| MPACT||16503||16503||16285(98.6790%)||13320(81.7931%)
 
|-
 
|-
 
| MPPI||1814||1814||1685(92.8886%)||825(48.9614%)
 
| MPPI||1814||1814||1685(92.8886%)||825(48.9614%)
 
|-
 
|-
−
| ALL||730845||630453||625149(99.1587%)||450760(72.1044%)
+
| CORUM||2104||2104||2102(99.9049%)||1917(91.1989%)
 +
|-
 +
| ALL||844127||743735||736837(99.0725%)|| 358599(48.6673%)
 
|}
 
|}
 +
*The value of total unique interactions was edited on 08June 2009. Please note that the sum of the "Unique RIGIDs" column is different from the figure given as the ALL.
  
−
== Assignment of protein interactors to ROGs (Table 3) ==
+
== Assignment of protein interactors to ROGs (Corresponds to Table 3 in PMID 18823568) ==
  
 
{|
 
{|
Line 81: Line 97:
 
|-
 
|-
 
| bind||285482||273644||95.8533||0||7742||4096||40738
 
| bind||285482||273644||95.8533||0||7742||4096||40738
 +
|-
 +
| CORUM||10316||10314||99.9806||0||0||2||3579
 +
|-
 +
| dip||19935||17773||89.1548||1198||393||571||19263
 
|-
 
|-
 
| grid||28943||18921||65.3733||9923||5||94||27164
 
| grid||28943||18921||65.3733||9923||5||94||27164
 +
|-
 +
| HPRD||9565||9494||99.2577||50||16||5||9539
 
|-
 
|-
 
| intact||97256||93646||96.2881||17||3367||226||41370
 
| intact||97256||93646||96.2881||17||3367||226||41370
 
|-
 
|-
 
| mint||80543||77276||95.9438||6||2780||481||28043
 
| mint||80543||77276||95.9438||6||2780||481||28043
 +
|-
 +
| MPACT||40349||40112||99.4126||0||0||237||4972
 
|-
 
|-
 
| MPPI||3628||3456||95.2591||0||27||145||858
 
| MPPI||3628||3456||95.2591||0||27||145||858
Line 92: Line 116:
 
| ophid||146423||145362||99.2754||103||699||259||9631
 
| ophid||146423||145362||99.2754||103||699||259||9631
 
|-
 
|-
−
| All||642275||612305||95.3338||10049||14620||5301||79389
+
| All||722440||689998||95.5094||11297||15029||6116||82657
 
|}
 
|}
  
−
== ROG summary ==
+
== ROG summary (Corresponds to Table 4 in PMID 18823568)==
  
 
{|
 
{|
 
| align="center" style="background:#f0f0f0;"|'''Decimal_score'''||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'''
 
| align="center" style="background:#f0f0f0;"|'''Decimal_score'''||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'''
 
|-
 
|-
−
| 778||000000001100001010||SVO+||-1||1||0.0002%||0||0||0||0||0||0||0||0
+
| 1||000000000000000001||P||1||564539||78.1434%||232690||7275||0||74838||0||125715||3023||30666
 
|-
 
|-
−
| 5386||000001010100001010||SVXL+||-1||1||0.0002%||0||0||0||0||0||0||0||0
+
| 130||000000000010000010||SM||1||546||0.0756%||0||546||0||0||0||0||0||0
 
|-
 
|-
−
| 196625||110000000000010001||PTNQ||-1||1||0.0002%||0||0||0||0||0||0||0||0
+
| 66||000000000001000010||SD||1||3||0.0004%||0||2||1||0||0||0||0||0
 
|-
 
|-
−
| 130||000000000010000010||SM||1||546||0.0850%||0||546||0||0||0||0||0||0
+
| 65||000000000001000001||PD||1||9522||1.3180%||8086||1417||0||19||0||0||0||0
 
|-
 
|-
−
| 129||000000000010000001||PM||1||522||0.0813%||473||1||0||0||0||0||32||0
+
| 42||000000000000101010||SVG||1||147||0.0203%||0||0||0||0||147||0||0||0
 
|-
 
|-
−
| 8193||000010000000000001||PI||1||58||0.0090%||0||2||0||0||0||0||0||0
+
| 8193||000010000000000001||PI||1||58||0.0080%||0||2||0||0||0||0||0||0
 
|-
 
|-
−
| 66||000000000001000010||SD||1||2||0.0003%||0||2||0||0||0||0||0||0
+
| 810||000000001100101010||SVGO+||1||58||0.0080%||0||0||0||0||58||0||0||0
 
|-
 
|-
−
| 65||000000000001000001||PD||1||9522||1.4825%||8086||1417||0||19||0||0||0||0
+
| 129||000000000010000001||PM||1||522||0.0723%||473||1||0||0||0||0||32||0
 
|-
 
|-
−
| 8194||000010000000000010||SI||1||12395||1.9299%||12336||59||0||0||0||0||0||0
+
| 8194||000010000000000010||SI||1||12395||1.7157%||12336||59||0||0||0||0||0||0
 
|-
 
|-
−
| 1||000000000000000001||P||1||533873||83.1222%||232690||7275||0||74838||0||125715||3023||0
+
| 10||000000000000001010||SV||1||90||0.0125%||0||0||83||0||0||0||0||0
 
|-
 
|-
−
| 10||000000000000001010||SV||1||7||0.0011%||0||0||0||0||0||0||0||0
+
| 2||000000000000000010||S||1||34020||4.7090%||0||7523||16598||242||2510||0||0||6927
 
|-
 
|-
−
| 2||000000000000000010||S||1||7985||1.2432%||0||7523||0||242||0||0||0||0
+
| 554||000000001000101010||SVGO||1||615||0.0851%||0||0||0||0||615||0||0||0
 
|-
 
|-
−
| 774||000000001100000110||SUO+||2||1||0.0002%||0||0||0||0||0||0||0||0
+
| 778||000000001100001010||SVO+||2||1||0.0001%||0||0||0||0||0||0||0||0
 
|-
 
|-
−
| 773||000000001100000101||PUO+||2||7||0.0011%||0||0||0||1||0||0||0||0
+
| 16385||000100000000000001||PE||2||211||0.0292%||0||0||0||0||0||0||0||0
 
|-
 
|-
−
| 5||000000000000000101||PU||2||20497||3.1913%||0||0||0||426||0||19520||320||0
+
| 16386||000100000000000010||SE||2||5402||0.7477%||5402||0||0||0||0||0||0||0
 
|-
 
|-
−
| 6||000000000000000110||SU||2||572||0.0891%||0||559||0||5||0||0||0||0
+
| 774||000000001100000110||SUO+||2||1||0.0001%||0||0||0||0||0||0||0||0
 
|-
 
|-
−
| 16386||000100000000000010||SE||2||5402||0.8411%||5402||0||0||0||0||0||0||0
+
| 773||000000001100000101||PUO+||2||7||0.0010%||0||0||0||1||0||0||0||0
 
|-
 
|-
−
| 16385||000100000000000001||PE||2||211||0.0329%||0||0||0||0||0||0||0||0
+
| 5||000000000000000101||PU||2||23016||3.1859%||0||0||0||426||0||19520||320||2519
 
|-
 
|-
−
| 8210||000010000000010010||STI||3||903||0.1406%||855||48||0||0||0||0||0||0
+
| 6||000000000000000110||SU||2||657||0.0909%||0||559||79||5||6||0||0||0
 
|-
 
|-
−
| 8209||000010000000010001||PTI||3||13||0.0020%||0||0||0||0||0||0||0||0
+
| 146||000000000010010010||STM||3||1||0.0001%||0||1||0||0||0||0||0||0
 
|-
 
|-
−
| 17||000000000000010001||PT||3||16259||2.5315%||11871||0||0||1739||0||122||46||0
+
| 8210||000010000000010010||STI||3||903||0.1250%||855||48||0||0||0||0||0||0
 
|-
 
|-
−
| 146||000000000010010010||STM||3||1||0.0002%||0||1||0||0||0||0||0||0
+
| 8209||000010000000010001||PTI||3||13||0.0018%||0||0||0||0||0||0||0||0
 
|-
 
|-
−
| 18||000000000000010010||ST||3||1490||0.2320%||0||1487||0||0||0||0||0||0
+
| 17||000000000000010001||PT||3||26549||3.6749%||11871||0||0||1739||0||122||46||0
 
|-
 
|-
−
| 145||000000000010010001||PTM||3||168||0.0262%||132||0||0||0||0||0||35||0
+
| 18||000000000000010010||ST||3||8645||1.1966%||0||1487||1009||0||6146||0||0||0
 
|-
 
|-
−
| 81||000000000001010001||PTD||3||1484||0.2311%||1484||0||0||0||0||0||0||0
+
| 26||000000000000011010||SVT||3||1||0.0001%||0||0||0||0||0||0||0||0
 
|-
 
|-
−
| 26||000000000000011010||SVT||3||1||0.0002%||0||0||0||0||0||0||0||0
+
| 81||000000000001010001||PTD||3||1484||0.2054%||1484||0||0||0||0||0||0||0
 
|-
 
|-
−
| 789||000000001100010101||PUTO+||4||14||0.0022%||0||0||0||0||0||0||0||0
+
| 145||000000000010010001||PTM||3||168||0.0233%||132||0||0||0||0||0||35||0
 
|-
 
|-
−
| 16402||000100000000010010||STE||4||315||0.0490%||315||0||0||0||0||0||0||0
+
| 22||000000000000010110||SUT||4||15||0.0021%||0||1||3||0||11||0||0||0
 
|-
 
|-
−
| 16401||000100000000010001||PTE||4||3||0.0005%||0||0||0||0||0||0||0||0
+
| 16401||000100000000010001||PTE||4||3||0.0004%||0||0||0||0||0||0||0||0
 
|-
 
|-
−
| 22||000000000000010110||SUT||4||1||0.0002%||0||1||0||0||0||0||0||0
+
| 16402||000100000000010010||STE||4||315||0.0436%||315||0||0||0||0||0||0||0
 
|-
 
|-
−
| 4482||000001000110000010||SML+||5||394||0.0613%||0||394||0||0||0||0||0||0
+
| 790||000000001100010110||SUTO+||4||1||0.0001%||0||0||0||0||1||0||0||0
 +
|-
 +
| 789||000000001100010101||PUTO+||4||14||0.0019%||0||0||0||0||0||0||0||0
 
|-
 
|-
 
| 131073||100000000000000001||PQ||5||2||0.0003%||0||0||0||0||0||0||0||0
 
| 131073||100000000000000001||PQ||5||2||0.0003%||0||0||0||0||0||0||0||0
 
|-
 
|-
−
| 131077||100000000000000101||PUQ||5||1||0.0002%||0||0||0||0||0||0||0||0
+
| 21||000000000000010101||PUT||5||35||0.0048%||0||0||0||6||0||5||0||0
 +
|-
 +
| 12546||000011000100000010||SLI+||5||6562||0.9083%||0||6562||0||0||0||0||0||0
 +
|-
 +
| 131077||100000000000000101||PUQ||5||1||0.0001%||0||0||0||0||0||0||0||0
 +
|-
 +
| 131089||100000000000010001||PTQ||5||38||0.0053%||0||0||0||0||0||0||0||0
 +
|-
 +
| 4373||000001000100010101||PUTL+||5||9||0.0012%||0||0||0||1||0||0||0||0
 +
|-
 +
| 4362||000001000100001010||SVL+||5||36||0.0050%||0||0||36||0||0||0||0||0
 +
|-
 +
| 4357||000001000100000101||PUL+||5||84||0.0116%||0||0||0||0||0||84||0||0
 +
|-
 +
| 4354||000001000100000010||SL+||5||4077||0.5643%||0||2967||1110||0||0||0||0||0
 +
|-
 +
| 4374||000001000100010110||SUTL+||5||52||0.0072%||0||0||52||0||0||0||0||0
 
|-
 
|-
−
| 131089||100000000000010001||PTQ||5||38||0.0059%||0||0||0||0||0||0||0||0
+
| 4394||000001000100101010||SVGL+||5||47||0.0065%||0||0||0||0||47||0||0||0
 
|-
 
|-
−
| 4357||000001000100000101||PUL+||5||84||0.0131%||0||0||0||0||0||84||0||0
+
| 4482||000001000110000010||SML+||5||394||0.0545%||0||394||0||0||0||0||0||0
 
|-
 
|-
−
| 4373||000001000100010101||PUTL+||5||9||0.0014%||0||0||0||1||0||0||0||0
+
| 5381||000001010100000101||PUXL+||5||32||0.0044%||0||0||0||5||0||19||0||0
 
|-
 
|-
−
| 5381||000001010100000101||PUXL+||5||32||0.0050%||0||0||0||5||0||19||0||0
+
| 5382||000001010100000110||SUXL+||5||3||0.0004%||0||0||0||0||3||0||0||0
 
|-
 
|-
−
| 21||000000000000010101||PUT||5||11||0.0017%||0||0||0||6||0||5||0||0
+
| 5386||000001010100001010||SVXL+||5||1||0.0001%||0||0||0||0||0||0||0||0
 
|-
 
|-
−
| 12546||000011000100000010||SLI+||5||6562||1.0217%||0||6562||0||0||0||0||0||0
+
| 86274||010101000100000010||SLEN+||6||3||0.0004%||0||2||1||0||0||0||0||0
 
|-
 
|-
−
| 4354||000001000100000010||SL+||5||2967||0.4620%||0||2967||0||0||0||0||0||0
+
| 82034||010100000001110010||STGDEN||6||2||0.0003%||0||0||0||0||2||0||0||0
 
|-
 
|-
−
| 86274||010101000100000010||SLEN+||6||2||0.0003%||0||2||0||0||0||0||0||0
+
| 81938||010100000000010010||STEN||6||24||0.0033%||24||0||0||0||0||0||0||0
 
|-
 
|-
−
| 81938||010100000000010010||STEN||6||24||0.0037%||24||0||0||0||0||0||0||0
+
| 81937||010100000000010001||PTEN||6||5||0.0007%||3||0||0||0||0||0||2||0
 
|-
 
|-
−
| 81922||010100000000000010||SEN||6||5374||0.8367%||5371||3||0||0||0||0||0||0
+
| 81922||010100000000000010||SEN||6||5708||0.7901%||5371||3||334||0||0||0||0||0
 
|-
 
|-
−
| 81921||010100000000000001||PEN||6||2746||0.4275%||2343||0||0||53||0||98||25||0
+
| 81921||010100000000000001||PEN||6||2755||0.3813%||2343||0||0||59||0||98||25||0
 
|-
 
|-
−
| 65601||010000000001000001||PDN||6||1||0.0002%||1||0||0||0||0||0||0||0
+
| 65601||010000000001000001||PDN||6||1||0.0001%||1||0||0||0||0||0||0||0
 
|-
 
|-
−
| 65553||010000000000010001||PTN||6||10||0.0016%||0||0||0||0||0||0||0||0
+
| 65553||010000000000010001||PTN||6||10||0.0014%||0||0||0||0||0||0||0||0
 
|-
 
|-
−
| 65537||010000000000000001||PN||6||6457||1.0053%||0||0||0||2727||0||601||0||0
+
| 65537||010000000000000001||PN||6||6520||0.9025%||0||0||58||2721||14||601||0||0
 
|-
 
|-
−
| 81937||010100000000010001||PTEN||6||5||0.0008%||3||0||0||0||0||0||2||0
+
| 196625||110000000000010001||PTNQ||6||1||0.0001%||0||0||0||0||0||0||0||0
 
|}
 
|}
  
−
== Scores (Table 2) ==
+
== Scores (Corresponds to Table 2 in PMID 18823568) ==
  
 
{|
 
{|
 
| 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'''
 
| 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.||11009(1.7283%)
+
| 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.||11012(1.5373%)
 
|-
 
|-
−
| E||The protein reference was a retired NCBI Identifier. NCBI's eUtils (E) were used to retrieve the current accession and/or sequence.||14082(2.2108%)
+
| E||The protein reference was a retired NCBI Identifier. NCBI's eUtils (E) were used to retrieve the current accession and/or sequence.||14428(2.0142%)
 
|-
 
|-
−
| 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%)
+
| 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.||869(0.1213%)
 
|-
 
|-
−
| L||More than one possible assignment is possible (see + above). The assignment with the largest (L) SEGUID is arbitrarily chosen (see Methods)||10051(1.5779%)
+
| L||More than one possible assignment is possible (see + above). The assignment with the largest (L) SEGUID is arbitrarily chosen (see Methods)||11300(1.5775%)
 
|-
 
|-
−
| M||The protein reference listed by the interaction record was a typographical modification (M) of a known accession. In specific cases, this variation istolerated and the assignment is made.||1631(0.2561%)
+
| 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.||1631(0.2277%)
 
|-
 
|-
−
| +||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).||10074(1.5815%)
+
| +||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).||11382(1.5889%)
 
|-
 
|-
−
| 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.||14620(2.2952%)
+
| 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.||15029(2.0981%)
 
|-
 
|-
−
| 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.||23(0.0036%)
+
| 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.||697(0.0973%)
 
|-
 
|-
−
| I||The protein reference used was an NCBI GenInfo Identifier (I).||19931(3.129%)
+
| I||The protein reference used was an NCBI GenInfo Identifier (I).||19931(2.7824%)
 
|-
 
|-
−
| 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.||21229(3.3328%)
+
| 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.||23927(3.3402%)
 
|-
 
|-
−
| 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||20750(3.2576%)
+
| 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||38288(5.3451%)
 
|-
 
|-
−
| 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.||10(0.0016%)
+
| 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.||996(0.139%)
 
|-
 
|-
−
| 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%)
+
| 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(0.0059%)
 
|-
 
|-
−
| P||The interaction record's primary (P) reference for the protein was used to make the assignment||592028(92.9438%)
+
| P||The interaction record's primary (P) reference for the protein was used to make the assignment||635599(88.7307%)
 
|-
 
|-
−
| S||One of the interaction record's secondary (S) references for the protein was used to make the assignment||44946(7.0562%)
+
| S||One of the interaction record's secondary (S) references for the protein was used to make the assignment||80725(11.2693%)
 
|-
 
|-
−
| 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||33(0.0052%)
+
| 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||36(0.0050%)
 
|}
 
|}
  
 
[[Category:iRefIndex]]
 
[[Category:iRefIndex]]

Latest revision as of 14:39, 8 June 2009

Summary

  • Total distinct interactions : 358, 599
  • Total distinct proteins : 77,821

The present collection includes 105,342 distinct human interactions and complexes involving 20,289 distinct human proteins.

Interactions (Corresponds to Table 6 in PMID 18823568)

BIND 62831
BIOGRID 20701 155527
DIP 25938 29041 55126
HPRD 2882 1903 753 37956
INTACT 24375 25775 24853 8021 110545
MINT 22409 32693 30271 6927 42208 73729
MPACT 6904 8427 6777 0 6079 6458 13320
MPPI 385 26 31 305 88 106 0 825
OPHID 2201 1309 809 17895 7177 7141 0 183 47303
CORUM 112 19 22 386 120 65 0 9 158 1917
BIND BIOGRID DIP HPRD INTACT MINT MPACT MPPI OPHID CORUM
(25768) (103361) (12549) (15276) (56308) (15199) (1136) (227) (26529) (1409)

Interactors

BIND 40738
BIOGRID 14397 27164
DIP 15136 12915 19263
HPRD 3281 2419 1026 9539
INTACT 18079 16677 15356 5749 41370
MINT 16296 14899 14788 4695 22877 28043
MPACT 4638 4494 4630 0 4857 4728 4972
MPPI 669 209 252 430 575 551 0 858
OPHID 3210 2261 1027 7339 5720 4807 1 422 9631
CORUM 1536 736 528 1843 2289 1750 0 321 1849 3579
BIND BIOGRID DIP HPRD INTACT MINT MPACT MPPI OPHID CORUM
(18505) (8050) (1498) (1078) (12260) (3191) (17) (38) (1293) (626)

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 91179(97.0433%) 62831(68.9095%)
grid 229399 229399 229101(99.8701%) 155527(67.8858%)
dip 56638 56638 55275(97.5935%) 55126(99.7304%)
intact 127880 127179 126757(99.6682%) 110545(87.2102%)
mint 104847 104847 103520(98.7343%) 73729(71.2220%)
HPRD 38037 38037 38026(99.9711%) 37956(99.8159%)
ophid 73257 73257 72907(99.5222%) 47303(64.8813%)
MPACT 16503 16503 16285(98.6790%) 13320(81.7931%)
MPPI 1814 1814 1685(92.8886%) 825(48.9614%)
CORUM 2104 2104 2102(99.9049%) 1917(91.1989%)
ALL 844127 743735 736837(99.0725%) 358599(48.6673%)
  • The value of total unique interactions was edited on 08June 2009. Please note that the sum of the "Unique RIGIDs" column is different from the figure given as the ALL.

Assignment of protein interactors to ROGs (Corresponds to Table 3 in PMID 18823568)

Source Protein_Intractors Assigned % Arbitrary New Unassigned Unique proteins
bind 285482 273644 95.8533 0 7742 4096 40738
CORUM 10316 10314 99.9806 0 0 2 3579
dip 19935 17773 89.1548 1198 393 571 19263
grid 28943 18921 65.3733 9923 5 94 27164
HPRD 9565 9494 99.2577 50 16 5 9539
intact 97256 93646 96.2881 17 3367 226 41370
mint 80543 77276 95.9438 6 2780 481 28043
MPACT 40349 40112 99.4126 0 0 237 4972
MPPI 3628 3456 95.2591 0 27 145 858
ophid 146423 145362 99.2754 103 699 259 9631
All 722440 689998 95.5094 11297 15029 6116 82657

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 MIIP MPACT
1 000000000000000001 P 1 564539 78.1434% 232690 7275 0 74838 0 125715 3023 30666
130 000000000010000010 SM 1 546 0.0756% 0 546 0 0 0 0 0 0
66 000000000001000010 SD 1 3 0.0004% 0 2 1 0 0 0 0 0
65 000000000001000001 PD 1 9522 1.3180% 8086 1417 0 19 0 0 0 0
42 000000000000101010 SVG 1 147 0.0203% 0 0 0 0 147 0 0 0
8193 000010000000000001 PI 1 58 0.0080% 0 2 0 0 0 0 0 0
810 000000001100101010 SVGO+ 1 58 0.0080% 0 0 0 0 58 0 0 0
129 000000000010000001 PM 1 522 0.0723% 473 1 0 0 0 0 32 0
8194 000010000000000010 SI 1 12395 1.7157% 12336 59 0 0 0 0 0 0
10 000000000000001010 SV 1 90 0.0125% 0 0 83 0 0 0 0 0
2 000000000000000010 S 1 34020 4.7090% 0 7523 16598 242 2510 0 0 6927
554 000000001000101010 SVGO 1 615 0.0851% 0 0 0 0 615 0 0 0
778 000000001100001010 SVO+ 2 1 0.0001% 0 0 0 0 0 0 0 0
16385 000100000000000001 PE 2 211 0.0292% 0 0 0 0 0 0 0 0
16386 000100000000000010 SE 2 5402 0.7477% 5402 0 0 0 0 0 0 0
774 000000001100000110 SUO+ 2 1 0.0001% 0 0 0 0 0 0 0 0
773 000000001100000101 PUO+ 2 7 0.0010% 0 0 0 1 0 0 0 0
5 000000000000000101 PU 2 23016 3.1859% 0 0 0 426 0 19520 320 2519
6 000000000000000110 SU 2 657 0.0909% 0 559 79 5 6 0 0 0
146 000000000010010010 STM 3 1 0.0001% 0 1 0 0 0 0 0 0
8210 000010000000010010 STI 3 903 0.1250% 855 48 0 0 0 0 0 0
8209 000010000000010001 PTI 3 13 0.0018% 0 0 0 0 0 0 0 0
17 000000000000010001 PT 3 26549 3.6749% 11871 0 0 1739 0 122 46 0
18 000000000000010010 ST 3 8645 1.1966% 0 1487 1009 0 6146 0 0 0
26 000000000000011010 SVT 3 1 0.0001% 0 0 0 0 0 0 0 0
81 000000000001010001 PTD 3 1484 0.2054% 1484 0 0 0 0 0 0 0
145 000000000010010001 PTM 3 168 0.0233% 132 0 0 0 0 0 35 0
22 000000000000010110 SUT 4 15 0.0021% 0 1 3 0 11 0 0 0
16401 000100000000010001 PTE 4 3 0.0004% 0 0 0 0 0 0 0 0
16402 000100000000010010 STE 4 315 0.0436% 315 0 0 0 0 0 0 0
790 000000001100010110 SUTO+ 4 1 0.0001% 0 0 0 0 1 0 0 0
789 000000001100010101 PUTO+ 4 14 0.0019% 0 0 0 0 0 0 0 0
131073 100000000000000001 PQ 5 2 0.0003% 0 0 0 0 0 0 0 0
21 000000000000010101 PUT 5 35 0.0048% 0 0 0 6 0 5 0 0
12546 000011000100000010 SLI+ 5 6562 0.9083% 0 6562 0 0 0 0 0 0
131077 100000000000000101 PUQ 5 1 0.0001% 0 0 0 0 0 0 0 0
131089 100000000000010001 PTQ 5 38 0.0053% 0 0 0 0 0 0 0 0
4373 000001000100010101 PUTL+ 5 9 0.0012% 0 0 0 1 0 0 0 0
4362 000001000100001010 SVL+ 5 36 0.0050% 0 0 36 0 0 0 0 0
4357 000001000100000101 PUL+ 5 84 0.0116% 0 0 0 0 0 84 0 0
4354 000001000100000010 SL+ 5 4077 0.5643% 0 2967 1110 0 0 0 0 0
4374 000001000100010110 SUTL+ 5 52 0.0072% 0 0 52 0 0 0 0 0
4394 000001000100101010 SVGL+ 5 47 0.0065% 0 0 0 0 47 0 0 0
4482 000001000110000010 SML+ 5 394 0.0545% 0 394 0 0 0 0 0 0
5381 000001010100000101 PUXL+ 5 32 0.0044% 0 0 0 5 0 19 0 0
5382 000001010100000110 SUXL+ 5 3 0.0004% 0 0 0 0 3 0 0 0
5386 000001010100001010 SVXL+ 5 1 0.0001% 0 0 0 0 0 0 0 0
86274 010101000100000010 SLEN+ 6 3 0.0004% 0 2 1 0 0 0 0 0
82034 010100000001110010 STGDEN 6 2 0.0003% 0 0 0 0 2 0 0 0
81938 010100000000010010 STEN 6 24 0.0033% 24 0 0 0 0 0 0 0
81937 010100000000010001 PTEN 6 5 0.0007% 3 0 0 0 0 0 2 0
81922 010100000000000010 SEN 6 5708 0.7901% 5371 3 334 0 0 0 0 0
81921 010100000000000001 PEN 6 2755 0.3813% 2343 0 0 59 0 98 25 0
65601 010000000001000001 PDN 6 1 0.0001% 1 0 0 0 0 0 0 0
65553 010000000000010001 PTN 6 10 0.0014% 0 0 0 0 0 0 0 0
65537 010000000000000001 PN 6 6520 0.9025% 0 0 58 2721 14 601 0 0
196625 110000000000010001 PTNQ 6 1 0.0001% 0 0 0 0 0 0 0 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. 11012(1.5373%)
E The protein reference was a retired NCBI Identifier. NCBI's eUtils (E) were used to retrieve the current accession and/or sequence. 14428(2.0142%)
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. 869(0.1213%)
L More than one possible assignment is possible (see + above). The assignment with the largest (L) SEGUID is arbitrarily chosen (see Methods) 11300(1.5775%)
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. 1631(0.2277%)
+ 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). 11382(1.5889%)
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. 15029(2.0981%)
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. 697(0.0973%)
I The protein reference used was an NCBI GenInfo Identifier (I). 19931(2.7824%)
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. 23927(3.3402%)
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 38288(5.3451%)
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. 996(0.139%)
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(0.0059%)
P The interaction record's primary (P) reference for the protein was used to make the assignment 635599(88.7307%)
S One of the interaction record's secondary (S) references for the protein was used to make the assignment 80725(11.2693%)
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 36(0.0050%)
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