Difference between revisions of "Statistics iRefIndex 5.0"

From irefindex
(New page: == Summary == *Total distinct interactions : 369,457 *Total distinct proteins : 83,388 This page lists statistics for our internal version of iRefIndex that includes all of the data fro...)
 
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== Summary ==
 
== Summary ==
  
−
*Total distinct interactions : 369,457
+
*Total interactions : 871,172
−
*Total distinct proteins :  83,388
+
*Total distinct interactions (based on RIGID): 357,156
 +
*Total distinct proteins (based on ROGID)    :  83,938
  
 
This page lists statistics for our internal version of iRefIndex that includes all of the data from sources used for the current build [[Sources_iRefIndex_4.0]].  This full build of the iRefIndex contains data that cannot be redistributed according to usage policies of the source databases (namely, from DIP, HPRD and MPact databases).  Please contact  ian.donaldson at biotek.uio.no if you would like to obtain a copy of the full iRefIndex build under an academic, collaborative agreement.
 
This page lists statistics for our internal version of iRefIndex that includes all of the data from sources used for the current build [[Sources_iRefIndex_4.0]].  This full build of the iRefIndex contains data that cannot be redistributed according to usage policies of the source databases (namely, from DIP, HPRD and MPact databases).  Please contact  ian.donaldson at biotek.uio.no if you would like to obtain a copy of the full iRefIndex build under an academic, collaborative agreement.
Line 9: Line 10:
  
 
== Interactions available from major taxonomies ==
 
== Interactions available from major taxonomies ==
−
{| {{table}}
+
 
−
| align="center" style="background:#f0f0f0;"|'''Taxonomy'''
+
 
−
| align="center" style="background:#f0f0f0;"|'''Number of interactions'''
 
−
|-
 
−
| 562 (''Escherichia coli'' )||1243||
 
−
|-
 
−
| 4932 (''Saccharomyces cerevisiae'' )||116321||
 
−
|-
 
−
| 6239 (''Caenorhabditis elegans'')||11912||
 
−
|-
 
−
| 7227 (''Drosophila melanogaster'')||46794||
 
−
|-
 
−
| 9606 (''Homo sapiens'')||117535||
 
−
|-
 
−
| 10090 (''Mus musculus)''||10098||
 
−
|-
 
−
| 10116 (''Rattus norvegicus'')||3372||
 
−
|-
 
−
|
 
−
|}
 
 
* for the full list :http://irefindex.uio.no/wikifiles//images/2/20/Interactions_by_taxonomy_beta4_full.pdf
 
* for the full list :http://irefindex.uio.no/wikifiles//images/2/20/Interactions_by_taxonomy_beta4_full.pdf
  
 
== Interactions  (Corresponds to Table 6 in PMID 18823568)==
 
== Interactions  (Corresponds to Table 6 in PMID 18823568)==
  
−
{|
+
 
−
| BIND||62921
 
−
|-
 
−
| BioGrid||20497  || 163891
 
−
|-
 
−
| DIP||25914  || 28969  || 56441
 
−
|-
 
−
| HPRD||2893  || 1958  || 839  || 37956
 
−
|-
 
−
| INTACT||24239  || 25653  || 24807  || 8075  || 111235
 
−
|-
 
−
| MINT||21991  || 34654  || 29988  || 6270  || 45260  || 76607
 
−
|-
 
−
| MPACT||6904  || 8489  || 6777  || 0  || 6087  || 6426  || 13321
 
−
|-
 
−
| MPPI||385  || 26  || 41  || 303  || 89  || 71  || 0  || 829
 
−
|-
 
−
| OPHID||2210  || 1333  || 887  || 17913  || 7196  || 6396  || 0  || 183  || 47297
 
−
|-
 
−
| CORUM||113  || 18  || 29  || 390  || 121  || 66  || 0  || 9  || 158  || 1919
 
−
|-
 
−
| ||BIND||BioGrid||DIP||HPRD||INTACT||MINT||MPACT||MPPI||OPHID||CORUM
 
−
|-
 
−
| ||(25903)||(111633)||(13594)||(15201)||(55807)||(15712)||(1137)||(238)||(26571)||(1403)
 
−
|}
 
  
 
== Interactors ==
 
== Interactors ==
  
−
{|
 
−
| BIND||40801
 
−
|-
 
−
| BioGrid||14442  || 27471
 
−
|-
 
−
| DIP||15395  || 13084  || 20111
 
−
|-
 
−
| HPRD||3320  || 2472  || 1249  || 9539
 
−
|-
 
−
| INTACT||18121  || 16827  || 15687  || 5792  || 41587
 
−
|-
 
−
| MINT||16178  || 15064  || 14987  || 4620  || 23418  || 28428
 
−
|-
 
−
| MPACT||4638  || 4560  || 4632  || 0  || 4859  || 4756  || 4972
 
−
|-
 
−
| MPPI||671  || 212  || 292  || 429  || 575  || 504  || 0  || 862
 
−
|-
 
−
| OPHID||3242  || 2300  || 1241  || 7357  || 5747  || 4709  || 1  || 421  || 9629
 
−
|-
 
−
| CORUM||1551  || 746  || 670  || 1845  || 2293  || 1733  || 0  || 321  || 1849  || 3581
 
−
|-
 
−
| ||BIND||BioGrid||DIP||HPRD||INTACT||MINT||MPACT||MPPI||OPHID||CORUM
 
−
|-
 
−
| ||(18591)||(8169)||(1838)||(1040)||(11893)||(3241)||(17)||(45)||(1280)||(626)
 
−
|}
 
  
 
==Summary of mapping interaction records to RIGs (Corresponds to Table 5 in PMID 18823568) ==
 
==Summary of mapping interaction records to RIGs (Corresponds to Table 5 in PMID 18823568) ==
  
−
{|
+
 
−
| align="center" style="background:#f0f0f0;"|'''Source'''||align="center" style="background:#f0f0f0;"|'''Total records'''||align="center" style="background:#f0f0f0;"|'''Protein-only interactors'''||align="center" style="background:#f0f0f0;"|'''PPI Assigned to RIGID'''||align="center" style="background:#f0f0f0;"|'''Unique RIGIDs'''
 
−
|-
 
−
| BIND||193648||93957||91291(97.1625%)||62921 (68.9236%)
 
−
|-
 
−
| BioGrid||240501||240501||240197(99.8736%)||163891 (68.2319%)
 
−
|-
 
−
| dip||57675||57675||56608(98.1500%)||56441 (99.7050%)
 
−
|-
 
−
| intact||129092||128326||127893(99.6626%)||111235 (86.9750%)
 
−
|-
 
−
| mint||109412||109412||107823(98.5477%)||76607 (71.0488%)
 
−
|-
 
−
| HPRD||38037||38037||38028(99.9763%)||37956 (99.8107%)
 
−
|-
 
−
| ophid||73257||73257||72907(99.5222%)||47297 (64.8731%)
 
−
|-
 
−
| MPACT||16504||16504||16286(98.6791%)||13321 (81.7942%)
 
−
|-
 
−
| MPPI||1814||1814||1697(93.5502%)||829 (48.8509%)
 
−
|-
 
−
| CORUM||2104||2104||2104(100.0000%)||1919 (91.2072%)
 
−
|-
 
−
| ALL||862044||761587||754834(99.1133%)||369457 (48.9455%)
 
−
|}
 
  
 
== Assignment of protein interactors to ROGs (Corresponds to Table 3 in PMID 18823568)  ==
 
== Assignment of protein interactors to ROGs (Corresponds to Table 3 in PMID 18823568)  ==
  
−
{|
 
−
| align="center" style="background:#f0f0f0;"|'''Source'''||align="center" style="background:#f0f0f0;"|'''Protein_Intractors'''||align="center" style="background:#f0f0f0;"|'''Assigned'''||align="center" style="background:#f0f0f0;"|'''%'''||align="center" style="background:#f0f0f0;"|'''Arbitrary'''||align="center" style="background:#f0f0f0;"|'''New'''||align="center" style="background:#f0f0f0;"|'''Unassigned'''||align="center" style="background:#f0f0f0;"|'''Unique proteins'''
 
−
|-
 
−
| BIND||285482||273646||95.8540||0||7942||3894||40801
 
−
|-
 
−
| CORUM||10316||10314||99.9806||0||2||0||3581
 
−
|-
 
−
| dip||20728||18513||89.3140||1261||479||475||20111
 
−
|-
 
−
| BioGrid||29318||19162||65.3592||10053||5||98||27471
 
−
|-
 
−
| HPRD||9565||9493||99.2473||53||15||4||9539
 
−
|-
 
−
| intact||97988||94387||96.3251||18||3347||236||41587
 
−
|-
 
−
| mint||76908||73745||95.8873||2||2689||472||28428
 
−
|-
 
−
| MPACT||40349||40112||99.4126||0||0||237||4972
 
−
|-
 
−
| MPPI||3628||3456||95.2591||0||39||133||862
 
−
|-
 
−
| ophid||146423||145362||99.2754||103||699||259||9629
 
−
|-
 
−
| All||720705||688190||95.4884||11490||15217||5808||83388
 
−
|}
 
  
 
==  ROG summary (Corresponds to Table 4 in PMID 18823568) ==
 
==  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;"|'''MPPI'''||align="center" style="background:#f0f0f0;"|'''MPACT'''||align="center" style="background:#f0f0f0;"|'''IntAct'''||align="center" style="background:#f0f0f0;"|'''CORUM'''
 
−
|-
 
−
| 1||000000000000000001||P||1||562341||78.0265%||232685||7503||0||71616||0||125715||3023||30666||91133||0
 
−
|-
 
−
| 130||000000000010000010||SM||1||551||0.0765%||0||551||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 66||000000000001000010||SD||1||2||0.0003%||0||2||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 65||000000000001000001||PD||1||9533||1.3227%||8084||1446||0||3||0||0||0||0||0||0
 
−
|-
 
−
| 42||000000000000101010||SVG||1||149||0.0207%||0||0||0||0||149||0||0||0||0||0
 
−
|-
 
−
| 8193||000010000000000001||PI||1||48||0.0067%||0||2||0||0||0||0||0||0||46||0
 
−
|-
 
−
| 8194||000010000000000010||SI||1||12395||1.7198%||12336||59||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 129||000000000010000001||PM||1||523||0.0726%||473||1||0||0||0||0||32||0||17||0
 
−
|-
 
−
| 554||000000001000101010||SVGO||1||611||0.0848%||0||0||0||0||611||0||0||0||0||0
 
−
|-
 
−
| 10||000000000000001010||SV||1||13||0.0018%||0||0||2||4||0||0||0||0||7||0
 
−
|-
 
−
| 2||000000000000000010||S||1||34755||4.8224%||0||7402||17432||242||2510||0||0||6927||242||0
 
−
|-
 
−
| 773||000000001100000101||PUO+||2||9||0.0012%||0||0||0||3||0||0||0||0||6||0
 
−
|-
 
−
| 774||000000001100000110||SUO+||2||1||0.0001%||0||0||0||0||0||0||0||0||1||0
 
−
|-
 
−
| 778||000000001100001010||SVO+||2||1||0.0001%||0||0||0||0||0||0||0||0||1||0
 
−
|-
 
−
| 5||000000000000000101||PU||2||22818||3.1661%||0||0||0||264||0||19520||320||2519||195||0
 
−
|-
 
−
| 6||000000000000000110||SU||2||737||0.1023%||0||659||60||4||6||0||0||0||8||0
 
−
|-
 
−
| 16385||000100000000000001||PE||2||189||0.0262%||0||0||0||0||0||0||0||0||189||0
 
−
|-
 
−
| 16386||000100000000000010||SE||2||5405||0.7500%||5405||0||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 146||000000000010010010||STM||3||1||0.0001%||0||1||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 145||000000000010010001||PTM||3||170||0.0236%||132||0||0||0||0||0||35||0||3||0
 
−
|-
 
−
| 8209||000010000000010001||PTI||3||13||0.0018%||0||0||0||0||0||0||0||0||13||0
 
−
|-
 
−
| 81||000000000001010001||PTD||3||1487||0.2063%||1486||0||0||1||0||0||0||0||0||0
 
−
|-
 
−
| 26||000000000000011010||SVT||3||1||0.0001%||0||0||0||0||0||0||0||0||1||0
 
−
|-
 
−
| 18||000000000000010010||ST||3||8651||1.2004%||0||1487||1015||0||6146||0||0||0||3||0
 
−
|-
 
−
| 17||000000000000010001||PT||3||26398||3.6628%||11876||0||0||1604||0||122||46||0||2460||10290
 
−
|-
 
−
| 8210||000010000000010010||STI||3||903||0.1253%||855||48||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 16401||000100000000010001||PTE||4||3||0.0004%||0||0||0||0||0||0||0||0||3||0
 
−
|-
 
−
| 16402||000100000000010010||STE||4||315||0.0437%||314||0||1||0||0||0||0||0||0||0
 
−
|-
 
−
| 789||000000001100010101||PUTO+||4||14||0.0019%||0||0||0||0||0||0||0||0||14||0
 
−
|-
 
−
| 790||000000001100010110||SUTO+||4||1||0.0001%||0||0||0||0||1||0||0||0||0||0
 
−
|-
 
−
| 22||000000000000010110||SUT||4||15||0.0021%||0||1||3||0||11||0||0||0||0||0
 
−
|-
 
−
| 4373||000001000100010101||PUTL+||5||9||0.0012%||0||0||0||1||0||0||0||0||8||0
 
−
|-
 
−
| 12546||000011000100000010||SLI+||5||6660||0.9241%||0||6660||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 810||000000001100101010||SVGO+||5||59||0.0082%||0||0||0||0||59||0||0||0||0||0
 
−
|-
 
−
| 21||000000000000010101||PUT||5||33||0.0046%||0||0||0||4||0||5||0||0||0||24
 
−
|-
 
−
| 131073||100000000000000001||PQ||5||2||0.0003%||0||0||0||0||0||0||0||0||2||0
 
−
|-
 
−
| 131077||100000000000000101||PUQ||5||1||0.0001%||0||0||0||0||0||0||0||0||1||0
 
−
|-
 
−
| 131089||100000000000010001||PTQ||5||38||0.0053%||0||0||0||0||0||0||0||0||38||0
 
−
|-
 
−
| 1802||000000011100001010||SVOX+||5||4||0.0006%||0||0||0||0||0||0||0||0||4||0
 
−
|-
 
−
| 4354||000001000100000010||SL+||5||4193||0.5818%||0||2984||1209||0||0||0||0||0||0||0
 
−
|-
 
−
| 5378||000001010100000010||SXL+||5||1||0.0001%||0||0||0||0||0||0||0||0||1||0
 
−
|-
 
−
| 4482||000001000110000010||SML+||5||409||0.0567%||0||409||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 4394||000001000100101010||SVGL+||5||50||0.0069%||0||0||0||0||50||0||0||0||0||0
 
−
|-
 
−
| 5381||000001010100000101||PUXL+||5||27||0.0037%||0||0||0||0||0||19||0||0||8||0
 
−
|-
 
−
| 5382||000001010100000110||SUXL+||5||3||0.0004%||0||0||0||0||3||0||0||0||0||0
 
−
|-
 
−
| 5386||000001010100001010||SVXL+||5||2||0.0003%||0||0||0||1||0||0||0||0||1||0
 
−
|-
 
−
| 4374||000001000100010110||SUTL+||5||52||0.0072%||0||0||52||0||0||0||0||0||0||0
 
−
|-
 
−
| 4357||000001000100000101||PUL+||5||84||0.0117%||0||0||0||0||0||84||0||0||0||0
 
−
|-
 
−
| 86274||010101000100000010||SLEN+||6||3||0.0004%||0||2||1||0||0||0||0||0||0||0
 
−
|-
 
−
| 82034||010100000001110010||STGDEN||6||2||0.0003%||0||0||0||0||2||0||0||0||0||0
 
−
|-
 
−
| 81938||010100000000010010||STEN||6||24||0.0033%||24||0||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 81937||010100000000010001||PTEN||6||5||0.0007%||3||0||0||0||0||0||2||0||0||0
 
−
|-
 
−
| 81922||010100000000000010||SEN||6||5823||0.8080%||5452||3||366||2||0||0||0||0||0||0
 
−
|-
 
−
| 81921||010100000000000001||PEN||6||2869||0.3981%||2462||0||0||49||0||98||37||0||221||2
 
−
|-
 
−
| 65601||010000000001000001||PDN||6||1||0.0001%||1||0||0||0||0||0||0||0||0||0
 
−
|-
 
−
| 65553||010000000000010001||PTN||6||26||0.0036%||0||0||0||0||0||0||0||0||26||0
 
−
|-
 
−
| 65537||010000000000000001||PN||6||6463||0.8968%||0||0||112||2638||13||601||0||0||3099||0
 
−
|-
 
−
| 196625||110000000000010001||PTNQ||6||1||0.0001%||0||0||0||0||0||0||0||0||1||0
 
−
|}
 
  
 
== Scores (Corresponds to Table 2 in PMID 18823568) ==
 
== 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'''
 
−
|-
 
−
| 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.||11025(1.5422%)
 
−
|-
 
−
| E||The protein reference was a retired NCBI Identifier. NCBI's eUtils (E) were used to retrieve the current accession and/or sequence.||14638(2.0476%)
 
−
|-
 
−
| 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.||871(0.1218%)
 
−
|-
 
−
| L||More than one possible assignment is possible (see + above). The assignment with the largest (L) SEGUID is arbitrarily chosen (see Methods)||11493(1.6076%)
 
−
|-
 
−
| 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.||1654(0.2314%)
 
−
|-
 
−
| +||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).||11582(1.6201%)
 
−
|-
 
−
| 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.||15217(2.1286%)
 
−
|-
 
−
| 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.||700(0.0979%)
 
−
|-
 
−
| I||The protein reference used was an NCBI GenInfo Identifier (I).||20019(2.8003%)
 
−
|-
 
−
| 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.||23804(3.3297%)
 
−
|-
 
−
| 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||38162(5.3381%)
 
−
|-
 
−
| 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.||890(0.1245%)
 
−
|-
 
−
| 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||633105(88.5589%)
 
−
|-
 
−
| S||One of the interaction record's secondary (S) references for the protein was used to make the assignment||81792(11.4411%)
 
−
|-
 
−
| 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||37(0.0052%)
 
−
|}
 
  
 
[[Category:iRefIndex]]
 
[[Category:iRefIndex]]

Revision as of 12:36, 23 July 2009

Summary

  • Total interactions : 871,172
  • Total distinct interactions (based on RIGID): 357,156
  • Total distinct proteins (based on ROGID) : 83,938

This page lists statistics for our internal version of iRefIndex that includes all of the data from sources used for the current build Sources_iRefIndex_4.0. This full build of the iRefIndex contains data that cannot be redistributed according to usage policies of the source databases (namely, from DIP, HPRD and MPact databases). Please contact ian.donaldson at biotek.uio.no if you would like to obtain a copy of the full iRefIndex build under an academic, collaborative agreement.

The data that are freely available at ftp://ftp.no.embnet.org/irefindex/data/current/ are a subset of the full build that we can freely redistribute according to the usage policies of the source databases. Please refer to http://irefindex.uio.no/wiki/Statistics_iRefIndex_free_4.0 for statistics that are applicable to this free dataset.

Interactions available from major taxonomies

Interactions (Corresponds to Table 6 in PMID 18823568)

Interactors

Summary of mapping interaction records to RIGs (Corresponds to Table 5 in PMID 18823568)

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

ROG summary (Corresponds to Table 4 in PMID 18823568)

Scores (Corresponds to Table 2 in PMID 18823568)

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