Difference between revisions of "Statistics iRefIndex 5.0"
From irefindex
| Line 172: | Line 172: | ||
== 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||273658||95.8582||0||7887||3937||40783 | ||
| + | |- | ||
| + | | CORUM||10316||10314||99.9806||0||2||0||3581 | ||
| + | |- | ||
| + | | dip||20728||18527||89.3815||1246||477||478||20108 | ||
| + | |- | ||
| + | | grid||29599||19354||65.3873||10141||6||98||27694 | ||
| + | |- | ||
| + | | HPRD||9773||9676||99.0075||55||42||0||9750 | ||
| + | |- | ||
| + | | intact||100752||97166||96.4408||19||3323||244||42061 | ||
| + | |- | ||
| + | | mint||76898||73745||95.8998||2||2678||473||28424 | ||
| + | |- | ||
| + | | MPACT||40349||40112||99.4126||0||0||237||4972 | ||
| + | |- | ||
| + | | MPPI||3628||3457||95.2867||0||30||141||861 | ||
| + | |- | ||
| + | | ophid||146423||145362||99.2754||103||699||259||9626 | ||
| + | |- | ||
| + | | All||723948||691371||95.5001||11566||15144||5867||83809 | ||
| + | |} | ||
== ROG summary (Corresponds to Table 4 in PMID 18823568) == | == ROG summary (Corresponds to Table 4 in PMID 18823568) == | ||
Revision as of 13:06, 23 July 2009
Contents
- 1 Summary
- 2 Interactions available from major taxonomies
- 3 Interactions (Corresponds to Table 6 in PMID 18823568)
- 4 Interactors
- 5 Summary of mapping interaction records to RIGs (Corresponds to Table 5 in PMID 18823568)
- 6 Assignment of protein interactors to ROGs (Corresponds to Table 3 in PMID 18823568)
- 7 ROG summary (Corresponds to Table 4 in PMID 18823568)
- 8 Scores (Corresponds to Table 2 in PMID 18823568)
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
Top 15 uncorrected taxonomy groups in iRefIndex (Taxonomy identifiers as they appear in original source)
| NCBI taxonomy identifier | Name | Number of interactions | |
| 4932 | Saccharomyces cerevisiae | 115570 | |
| 9606 | Homo sapiens | 103700 | |
| 7227 | Drosophila melanogaster | 46240 | |
| 40674 | Mammalia | 35023 | |
| 197 | Campylobacter jejuni | 11998 | |
| 6239 | Caenorhabditis elegans | 11793 | |
| 284812 | Schizosaccharomyces pombe 972h- | 11556 | |
| 10090 | Mus musculus | 9964 | |
| 562 | Escherichia coli | 8512 | |
| 3702 | Arabidopsis thaliana | 5348 | |
| 160 | Treponema pallidum | 3646 | |
| 83333 | Escherichia coli K-12 | 3490 | |
| 10116 | Rattus norvegicus | 3477 | |
| 1142 | Synechocystis | 3057 | |
| 36329 | Plasmodium falciparum 3D7 | 2731 | |
- for the full list :http://irefindex.uio.no/wikifiles//images/9/90/Interactions_by_taxonomy_beta5_full.pdf
Top 15 corrected taxonomy groups in iRefIndex (Taxonomy identifiers corrected using sequence database information)
| 4932 | Saccharomyces cerevisiae | 115562 |
| 9606 | Homo sapiens | 114618 |
| 7227 | Drosophila melanogaster | 46244 |
| 197 | Campylobacter jejuni | 11998 |
| 4896 | Schizosaccharomyces pombe | 11831 |
| 6239 | Caenorhabditis elegans | 11793 |
| 10090 | Mus musculus | 8569 |
| 83333 | Escherichia coli K-12 | 7482 |
| 3702 | Arabidopsis thaliana | 5354 |
| 155864 | Escherichia coli O157:H7 EDL933 | 4928 |
| 160 | Treponema pallidum | 3646 |
| 1148 | Synechocystis sp. PCC 6803 | 3166 |
| 36329 | Plasmodium falciparum 3D7 | 2731 |
| 10116 | Rattus norvegicus | 2650 |
| 85962 | Helicobacter pylori 26695 | 1598 |
- for the full list corrected :http://irefindex.uio.no/wikifiles//images/4/4e/Interactions_by_taxonomy_beta5_full_cor.pdf
Interactions (Corresponds to Table 6 in PMID 18823568)
| BIND | 62896 | |||||||||
| BIOGRID | 20564 | 164770 | ||||||||
| DIP | 25930 | 29004 | 56430 | |||||||
| HPRD | 2947 | 2016 | 858 | 39966 | ||||||
| INTACT | 24400 | 26946 | 25008 | 8442 | 113877 | |||||
| MINT | 22066 | 34683 | 30052 | 6563 | 45338 | 76602 | ||||
| MPACT | 6938 | 8489 | 6793 | 0 | 6132 | 6426 | 13321 | |||
| MPPI | 385 | 27 | 41 | 304 | 89 | 71 | 0 | 826 | ||
| OPHID | 2226 | 1357 | 899 | 18063 | 7248 | 6396 | 0 | 183 | 47297 | |
| CORUM | 116 | 18 | 29 | 403 | 122 | 66 | 0 | 9 | 158 | 1919 |
| BIND | BIOGRID | DIP | HPRD | INTACT | MINT | MPACT | MPPI | OPHID | CORUM | |
| (25793) | (111301) | (13496) | (16472) | (56805) | (15495) | (1132) | (235) | (26461) | (1398) |
Interactors
| BIND | 40783 | |||||||||
| BIOGRID | 14503 | 27694 | ||||||||
| DIP | 15398 | 13106 | 20108 | |||||||
| HPRD | 3357 | 2522 | 1251 | 9750 | ||||||
| INTACT | 18205 | 16989 | 15721 | 5967 | 42061 | |||||
| MINT | 16198 | 15112 | 14999 | 4669 | 23460 | 28424 | ||||
| MPACT | 4651 | 4560 | 4639 | 0 | 4874 | 4756 | 4972 | |||
| MPPI | 674 | 219 | 294 | 430 | 579 | 505 | 0 | 861 | ||
| OPHID | 3253 | 2325 | 1242 | 7426 | 5809 | 4708 | 1 | 422 | 9626 | |
| CORUM | 1561 | 756 | 671 | 1867 | 2312 | 1733 | 0 | 322 | 1849 | 3581 |
| BIND | BIOGRID | DIP | HPRD | INTACT | MINT | MPACT | MPPI | OPHID | CORUM | |
| (18529) | (8247) | (1834) | (1094) | (12125) | (3228) | (16) | (42) | (1257) | (620) |
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 | 91265(97.1349%) | 62896(68.9158%) |
| grid | 242126 | 242126 | 241823(99.8749%) | 164770(68.1366%) |
| dip | 57675 | 57675 | 56597(98.1309%) | 56430(99.7049%) |
| intact | 133302 | 132525 | 132077(99.6620%) | 113877(86.2202%) |
| mint | 109398 | 109398 | 107808(98.5466%) | 76602(71.0541%) |
| HPRD | 40075 | 40075 | 40075(100.0000%) | 39966(99.7280%) |
| ophid | 73257 | 73257 | 72907(99.5222%) | 47297(64.8731%) |
| MPACT | 16504 | 16504 | 16286(98.6791%) | 13321(81.7942%) |
| MPPI | 1814 | 1814 | 1688(93.0540%) | 826(48.9336%) |
| CORUM | 2104 | 2104 | 2104(100.0000%) | 1919(91.2072%) |
| ALL | 869903 | 769435 | 762630(99.1156%) | 372649(48.8637%) |
Assignment of protein interactors to ROGs (Corresponds to Table 3 in PMID 18823568)
| Source | Protein_Intractors | Assigned | % | Arbitrary | New | Unassigned | Unique proteins |
| bind | 285482 | 273658 | 95.8582 | 0 | 7887 | 3937 | 40783 |
| CORUM | 10316 | 10314 | 99.9806 | 0 | 2 | 0 | 3581 |
| dip | 20728 | 18527 | 89.3815 | 1246 | 477 | 478 | 20108 |
| grid | 29599 | 19354 | 65.3873 | 10141 | 6 | 98 | 27694 |
| HPRD | 9773 | 9676 | 99.0075 | 55 | 42 | 0 | 9750 |
| intact | 100752 | 97166 | 96.4408 | 19 | 3323 | 244 | 42061 |
| mint | 76898 | 73745 | 95.8998 | 2 | 2678 | 473 | 28424 |
| MPACT | 40349 | 40112 | 99.4126 | 0 | 0 | 237 | 4972 |
| MPPI | 3628 | 3457 | 95.2867 | 0 | 30 | 141 | 861 |
| ophid | 146423 | 145362 | 99.2754 | 103 | 699 | 259 | 9626 |
| All | 723948 | 691371 | 95.5001 | 11566 | 15144 | 5867 | 83809 |
