Statistics iRefIndex 8.0
From irefindex
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)
- 9 All iRefIndex Pages
Summary
Last updated: 2010-11-17
- Total interaction source records :
- Total distinct interactions (based on RIGID): ( % of total interactions)
- Total distinct proteins (based on ROGID) :
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_8.0.
Interactions available from major taxonomies
Top 15 uncorrected taxonomy groups in iRefIndex (Taxonomy identifiers as they appear in original source)
- Full list [[1]]
Top 15 corrected taxonomy groups in iRefIndex (Taxonomy identifiers corrected using sequence database information)
- Full list [[2]]
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)
| 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. | 11106(1.2054%) |
| 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, seeunce information obtained form UniProt. | 12693(1.3777%) |
| 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. | 8348(0.9061%) |
| 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) | 16937(1.8383%) |
| 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. | 712(0.0773%) |
| + | 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). | 17164(1.863%) |
| 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. | 6423(0.6971%) |
| 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. | 704(0.0764%) |
| I | The protein reference used was an NCBI GenInfo Identifier (I). | 167561(18.1868%) |
| 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. | 23872(2.591%) |
| 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 | 29603(3.2131%) |
| 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. | 15147(1.644%) |
| 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'. | 43(0.0047%) |
| P | The interaction record's primary (P) reference for the protein was used to make the assignment | 832046(90.309%) |
| S | One of the interaction record's secondary (S) references for the protein was used to make the assignment | 89286(9.691%) |
| Y | the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009) | 10230(1.1103%) |
| 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 | 38(0.0041%) |
All iRefIndex Pages
Follow this link for a listing of all iRefIndex related pages (archived and current).
