Statistics iRefIndex 14.0
These statistics apply to the extended version of iRefIndex. See the iRefIndex_Release_Notes for details.
Interactions available from major taxonomies (corrected)
Taxons of the protein interactors have been corrected to correspond to the taxon provided in the protein sequence record regardless of the taxon listed in the interaction record. See PMID 18823568 for details.
|NCBI taxonomy identifier||Scientific name||Number of interactions|
|559292||Saccharomyces cerevisiae S288c||122323|
|83333||Escherichia coli K-12||16450|
|192222||Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819||11971|
|284812||Schizosaccharomyces pombe 972h-||9387|
|381518||Influenza A virus (A/Wilson-Smith/1933(H1N1))||4087|
|243276||Treponema pallidum subsp. pallidum str. Nichols||3642|
|1111708||Synechocystis sp. PCC 6803 substr. Kazusa||3232|
Summary of mapping interaction records to RIGs (redundant interaction groups)
Source: Interaction data source. Total records: Total number of interaction records found in source. Protein-only interactors:Total number of interactions involving only protein interactors. PPI assigned to RIGID: Number of interactions where all protein interactors were assigned to a ROG. Percentage of column 3 is shown. Unique RIGIDs (interactions): Number of unique protein interactions and complexes (RIGID's) found in the data source (also expressed as a percentage of column 4). For a description of the term RIGs, see README_MITAB2.6_for_iRefIndex#Understanding_the_iRefIndex_MITAB_format and the original paper PMID 18823568.
|Source||Total records||Protein-related interactions||PPI assigned to RIGID||%||Unique RIGIDs||%|
Assignment of protein interactors to ROGs (redundant object group)
Source: Interaction data source (see methods). Protein interactors: Total number of interactors found in all interaction records. Assigned: Number of proteins assigned unambiguously to a ROG. Assignments listed in columns 5 and 6 are not included here. %: Column 3 expressed as a percentage of column 2. Arbitrary: Total number of ROG assignments that were ambiguous and resolved with an arbitrary method (see ROG scores with 'L'). Matching sequence: Total number of assignments made where a sequence in the interaction record matched a known sequence. Unassigned:Total number of protein interactors that could not be assigned to a ROG. Unique: Total number of unique proteins (ROG's). For a description of the term ROGs, see README_MITAB2.6_for_iRefIndex#Understanding_the_iRefIndex_MITAB_format and the original paper PMID 18823568.
|Source||Protein interactors||Assigned||%||Arbitrary||Matching sequence||New or obsolete sequence||Unassigned||Unique proteins|
Mapping score summary
See below for definitions of the mapping score codes.
Mapping score code definitions
|Character||Description of feature (when the value is 1)||align="center" style="background:#f0f0f0;"|
|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.|
|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, sequence information obtained from UniProt.|
|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.|
|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)|
|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.|
|+||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).|
|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.|
|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.|
|I||The protein reference used was an NCBI GenInfo Identifier (I).|
|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.|
|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|
|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.|
|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'.|
|P||The interaction record's primary (P) reference for the protein was used to make the assignment|
|S||One of the interaction record's secondary (S) references for the protein was used to make the assignment|
|Y||the accession was referring an accession which was removed from RefSeq or UniProt after beta3 build of iRefIndex (March 9th, 2009)|
|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|