| First Author | Mouse Genome Informatics (MGI) and National Center for Biotechnology Information (NCBI) | Year | 2008 |
| Journal | Database Download | Mgi Jnum | J:141210 |
| Mgi Id | MGI:3817419 | Citation | Mouse Genome Informatics (MGI) and National Center for Biotechnology Information (NCBI) (2008) Mouse Gene Trap Data Load from dbGSS. Database Download |
| abstractText | MGI regularly loads mouse gene trap sequence tag and cell line data from GenBank dbGSS. The load resolves biological source information present in gene trap sequence records to MGI controlled vocabularies, and identifies mutant cell line IDs and the organizations that provided the gene trap sequence data to dbGSS. For each unique gene trap cell line, MGI represents a mutant cell line record and an allele record. MGI also stores information about the parent stem cell line and the gene trap vector used to product each mutant. MGI associates all dbGSS sequence records from a given gene trap mutant cell line with the corresponding allele record. Gene Trap-to-Gene Association Process: MGI performs genome wide sequence alignments (BLAT) with gene trap sequence tags to obtain sequence tag genome coordinates, and computes a single point coordinate that best approximates the gene trap vector insertion site for each sequence tag. Gene trap sequence tag coordinates/strand are then compared to MGI gene coordinates/strand to detect trapped genes and to establish allele-to-gene relationships. Gene trap allele-to-gene associations are updated regularly. Gene Trap-to-Gene associations are not established in the following cases: 1) Where sequence tags for a gene trap allele overlap multiple genes in the trapped gene orientation, overlap one or more genes in reverse orientation (not disrupted by the gene trap mechanism), or overlap no known genes using current gene model coordinates. 2) Where gene trap sequence tags for an allele do not align with the reference mouse genome, or align equally well to multiple locations. 3) Mixed cell lines, characterized by multiple sequence tags for the same cell line that have good alignments to different locations in the genome. The MGI gene trap load integrates dbGSS sequence tag data with curated gene trap information from published literature, and MGI curators integrate published phenotype data for mice derived from gene trap cell lines with allele records generated from the load. |
