Table 4.
Summary of FANTOM2 Data Integration in MGI
| Procedure | FANTOM2 clones representing novel MGI genes | FANTOM2 clones representing existing MGI genes |
|---|---|---|
| Gene object created | Yes, for curated sequences and for uncurated multi-clone clusters | No |
| Gene nomenclature | Standardized RIKEN or derived from ortholog or paralog nomenclature | Existing or derived from ortholog or paralog nomenclature |
| DDBJ seqID-to-gene association | Yes, if not a problem sequence | Same as for novel MGI genes |
| Chromosome obtained from genome assembly | Yes, if no mapping conflicts between cluster members | Yes, if no mapping conflicts between cluster members or with existing Chr assignment in MGI |
| Mammalian ortholog record created | Yes, for curated orthologs | Same as for Novel MGI genes |
| Gene reference | FANTOM1 or FANTOM2 reference | Existing gene reference |
| Molecular segment object created | Yes, for all clones | Same as for Novel MGI genes |
| Molecular segment name | “RIKEN clone” RIKEN clonelD | Same as for novel MGI genes |
| Molecular segment attributes | Clone library name, mouse strain, tissue, age, sex | Same as for novel MGI genes |
| Molecular segment-to-gene association | Yes, for all clones associated to genes | Same as for novel MGI genes |
| DDBJ seqID-to-molecular segment association | Yes, for all clones with DDBJ seqIDs | Same as for novel MGI genes |
| Molecular segment reference | FANTOM1 or FANTOM2 reference | Same as for novel MGI genes |
| Molecular segment, problem sequence note | Yes, for problem sequences | Same as for novel MGI genes |
| Gene ontology (GO) annotation | Yes, if annotation source were: InterPro, SWISS-PROT/Trembl, paralogous MGI gene or expert confirmed | Same as for novel MGI genes |
The procedures carried out to integrate FANTOM2 data into MGI are compared for sequences representing novel and existing genes in MGI