Table 1.
Annotation Fields in the FANTOM2 Database, Their Corresponding Title in the CAS, and a Description of the Information They Carry
| Qualifier | Displayed title | Description |
|---|---|---|
| gene_name | Curated gene name | FANTOM gene name, which shows the function of protein products or the status of mRNA and is described in a sentence |
| gene_symbol | Curated gene symbol | gene symbol, if available, which shows the function in the several letters |
| synonym | Synonym | synonyms, if available |
| match_status1 | Match Status 1 | flags indicating whether a sequence represents a complete or partial gene, or a problem with the clone exists |
| match_status2 | Match Status 2 | flags for possible splice variants, and antisense transcripts |
| match_status3 | Match Status 3 | flags for possible frame shifts, unspliced introns, and chimeric sequences |
| cds_start | CDS start | CDS start position within the clone, in bp |
| cds_stop | CDS stop | CDS stop position within the clone, in bp |
| cds_status1 | CDS status 1 | flags for clones which may represent 5′UTR, 3′UTR, non-coding RNAs, or other artifacts |
| cds_status2 | CDS status 2 | flags for possible reverse complemented, 5′-truncated, or 3′-truncated sequences |
| cds_status3 | CDS status 3 | flags for possible frame shifts, immature transcripts or unexpected stop codon |
| cds_note | CDS Note | curator's note about the CDS |
| utr | UTR | curator's comment about UTR |
| expression_note | Expression Note | curator's comment about expression profile |
| antisense_hit | Antisense Hit | FANTOM gene names derived from a matched entry on the reverse complement strand |
| note | Note | curator's general comments |