| Version 89 (modified by , 6 years ago) (diff) |
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Qualitative Gene Expression Data
Annotations to qualitatively describe the transcript/protein level or the changes which occur in different conditions or at different phases in WT cells.
- Qualitative Expression annotation comprises of 5 pieces of data: Expression Type, Annotation extension( Relation), Level, Evidence and Reference
- Qualitative expression is currently curated in Artemis, but will eventually be captured in Canto
- Syntax /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:xxxxxxx); qualifier=increased; evidence=ECO:xxxx; db_xref=PMID:xxxxxxx; date=YYYYMMDD"
Expression Type
| Allowed Type | Comment |
| RNA level | A northern blot (for instance) can only tell you if there is RNA there |
| protein level | - |
| transcription | Requires a specific assay for transcription, not only presence of RNA, as could be decreased degradation |
| RNA degradation | Requires a specific assay for degradation |
| translation | - |
| protein degradation | - |
Annotation extension (Relation)
| Allowed relations | Syntax (Example) | comment |
| during | during(GO:0072690) | A GO biological process ID, commonly vegetative growth (GO:0072690), a specific cell cycle phase phases or a "response to specific stress condition" term |
| in_presence_of | in_presence_of(ChEBI ID) | GIVE EXAMPLES |
| occurs_in | occurs_in(cell type) | ADD THE CELL TYPE DETAILS |
Level (qualifier)
- allowed qualifiers: present, absent, unchanged, increased, decreased, constant, fluctuates
Evidence
| Evidence codes | |
| ECO:0000112 | Western blot assay |
| ECO:0000106 | Northern assay evidence |
| ECO:0000049 | reporter gene assay |
| ECO:0000108 | RT-PCR (reverse transcriptase) |
| ECO:0000110 | RNA protection assay evidence |
| ECO:0000058 | expression microarray evidence |
| ECO:0000231 | qPCR / (quantitative / real time pcr) |
| ECO:0000124 | fusion protein localization evidence |
| ECO:0000007 | immunofluorescence |
Or use the bulk upload format described here http://www.pombase.org/submit-data/qualitative-gene-expression-bulk-upload-file-format
Quantitative Data
Please use the spreadsheet file format described here: http://www.pombase.org/submit-data/quantitative-gene-expression-bulk-upload-file-format
