| Version 79 (modified by , 6 years ago) (diff) |
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Qualitative Gene Expression Data
Annotations to describe the amount of transcript/protein level or the changes in level 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 | Requiers 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), or a "response to specific stress condition" term |
| in_presence_of | In_presence_of(ChEBI ID) | - |
| occurs_in | (cell type) | - |
- Unstressed conditions include during "vegetative growth of single-celled organism" (=whole cell extract) or "mitotic/meiotic cell cycle" (= they looked at different phases))
- Unstressed conditions include growth on YE and MM unless there is a known difference between the two (in which case EMM might eg be a starvation condition
Level
- 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 |
Quantitative Data
File format for bulk upload
| Column | Content | Required | Cardinality | Example |
| 1. | Systematic ID | required | 1 | SPBC11B10.09 |
| 2. | Type | required | 1 | RNA OR protein |
| 3. | During* | required | 1 | GO:0072690 |
| 4. | Average copies per cell | required | 1 | 5 |
| 5. | Range (of copies/cell) | optional | 1 | 5-10 |
| 6. | Evidence | required | 1 | ECO:0000046 |
| 7. | Qualifier | required | 1 | "population wide" OR " "single cell" |
| 8. | Source | required | 1 | PMID:12345678 |
- will be converted to annotation_extension=during(GO:0072690)
A property value that captures whether the expression is determined at the level of a single cell or a population. Related but not identical to evidence (some kinds of evidence allow inferences about expression in an individual cell, whereas other evidence types only support population-level inferences). Property name is "qual_gene_ex_cell_distribution"; value can be "population wide" or "single cell".
