| Version 72 (modified by , 6 years ago) (diff) |
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Qualitative 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 4 pieces of data: Expression Type, Relation, Level and Evidence
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 | - |
Relation
| Allowed relations | Example | comment |
| during | during(GO biological process ID) | - |
| 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
- Level allowed qualifiers: present, absent, unchanged, increased, decreased, constant, fluctuates
Evidence codes
| 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 |
| Examples table | ||||
| type | relation | level | description | formal |
| RNA level | during(veg growth) | present | RNA detected during vegetative growth | term=gene expression, RNA level; annotation_extension=during(GO:0072690); qualifier=present; evidence=ECO:0000106; db_xref=PMID:1; date=YYYYMMDD" |
| RNA level | during(cell response to UV | increased | RNA amount increased during UV stress | term=gene expression, RNA level; annotation_extension=during(GO:0034644); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:1; date=YYYYMMDD" |
| protein level | during(cell response to UV | unchanged | protein level does not change during UV stress compared to unstressed | term=gene expression, protein level; annotation_extension=during(GO:0034644); qualifier=unchanged; evidence=ECO:0000112; db_xref=PMID:1; date=YYYYMMDD" |
| transcription | during(meiosis) | increased | transcription is increased during meiosis (as opposed to decreased degradation) | term=gene expression, transcription; annotation_extension=during(GO:0007126); qualifier=increased; evidence=ECO:0000108; db_xref=PMID:1; date=YYYYMMDD" |
Template Artemis: /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:xxxxxxx); qualifier=increased; evidence=ECO:xxxx; db_xref=; date=YYYYMMDD"
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".
