| Version 63 (modified by , 7 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.
*Qualitive Expression annotation comprises of 4 pieces of data:
- Expression type Allowed types: RNA level, protein level, transcription, RNA degradation, translation, protein degradation
- A northern blot (for instance) can only tell you if there is RNA there, and if the amount changes during different conditions. Other assays may tell you specifically if it is transcription or degradation that is affected (for instance, the amount of RNA could increase due to increased transcription or decreased degradation).
- Relation during(GO biological process ID) or 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 ECO:xxxxxxx
| 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"
| Evidence codes used | |
| 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".
