wiki:CapturingGeneExpression

Version 54 (modified by val_wood, 8 years ago) (diff)

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Qualitative Data

  • Each annotation must consist of these 4 bits of data:
    • Expression type Allowed types: RNA level, protein level, transcription, RNA degradation, translation, protein degradation
    • Relation during(GO biological process ID) or in_presence_of(ChEBI ID)
    • Level present, absent, unchanged, increased, decreased, constant
      • present during vegetative growth (if no unstressed control, the present during stress also ok)
      • unchanged/decreased/increased in stress
      • constant during cell cycle
    • Evidence ECO:xxxxxxx

  • 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).
  • 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
Examples table
typerelationleveldescriptionformal
RNA levelduring(veg growth)presentRNA detected during vegetative growthterm=gene expression, RNA level; annotation_extension=during(GO:0072690); qualifier=present; evidence=ECO:0000106; db_xref=PMID:1; date=YYYYMMDD"
RNA levelduring(cell response to UVincreasedRNA amount increased during UV stressterm=gene expression, RNA level; annotation_extension=during(GO:0034644); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:1; date=YYYYMMDD"
protein levelduring(cell response to UVunchangedprotein level does not change during UV stress compared to unstressedterm=gene expression, protein level; annotation_extension=during(GO:0034644); qualifier=unchanged; evidence=ECO:0000112; db_xref=PMID:1; date=YYYYMMDD"
transcriptionduring(meiosis)increasedtranscription 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:0000112Western blot assay
ECO:0000106Northern assay evidence
ECO:0000049reporter gene assay
ECO:0000108RT-PCR
ECO:0000110RNA protection assay evidence
ECO:0000058expression microarray evidence


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".