wiki:CapturingGeneExpression

Version 37 (modified by antonialock, 8 years ago) (diff)

--

Legacy Data

move to transcript features

  • alternative transcript, -> migrate to transcript features
  • alternative translation,
  • gene expression, antisense transcript detected
  • gene expression, meiosis-specific splicing
  • gene expression, promoter contains CCAAT element (these need migrating to sequence features attached to the genes they are regulating)

to migrate to extensions

  • gene expression, target genes transcriptionally co-regulated by Cdk9 (1)
  • gene expression, target genes transcriptionally co-regulated by Mcs6
  • gene expression, post transcriptional regulation of Tsn1 expression
  • gene expression, transcriptionally repressed by cAMP signaling pathway PMID:1849107 (0 Others)

move to something else?

  • gene expression, co-transcribed with divergently orientated functionally related gene

need to deal with

  • complexes
  • gene expression, consitutive
  • gene expression, expressed during meiosis, specifically
  • expressed only during (phase)
  • expressed in cell type
  • gene expression, expression autoregulated (move to GO annotation extension)
  • gene expression, cell cycle regulated (1)

Qualitative Data

  • Each annotation must consist of these 4 bits of data:
    • Expression type (mRNA or protein level)
    • Relation (happens_during(BP) or in_presence_of(ChEBI)
    • Level (present, absent, unchanged, increased, decreased
    • Evidence (ECO:xxxxxxx)

  • The expression type may, if it is known, be further subdivided into:
    • RNA level -> transcription or degradation
    • protein level -> translation or degradation
  • Unstressed conditions are currently paired with happens_during(vegetative growth on single-celled organism)
  • Unstressed conditions include growth on YE and MM unless there is a known difference between the two
  • Not sure how to deal with other carbon sources? Difference could be due to glucose starvation or response to other carbon source. Lets discuss if it crops up.
  • Use 'unchanged' if the level doesn't change during a condition compared to unstressed

Example Artemis string: /controlled_curation="term=gene expression, RNA level; annotation_extension=happens_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

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 optional 1 5-10
6. Evidence required 1 "population wide" OR " "single cell"
7. Source required 1 PMID:12345678