wiki:CapturingGeneExpression

Version 32 (modified by antonialock, 9 years ago) (diff)

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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

expression type detail level evidence
mRNA level|transcription|degradation|protein level|translation|degradation during phase or process (S, phase, meiosis, sporulation, cellular response to X)|in_response_to(CHEBI chemical) increased|decreased ECO:...
  • If a gene is present in a blot under normal growth conditions I use extension during(vegetative growth of single celled organism) + qualifier=present. I then set increased/decreased during other responses (veg growth may not be the optimal term to use but I've used it in the context of when growing in standard medium, rather than having elevated levels of some nonstandard compound in there, or starved of something, or any other arbitrarily abnormal condition)
  • if they don't show the level during vegetative growth use 'present' or 'absent' during a condition (nothing to compare to)
  • use 'unchanged' if level doesn't change during a condition
  • I use 'in_response_to(CHEBI chemical)' if there isn't a GO 'response to' term for the chemical

Syntax in Artemis:

/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(GO:xxxxx),in_response_to(CHEBI:xxxxxxx); qualifier=increased/decreased/unchanged/present/absent; 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