wiki:CapturingGeneExpression

Version 30 (modified by val_wood, 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
  • 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

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