wiki:CapturingGeneExpression

Version 24 (modified by antonialock, 9 years ago) (diff)

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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)

move to GO

  • gene expression, transcriptionally regulates genes involved in nitrogen metabolism (1) IN PROGRESS - GO term requested
  • gene expression, transcriptionally regulates genes involved in thiamin biosynthesis (2) IN PROGRESS - GO term requested
  • gene expression, transcriptionally regulates genes involved in vesicle mediated transport IN PROGRESS - GO term requested
  • gene expression, transcriptionally represses genes involved in cell surface adhesion (3) IN PROGRESS - GO term requested
  • gene expression, transcriptionally represses genes involved in glucose uptake (2) IN PROGRESS - GO term requested
  • gene expression, transcriptionally represses genes involved in iron uptake (2) IN PROGRESS - GO term requested
  • gene expression, transcriptionally represses genes involved in transport IN PROGRESS - GO term requested

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)

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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:...

use 'in_response_to(CHEBI chemical)' if there isn't a GO 'response to' term for the chemical and they won't add it. NOTE: increased/decreased may be a bit arbitrary...we should probably discuss this I have been using these in relation to WT grown in rich medium (so it's got nitrogen, thiamine, lots of glucose etc etc) under fairly 'normal' conditions (with regards to temp etc), I haven't made a distinction between agar or liquid....so yeah, a bit arbitrary. /AL

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