wiki:CapturingGeneExpression

Version 16 (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, post transcriptional regulation of Tsn1 expression
  • gene expression, transcriptionally repressed by cAMP signaling pathway PMID:1849107 (0 Others)
  • gene expression, transcriptionally activates genes required for anaerobic growth under oxygen-limiting conditions
  • gene expression, transcriptionally activates stress related genes convert to GO (pos reg of transcription involved in cellular response to stress)
  • gene expression, transcriptionally regulates genes involved in nitrogen metabolism (1) IN PROGRESS - request GO term if needed
  • gene expression, transcriptionally regulates genes involved in thiamin biosynthesis (2) IN PROGRESS - request GO term if needed
  • gene expression, transcriptionally regulates genes involved in vesicle mediated transport IN PROGRESS - request GO term if needed
  • gene expression, transcriptionally regulated by CCAAT complex DONE
  • gene expression, transcriptionally represses genes involved in cell surface adhesion (3) IN PROGRESS - request GO term if needed
  • gene expression, transcriptionally represses genes involved in glucose uptake (2) IN PROGRESS - request GO term if needed
  • gene expression, transcriptionally represses genes involved in iron uptake (2) IN PROGRESS - request GO term if needed
  • gene expression, transcriptionally represses genes involved in transport IN PROGRESS - request GO term if needed

to migrate to extensions

  • gene expression, target genes transcriptionally co-regulated by Cdk9 (1)
  • gene expression, target genes transcriptionally co-regulated by Mcs6
  • transcriptionally regulated by ->check represented as transcriptionally regulates, then infer. DONE for most; a few remaining to convert to new syntax

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|degradationprotein 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

Syntax in Artemis:

controlled_curation="gene expression, mRNA level; annotation_extension=during(GO:xxxxx),in_response_to(CHEBI:xxxxxxx); qualifier=increased/decreased; evidence=ECOXX"

Evidence codes used
ECO:0000112Western blot assay
ECO:0000106Northern assay evidence