wiki:CapturingGeneExpression

Version 47 (modified by antonialock, 8 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, constitutive
  • 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)
  • deletion mutant expression profiling (move to misc?)

Qualitative Data

  • Each annotation must consist of these 4 bits of data:
    • Expression type RNA or protein level
    • Relation during(BP) or in_presence_of(ChEBI)
    • Level present, absent, unchanged, increased, decreased, constant
      • present during vegetative growth,
      • unchanged/decreased/increased in stress
      • constant during cell cycle
    • 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 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.

Example Artemis string: /controlled_curation="term=gene expression, RNA level; annotation_extension=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
ECO:0000110RNA protection assay evidence
ECO:0000058expression microarray evidence


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 (of copies/cell) optional 1 5-10
6. Evidence required 1 ECO:0000046
7. Qualifier required 1 "population wide" OR " "single cell"
8. Source required 1 PMID:12345678
  • will be converted to annotation_extension=during(GO:0072690)

A property value that captures whether the expression is determined at the level of a single cell or a population. Related but not identical to evidence (some kinds of evidence allow inferences about expression in an individual cell, whereas other evidence types only support population-level inferences). Property name is "qual_gene_ex_cell_distribution"; value can be "population wide" or "single cell".