wiki:CapturingGeneExpression

Version 48 (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 (if no unstressed control, the present during stress also ok)
      • 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 include during "vegetative growth of single-celled organism" (=whole cell extract) or "mitotic/meiotic cell cycle" (= they looked at different phases))
  • Unstressed conditions include growth on YE and MM unless there is a known difference between the two

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".