wiki:CapturingGeneExpression

Version 74 (modified by vw253, 6 years ago) (diff)

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Qualitative Data

Annotations to describe the amount of transcript/protein level or the changes in level which occur in different conditions or at different phases in WT cells.

  • Qualitative Expression annotation comprises of 4 pieces of data: Expression Type, Relation, Level and Evidence
  • Qualtative expression is currently curated in Artemis, but will eventually be captured in Canto

Syntax /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:xxxxxxx); qualifier=increased; evidence=ECO:xxxx; db_xref=; date=YYYYMMDD"

Expression Type

Allowed TypeComment
RNA level A northern blot (for instance) can only tell you if there is RNA there
protein level -
transcriptionRequires a specific assay for transcription, not only presence of RNA, as could be decreased degradation
RNA degradationRequiers a specific assay for degradation
translation-
protein degradation-

Relation

Allowed relationsExample comment
duringduring(GO biological process ID) -
in_presence_ofIn_presence_of(ChEBI ID)-
occurs_in(cell type)-
  • 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 (in which case EMM might eg be a starvation condition

Level

  • Level allowed qualifiers: present, absent, unchanged, increased, decreased, constant, fluctuates

Evidence

Evidence codes
ECO:0000112Western blot assay
ECO:0000106Northern assay evidence
ECO:0000049reporter gene assay
ECO:0000108RT-PCR (reverse transcriptase)
ECO:0000110RNA protection assay evidence
ECO:0000058expression microarray evidence
ECO:0000231qPCR / (quantitative / real time pcr)
ECO:0000124fusion protein localization evidence
ECO:0000007immunofluorescence
Examples table
typerelationleveldescriptionformal
RNA levelduring(veg growth)presentRNA detected during vegetative growthterm=gene expression, RNA level; annotation_extension=during(GO:0072690); qualifier=present; evidence=ECO:0000106; db_xref=PMID:1; date=YYYYMMDD"
RNA levelduring(cell response to UVincreasedRNA amount increased during UV stressterm=gene expression, RNA level; annotation_extension=during(GO:0034644); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:1; date=YYYYMMDD"
protein levelduring(cell response to UVunchangedprotein level does not change during UV stress compared to unstressedterm=gene expression, protein level; annotation_extension=during(GO:0034644); qualifier=unchanged; evidence=ECO:0000112; db_xref=PMID:1; date=YYYYMMDD"
transcriptionduring(meiosis)increasedtranscription is increased during meiosis (as opposed to decreased degradation)term=gene expression, transcription; annotation_extension=during(GO:0007126); qualifier=increased; evidence=ECO:0000108; db_xref=PMID:1; date=YYYYMMDD"


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".