wiki:CapturingGeneExpression

Version 81 (modified by vw253, 6 years ago) (diff)

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Qualitative Gene Expression 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 5 pieces of data: Expression Type, Annotation extension( Relation), Level, Evidence and reference
  • Qualitative 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=PMID:xxxxxxx; 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-

Annotation extension (Relation)

Allowed relationsSyntax (Example) comment
duringduring(GO:0072690) A GO biological process ID , Commonly vegetative growth (GO:0072690), or a "response to specific stress condition" term
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 (qualifier)

  • 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

Or sue the bulk upload format described here http://www.pombase.org/submit-data/qualitative-gene-expression-bulk-upload-file-format


Quantitative Data

Please use the spreadsheet file format described here: http://www.pombase.org/submit-data/quantitative-gene-expression-bulk-upload-file-format