wiki:CapturingGeneExpression

Qualitative Gene Expression Data

Annotations to qualitatively describe the transcript/protein level or the changes 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 degradationRequires 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), a specific cell cycle phase or a response to specific stress condition
in_presence_ofin_presence_of(ChEBI ID)Used when there is no "cellular response to" term for the compound in question
in_absence_ofin_presence_of(ChEBI ID)Used when there is no "cellular response to" term for the compound in question
occurs_inoccurs_in(cell type)H+=CL:0002675, H-=CL:0002674

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
ECO:0000048transcript expression level evidence

Or use 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

Last modified 5 years ago Last modified on Jul 14, 2015, 10:36:18 PM