Ontology meeting 2014-03-27

Attendees:

Minutes:

gene expression/transcription 'involved in' terms

Following a discussion with Ruth and Rachael, it seems that using the TG 'involved in' template for gene expression/transcription may have been wrong e.g. 'regulation of gene expression involved in extracellular matrix organization'. Here the regulation of gene expression shouldn't be part of the process extracellular matrix organization, I think instead it should be 'causally_upstream_of'.

Here is the full list of terms:

GO:0060807	regulation of transcription from RNA polymerase II promoter involved in definitive endodermal cell fate specification
GO:2000976	regulation of transcription from RNA polymerase II promoter involved in detection of glucose
GO:1900094	regulation of transcription from RNA polymerase II promoter involved in determination of left/right symmetry
GO:0003258	regulation of transcription from RNA polymerase II promoter involved in endocardial precursor cell differentiation
GO:0021882	regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment
GO:1901213	regulation of transcription from RNA polymerase II promoter involved in heart development
GO:0060994	regulation of transcription from RNA polymerase II promoter involved in kidney development
GO:0060500	regulation of transcription from RNA polymerase II promoter involved in lung bud formation
GO:0060597	regulation of transcription from RNA polymerase II promoter involved in mammary gland formation
GO:0061216	regulation of transcription from RNA polymerase II promoter involved in mesonephros development
GO:0072212	regulation of transcription from RNA polymerase II promoter involved in metanephros development
GO:0003256	regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation
GO:0021918	regulation of transcription from RNA polymerase II promoter involved in somatic motor neuron fate commitment
GO:0090236	regulation of transcription from RNA polymerase II promoter involved in somitogenesis
GO:1902064	regulation of transcription from RNA polymerase II promoter involved in spermatogenesis
GO:0021909	regulation of transcription from RNA polymerase II promoter involved in spinal cord anterior-posterior patterning
GO:0021920	regulation of transcription from RNA polymerase II promoter involved in spinal cord association neuron specification
GO:0021912	regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification
GO:0021913	regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification
GO:0090019	regulation of transcription involved in anterior neural plate formation
GO:0044324	regulation of transcription involved in anterior/posterior axis specification
GO:0060850	regulation of transcription involved in cell fate commitment
GO:0060899	regulation of transcription involved in eye field cell fate commitment of camera-type eye
GO:0000083	regulation of transcription involved in G1/S transition of mitotic cell cycle
GO:0000117	regulation of transcription involved in G2/M transition of mitotic cell cycle
GO:0060849	regulation of transcription involved in lymphatic endothelial cell fate commitment
GO:0090020	regulation of transcription involved in posterior neural plate formation
GO:0060796	regulation of transcription involved in primary germ layer cell fate commitment
GO:0060852	regulation of transcription involved in venous endothelial cell fate commitment
GO:1901311    regulation of gene expression involved in extracellular matrix organization

The cell cycle ones may be a special case, I'll need to confer with Val. But what about the development ones? Is the transcription regulation really part of the process or is it really upstream?