Electronic jamboree feb22-2010

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  • 4pm BST/11 am eastern/8 am pacific to 6pm BST/1pm eastern/10 am pacific

Conference call planned using the GO Consortium's phone conference line, to link up with different Reference Genomes annotation groups to discuss the issues that have arisen during the annotation of the two selected target genes.

SLIT2 annotation

Chair: Pascale Gaudet

Minutes: Emily Dimmer

ppod page

Reference Genome annotations are available at:

http://gowiki.tamu.edu/wiki/index.php/Category:RefGenome_Electronic_Jamboree_2010-02_SLIT2

Source Forge Requests


  • Accepted:*

NTR: smooth muscle cell chemotaxis GO:0071670 (SourceForge ID:2952208; Ruth) [1]

NTR:regulation of smooth muscle cell chemotaxis GO:0071671

NTR:negative regulation of smooth muscle cell chemotaxis GO:0071672

NTR:positive regulation of smooth muscle cell chemotaxis GO:0071673

NTR:mononuclear cell migration GO:0071674 (SourceForge ID:952217; Ruth)[2]

NTR:regulation of mononuclear cell migration GO:0071675

NTR:negative regulation of mononuclear cell migration GO:0071676

NTR:positive regulation of mononuclear cell migration GO:0071677

NTR:olfactory bulb axon guidance GO:0071678 (SourceForge ID: 2952671; Varsha)[3]. PMID 10102269

NTR:commissural neuron axon guidance GO:0071679

NTR:Slit-Robo signaling complex GO:0071666 (SourceForge ID:2950516; Susan)[4]

NTR: negative regulation of retinal ganglion cell axon guidance (SourceForge ID:2942137 [5]; Yasmin)

  • Unresolved:*

NTR: Roundabout receptor signaling pathway (SourceForge ID:2952646; Varsha)[6]

NTR: initiation of SLIT signal transduction

NTR: termination of SLIT signal transduction

NTR: negative regulation of cellular response to growth factor (SourceForge ID:2952222; Ruth)[7]

NTR: negative regulation of chemokine receptor expression (SourceForge ID:2952897; Varsha)[8] PMID 18829537 Planning to use this with col 16 (CXCR4 & CXCR12) from PMID: 18829537 This is a general term to describe the regulation of a class of proteins - is this appropriate for GO? Or is GO:0070100 negative regulation of chemokine-mediated signaling pathway more appropriate here?

regulation of gene expression GO:0010468 (SourceForge ID:2952691; Varsha) Would it be possible to widen the name of the term GO:0010468 to include 'gene product'? i.e. GO:0010468 regulation of gene or gene product expression. We feel this would make it clear that the term is used for the regulation of all aspects of protein production as well as the regulation of mRNA production.

Improving guidance and chemotaxis relationships (SourceForge ID:2952195&; Ruth)[9] During the UK annotation of the jamboree gene SLIT2 we felt that embryonic olfactory bulb interneuron migration (GO:0021834) should be have 'part_of' guidance parents that bring in the aspect of guidance and that there should be more general terms available to link specific guidance and chemotaxis terms. For example the term GO:0021834 embryonic olfactory bulb interneuron migration should have a 'part_of' term embryonic olfactory bulb interneuron guidance, and perhaps the more general (grand)parent terms, neuron guidance, interneuron guidance, perhaps also embryonic interneuron guidance. And that the term GO:0050919 negative chemotaxis should have more general child terms: chemorepulsion of somatic cell (as we have GO:0035233 germ cell repulsion) as well as negative chemotaxis of neuron (and for axon too) which would have child terms such as 'chemorepulsion involved in precerebellar neuron migration'. The negative chemotaxis of neuron term would then be a 'part_of' child to the new term 'neuron guidance', axon guidance is already present in GO and should be 'part_of' parent to the axon chemotaxis term. Positive chemotaxis would also be required for these terms. There are already examples of a link between guidance and chemotaxis eg GO:0021842 chemorepulsion involved in interneuron migration from the subpallium to the cortex. However the creation of logical general terms in this area would help with the creation or placement of the more specific terms within the ontology and with the annotation of genes involved in these processes.

Annotation Queries*

1. PMID:11748139 Paper shows that Slit causes chemorepulsion in vitro, but authors concerned about in vivo relevance. Should data from this be annotated? Annotate to chemorepulsion and then make a NOT annotation to the more specific term chemorepulsion olfactory bulb axons using this paper? (Rachael)

2. Is SLIT2 regulating axon guidance or involved in the process of axon guidance? SLIT2 negatively regulates axon migration and is a central part of axon guidance. Surely axon guidance is a regulatory pathway unlike axon migration (which can be random or directed).

3. growth cone guidance/axon pathfinding : should these be added as synonyms for axon guidance?

4. 'growth cone collapse' [10] is this negative regulation of axon guidance? If axon guidance is a regulatory process perhaps collapse should be a child of axon guidance; being part of the process of axon guidance. (Rachael) PMID 17062560 to describe retinal growth cone collapse.


Minutes: http://gowiki.tamu.edu/wiki/index.php/Category:RefGenome_Electronic_Jamboree_2010-02_SLIT2#Minutes

NIPBL annotation

Chair: Emily Dimmer

Minutes: Dianna Fisk

ppod page

Reference Genome annotations are available at:

http://gowiki.tamu.edu/wiki/index.php/Category:RefGenome_Electronic_Jamboree_2010-02_NIPBL

Source Forge Requests

  • NTR: transcriptionally active chromatin binding [11]
  • NTR: long-range enhancer-promoter communication [12]
  • NTR: enhancer binding [13]
  • placement of Transcription cofactor activity [14]
  • NTR: abdominal wall muscle cell development [15]. This term was rejected as it was decided at the UK ref genome jamboree meeting (10/02/2010) that it should not have been requested based on the one patient study as reported in PMID 16957487.


Minutes: http://gowiki.tamu.edu/wiki/index.php/Category:RefGenome_Electronic_Jamboree_2010-02_NIPBL#Minutes