Electronic jamboree oct-2008 (Archived)

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Planning of the day

  • On Thursday (or before!), US people can start looking at annotations for chosen gene sets
  • UK people will meet at 9:30
  • 4pm BST/11 am eastern/8 am pacific to 6pm BST/1pm eastern/10 am pacific

Conference call using webex and phone conference - link up with US on eastern and central time. discuss annotation issues that have arisen, go round the groups to find out if any species have found any interesting differences in their annotation set.

  • annotations are to be temporarily stored in the GOnuts wiki:

http://gowiki.tamu.edu/wiki/index.php/Category:Refgenome_Electronic_Jamborees


4 PM BST/11 AM eastern/8 AM pacific - NEDD4 annotation

http://gowiki.tamu.edu/wiki/index.php/RefGenome_Electronic_Jamboree_2008-10_NEDD4

GONUTs talk page


5 PM BST/12 AM eastern/9 AM pacific - PFKL annotation

http://gowiki.tamu.edu/wiki/index.php/RefGenome_Electronic_Jamboree_2008-10_PFKL

GONUTs talk page

Selected genes

Nedd4 yeast http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO0/ORTHOMCL2003 (Stacia, SGD)

  • hits in worm, Danio, Drosophila, chicken, human (WWP1), Mus, Rattus, Saccharomyces, pombe

NEDD4 human http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO0/ORTHOMCL4386 a human HECT E3 that is involved in a congenital human hypertensive disorder known as Liddle syndrome

  • hits in worm, Danio, Drosophila, chicken, human, Mus, Rattus, but

not Saccharomyces, pombe and E.coli.


PFKL (UniProtKB:P17858; OMIM:171860) 6-phosphofructokinase, liver type Catalyses; ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6- bisphosphate http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO0/ORTHOMCL450

  • hits in worm, zebrafish, E.coli, Drosophila, chicken, human, Mus, Rattus, Saccharomyces, pombe

Suggested genes

Please list your name and a small justification for selecting the gene.

PFKL (UniProtKB:P17858; OMIM:171860) 6-phosphofructokinase, liver type Catalyses; ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6- bisphosphate http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO0/ORTHOMCL450

  • hits in worm, zebrafish, E.coli, Drosophila, chicken, human, Mus, Rattus, Saccharomyces, pombe

From the PPOD clusters it looks like there are orthologs for all species. (Rachael, GOA)


ADD3 (UniProtKB:Q9UEY8; OMIM:601568) Gamma adducin Membrane-cytoskeleton-associated protein that promotes the assembly of the spectrin-actin network. Binds to calmodulin.

Orthologs in mouse, rat, chicken, zebrafish, Drosophila (from HCOP) and is also in the conserved Hs-E.coli list. (Rachael, GOA).

(Note from Eurie, SGD:PPOD does not list a S. cerevisiae gene for ADD3. Am looking for suggestions but PPOD doesn't not list very many from the HS-E.coli list.)

(Note from Debby: I can't access the conserved HS-E.coli spreadsheet, so I can't double check what is written there, but I can't find an E. coli ortholog for ADD3. E. coli does have a gene named add, but it codes for an adenosine deaminase. The human ortholog is UniProtKB:P00813.)

COX18 http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO0/ORTHOMCL5423 (Stacia, SGD) conserved from E.coli to human, but i don't see E.coli in the PPOD results

  • hits in worm, Drosophila, chicken, human, Mus, Rattus, Saccharomyces, pombe

Nedd4 http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO0/ORTHOMCL2003 (Stacia, SGD) a human HECT E3 that is involved in a congenital human hypertensive disorder known as Liddle syndrome

  • hits in worm, Danio, Drosophila, chicken, human, Mus, Rattus, Saccharomyces, pombe

PI4K2B http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO0/ORTHOMCL1986 (Stacia, SGD) Phosphatidylinositol 4-kinase type 2-beta

  • hits in worm, Danio, Drosophila, chicken, human, Mus, Rattus, Saccharomyces, pombe

PIK4CB http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO0/ORTHOMCL2133 (Stacia, SGD) Phosphatidylinositol 4-kinase beta

  • hits in Arabidopsis, worm, Danio, Dicty, Drosophila, chicken, human, Mus, Rattus, Saccharomyces, pombe

PIK4CA http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO0/ORTHOMCL3102 (Stacia, SGD) Phosphatidylinositol 4-kinase alpha

  • hits in Arabidopsis, worm, Dicty, Drosophila, chicken, human, Mus, Rattus, Saccharomyces, and pombe

Phosphatidylinositol 4-kinases (ATP:phosphatidylinositol-4-phosphotransferase, EC 2.7.1.67) are evolutionarily conserved enzymes that catalyze the formation of phosphatidylinositol 4-phosphate and ADP from phosphatidylinositol (PtdIns or PI) and ATP, the first step in the synthesis of phosphatidylinositol phosphates.

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