Difference between revisions of "Electronic jamboree oct-2008 (Archived)"

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[[Category:Reference Genome]][[Category:Archived]]
 
==Planning of the day==
 
==Planning of the day==
  
 
* On Thursday (or before!), US people can start looking at annotations for chosen gene sets
 
* On Thursday (or before!), US people can start looking at annotations for chosen gene sets
* UK people will meet at 9;30
+
* UK people will meet at 9:30
* 3pm BST/10 am eastern/7 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.
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* 4pm BST/11 am eastern/8 am pacific to 6pm BST/1pm eastern/10 am pacific <br>
* 5pm/12 eastern/9 am pacific - west coast (PTZ) will join phone conference until 6 pm
+
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/Electronic_Jamboree http://gowiki.tamu.edu/wiki/index.php/Electronic_Jamboree]
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* annotations are to be temporarily stored in the GOnuts wiki:  
(Is the URL still valid??) 
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[http://gowiki.tamu.edu/wiki/index.php/Category:Refgenome_Electronic_Jamborees http://gowiki.tamu.edu/wiki/index.php/Category:Refgenome_Electronic_Jamborees]
The above URL is for the July electronic jamboree.  I'll make a new page for the October Electronic Jamboree and past the URL here:
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----
  
http://gowiki.tamu.edu/wiki/index.php/Electronic_Jamboree_Oct_2008
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=== 4 PM BST/11 AM eastern/8 AM pacific - NEDD4 annotation===
 +
http://gowiki.tamu.edu/wiki/index.php/RefGenome_Electronic_Jamboree_2008-10_NEDD4
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[http://gowiki.tamu.edu/wiki/index.php/Talk:RefGenome_Electronic_Jamboree_2008-10_NEDD4#Issues GONUTs talk page]
 +
----
 +
 
 +
=== 5 PM BST/12 AM eastern/9 AM pacific - PFKL annotation ===
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 +
http://gowiki.tamu.edu/wiki/index.php/RefGenome_Electronic_Jamboree_2008-10_PFKL
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 +
[http://gowiki.tamu.edu/wiki/index.php/RefGenome_Electronic_Jamboree_2008-10_PFKL GONUTs talk page]
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 +
==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
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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)
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6-phosphofructokinase, liver type
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Catalyses; ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6- bisphosphate
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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==
 
==Suggested genes==
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6-phosphofructokinase, liver type
 
6-phosphofructokinase, liver type
 
Catalyses; ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6- bisphosphate
 
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)
 +
  
From the PPOD clusters it looks like there are orthologs for all species. (Rachael, GOA)
 
  
 
'''ADD3''' (UniProtKB:Q9UEY8; OMIM:601568)
 
'''ADD3''' (UniProtKB:Q9UEY8; OMIM:601568)
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(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 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.)
+
(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)
 
'''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
 
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)
 
'''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
 
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)
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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.
  
 
Return to [[Reference_Genome_Annotation_Project]]
 
Return to [[Reference_Genome_Annotation_Project]]

Latest revision as of 08:47, 16 January 2018

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.

Return to Reference_Genome_Annotation_Project