PAINT annotation guidelines: Difference between revisions

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=== HPRT Family done by Kara ===
=== HPRT Family done by Kara ===
Based on SourceForge 1893061 and 1893082, looking at UniProtKB:P00492
Coming in via human protein UniProtKB:P00492, HPRT1, a hypoxanthine guanine phosphoribosyltransferase.
In old version of PAINT, this is BookPTHR22573.
See SourceForge 1893061 and 1893082, in old version of PAINT, this is BookPTHR22573.
Human protein UniProtKB:P00492, HPRT1, a hypoxanthine guanine phosphoribosyltransferase
 
Panther family large and with this PAINT version could not easily get to GO annotations, so used PPOD to look at more managable chunks of the larger Panther family:
General notes: The Panther family is very large and with this old PAINT version could not easily get to GO annotations, so used PPOD to look at more managable chunks of the larger Panther family:


==== Molecular Function ====
==== Molecular Function ====
* [[http://ppod.princeton.edu/cgi-bin/ppod.cgi/j04/Jaccard1673 PPOD Jaccard1673]]: not enough experimental annotations (only human protein UniProtKB:P00492 had exp. ann.) in this subsection of the big PANTHER family, so could not do transfer.
* [[http://ppod.princeton.edu/cgi-bin/ppod.cgi/j04/Jaccard1673 PPOD Jaccard1673]]: not enough experimental annotations (only human protein UniProtKB:P00492 had exp. ann.) in this subsection of the big PANTHER family, so could not do transfer.


* [[http://ppod.princeton.edu/cgi-bin/ppod.cgi/j04/Jaccard548 PPOD Jaccard548]]: in the top half of the graph, PGM1 and PGM2 in cerevisiae have experimental annotations.  Mouse has experimental as well; however, mouse PGM5 has a NOT annotation while mouse PGM2 has a positive annotation. Other organisms checked do not have experimental annotation.
* [[http://ppod.princeton.edu/cgi-bin/ppod.cgi/j04/Jaccard548 PPOD Jaccard548]]:  


cerevisiae PGM3 part of graph: cerevisiae PGM3 has exp. annotation.  Mouse Pgm1 has annotation as well.  Could transfer to worm, pombe, dicty, drosophila, rat, human, chicken, fish based on common ancestor
The three cervevisiae proteins, PGM1, PGM2, and PGM3, the mouse proteins PGM1 and PGM2, and the fly protein Pgm (last one on the graph) all have experimental annotations to phosphoglucomutase activity.  However, the mouse PGM5 has a NOT annotation to this activity and the human also has a NOT (but also a positive annotation(!)).


bottom fly protein has exp. annotation for function as well: can we transfer to everything except the NOT section???
Propagation proposal:
Propagate to all proteins except for the clade with the NOT annotations (mouse and human PGM5) and the three C. elegans proteins that are part of an outgroup (top of graph).  Pending info from MOD curators (see below), we might propagate that NOT to the rat proteins in that clade as well.


Suggestions for MOD annotators:
Suggestions for MOD annotators:
* ask about human NOT, ISO from NAS


* ask E. coli to possibly add experimental annotation based on PubMed: 12351653
* ask E. coli to possibly add experimental annotation based on PubMed: 12351653

Revision as of 14:55, 17 March 2009

PAINT

A central repository for PAINT developer info, announcements, and technical information.

Temporary SOP while awaiting PAINT release

We can stash notes here on how we annotate the first few trees to come up with an SOP. General SOP:

1) examine existing MOD annotations, in particular experimental annotations, in context of evolutionary trees.

2) if necessary, contact MOD curators about questions, suggestions for additions, etc.

3) determine annotations that can be propagated. Send each MOD a GAF of proposed annotations, with a suggestion for incorporation within two weeks.

MSH Family done by Mike

HPRT Family done by Kara

Coming in via human protein UniProtKB:P00492, HPRT1, a hypoxanthine guanine phosphoribosyltransferase. See SourceForge 1893061 and 1893082, in old version of PAINT, this is BookPTHR22573.

General notes: The Panther family is very large and with this old PAINT version could not easily get to GO annotations, so used PPOD to look at more managable chunks of the larger Panther family:

Molecular Function

  • [PPOD Jaccard1673]: not enough experimental annotations (only human protein UniProtKB:P00492 had exp. ann.) in this subsection of the big PANTHER family, so could not do transfer.

The three cervevisiae proteins, PGM1, PGM2, and PGM3, the mouse proteins PGM1 and PGM2, and the fly protein Pgm (last one on the graph) all have experimental annotations to phosphoglucomutase activity. However, the mouse PGM5 has a NOT annotation to this activity and the human also has a NOT (but also a positive annotation(!)).

Propagation proposal: Propagate to all proteins except for the clade with the NOT annotations (mouse and human PGM5) and the three C. elegans proteins that are part of an outgroup (top of graph). Pending info from MOD curators (see below), we might propagate that NOT to the rat proteins in that clade as well.

Suggestions for MOD annotators:

  • ask about human NOT, ISO from NAS
  • ask E. coli to possibly add experimental annotation based on PubMed: 12351653

Code and Trackers

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