PAINT annotation guidelines: Difference between revisions
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In old version of PAINT, this is BookPTHR22573. | In old version of PAINT, this is BookPTHR22573. | ||
Human protein UniProtKB:P00492, HPRT1, a hypoxanthine guanine phosphoribosyltransferase | 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 | 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: | ||
==== 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. | ||
Revision as of 15:37, 16 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.
HPRT Family done by Kara
Based on SourceForge 1893061 and 1893082, looking at UniProtKB:P00492 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:
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.
- [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.
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
bottom fly protein has exp. annotation for function as well: can we transfer to everything except the NOT section???
Suggestions for MOD annotators:
- ask E. coli to possibly add experimental annotation based on PubMed: 12351653
Code and Trackers
- PAINT: Getting the Source Code
- [ https://sourceforge.net/tracker2/?group_id=184610&atid=1126622 Bug Tracker]
- [ https://sourceforge.net/tracker2/?group_id=184610&atid=1126623 Feature Tracker]
- Browse PAINT code in SourceForge SVN repository
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