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

Protein Family Annotation To-Do Lists

We are working from two to-do lists right now:

1) The "finished" sets on the Source Forge Tracker.

2) Recent monthly target lists at Google docs.

Standard Operating Procedures for annotating in PAINT

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 (emailed relevant curators March 18)
  • ask E. coli to possibly add experimental annotation based on PubMed: 12351653 (emailed Debby March 18)

Software Developer testing checklist prior to releasing PAINT

  1. Collapse a node
    1. Collapsing a node selects the node, and the selection is shown by a faint highlight
  2. "re-root to node"
  3. "output seq id's for leaves"# Edit --> Find... --> Search text
  4. Tree --> Scale...
  5. Tree --> Reset root to main
  6. Default sort order for GO terms is (1) by ontology and (2) by GOid.
  7. After selecting term and clicking "Propagate" button, term moves to top of list.

Code and Trackers

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