Review of trees-based annotations (Retired): Difference between revisions

From GO Wiki
Jump to navigation Jump to search
No edit summary
mNo edit summary
 
(70 intermediate revisions by 5 users not shown)
Line 1: Line 1:
== MSH family ([[Panther ID:11361]])==
[[Category:PAINT Archived]]
[[Media:MSH_annotations_final.xls]]
This is the central site for viewing/reviewing the tree based annotations done via PAINT.


This is a GAF file containing suggested annotations for the MSH6 family of proteins (PTHR11361) produced by protein family annotators using the PANTHER method, June 2009.  It is an Excel worksheet with Autofilter turned on and the splitscreen frozen to show a header row.
== Families ready for or under review by MODs ==


There are 2 types of annotations:
Coming soon
*Up-propagation (in boldface): Annotations to hypothetical ancestral proteins showing a consensus parental GOID (column E) and the proteins on which these annotations are based (column H).
*Down-propagation (in plaintext, following the corresponding up-propagation): Annotations to real proteins based on their descent from the hypothetical ancestors (column H).
This file contains suggested annotations for '''all RefGenome organisms except E. coli.'''  There are 37 up-propagations and 584 down-propagations spanning 16 unique GO terms.


Problems detected and fixed through annotation of this family:
== Families ready for review by 2nd set of PAINT curators ==
*GO:32300 "mismatch repair complex" was found to be a child of "nucleus" even though it is also found in bacteria32300 was moved to be a child of "intracellular part (GO:44424).
 
*Mouse Msh2 had an annotation to GO:6928 "cell motion," but it was a typo and should have been GO:6298 "mismatch repair."
All GAF files can be found in following directory under gocvs/:
*PMID 8492116 had annotations to "hypoxanthine phosphoribosyltransferase activity" and "purine nucleotide biosynthetic process" for mouse Msh2Neither was shown in this paperThese annotations were removed.
 
*PMID 11005803 contained several annotations to human MSH3 and MSH6 which should have been attributed to PCNA insteadThe following annotations were removed from MSH3 and MSH6 and added to PCNA:
????
**GO:0032139 dinucleotide insertion or deletion binding IMP (and changed to IDA)
 
**GO:0000701  purine-specific mismatch base pair DNA N-glycosylase activity IMP (and changed to IDA)
 
**GO:0006298  mismatch repair  IDA
Notes for each family can be found on the following wiki pages:
 
* CPS1 Family: [[Panther ID:11014]], done by Mike Livstone, Done July 2009
 
* ACHE family :[[Panther ID:11559]], Mike LivstoneDone August 4, 2009.
 
* FOXE1/Forkhead/Forkhead box family: [[Panther ID:11829]], Kara Dolinski. Done 21-Aug-2009
 
* Dicer family: [[PANTHER14950]], Mike Livstone. Completed 8/26/09.
 
* Striatin family: [[PANTHER15653]], Mike Livstone. Completed 10/22/09.
 
* RDH10 family: [[PTHR24316]], Mike LivstoneCompleted 3/22/10LUNG TARGET.
 
* LONP1, LONP2: [[Panther ID:10046]], Kara Dolinski. Feb. 2009 jamboreeDone July 2009
 
* HPRT Phosphoglucomutase family: [[Panther ID:22573]], Kara Dolinski. Done July 2009
 
* MVD Family: [[PANTHER10977]], done by Kara
 
== PENDING ==
 
 
 
 
 
* MSH family : [[Panther ID:11361]], Mike Livstone. Done July 2009.
 
* GRIN1 family : [[Panther ID:18966]], Mike Livstone.  Done July 2009.
 
* PSEN2 family: [[Panther ID:10202]], Mike Livstone.  Done ~8/17/09.
 
*[[PANTHER17602]]: RRS1 family, Mike Livstone. Completed 8/24/09.  No annotations inferred. //
** Modification: can annotate to nucleolus based on pombe, human annotations. Pascale Gaudet 12/15/2009
 
 
'''Families based on recent Ref Genome gene targets:'''
 
July Targets
 
*[[PANTHER14950]]: Mike
 
*[[PANTHER17602]]: Mike
 
 
* TPP1(CLN2) family : [[Panther ID:14218]], Pascale Gaudet. Done for now (no GAF file- can only propagate in mammals) PG 14-Jul-2009
 
== TO-DO LIST (based on monthly Reference Genome gene targets) ==
 
Lung development targets
(coming soon)
 
July
*[[PANTHER11544]]: Mike
*[[PANTHER10314]]: Kara
*[[PANTHER10146]]: Kara
*[[PANTHER12732]]
*[[PANTHER10010]]
 
August
*[[PTHR12383]]
*[[PTHR11679]]
*[[PTHR11200]]
 
== DONE: incorporated into the MODs ==

Latest revision as of 10:37, 12 April 2019

This is the central site for viewing/reviewing the tree based annotations done via PAINT.

Families ready for or under review by MODs

Coming soon

Families ready for review by 2nd set of PAINT curators

All GAF files can be found in following directory under gocvs/:

????


Notes for each family can be found on the following wiki pages:

  • FOXE1/Forkhead/Forkhead box family: Panther ID:11829, Kara Dolinski. Done 21-Aug-2009
  • Dicer family: PANTHER14950, Mike Livstone. Completed 8/26/09.
  • Striatin family: PANTHER15653, Mike Livstone. Completed 10/22/09.
  • RDH10 family: PTHR24316, Mike Livstone. Completed 3/22/10. LUNG TARGET.
  • LONP1, LONP2: Panther ID:10046, Kara Dolinski. Feb. 2009 jamboree. Done July 2009

PENDING

  • PANTHER17602: RRS1 family, Mike Livstone. Completed 8/24/09. No annotations inferred. //
    • Modification: can annotate to nucleolus based on pombe, human annotations. Pascale Gaudet 12/15/2009


Families based on recent Ref Genome gene targets:

July Targets


  • TPP1(CLN2) family : Panther ID:14218, Pascale Gaudet. Done for now (no GAF file- can only propagate in mammals) PG 14-Jul-2009

TO-DO LIST (based on monthly Reference Genome gene targets)

Lung development targets (coming soon)

July

August

DONE: incorporated into the MODs