Review of trees-based annotations (Retired)

MSH family (Panther ID:11361)

Media:MSH_annotations_final.xls

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.

There are 2 types of annotations:

• 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 unique suggestions of 16 unique GO terms propagated to a total of 621 lines.

Problems detected and fixed through annotation of this family:

• GO:32300 "mismatch repair complex" was found to be a child of "nucleus" even though it is also found in bacteria. 32300 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."
• PMID 8492116 had annotations to "hypoxanthine phosphoribosyltransferase activity" and "purine nucleotide biosynthetic process" for mouse Msh2. Neither was shown in this paper. These annotations were removed.
• PMID 11005803 contained several annotations to human MSH3 and MSH6 which should have been attributed to PCNA instead. The 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