# molecular_function
20140508: DROME_Unc-89 lost/modified myosin light chain kinase activity (GO:0004687) capacity
20140508: DROME_Unc-89 lost/modified calmodulin-dependent protein kinase activity (GO:0004683) capacity
20140306: Has function actin filament binding (GO:0051015) in Bilateria_PTN001491415
20140306: Has function myosin light chain kinase activity (GO:0004687) in Bilateria_PTN000539674
20140306: Has function calmodulin-dependent protein kinase activity (GO:0004683) in Eukaryota_PTN000539670
# cellular_component
20140306: Has function Z disc (GO:0030018) in Bilateria_PTN001491415
# biological_process
20140508: DROME_Unc-89 lost/modified actin filament organization (GO:0007015) capacity
20140508: Euteleostomi_PTN001491431 lost/modified regulation of apoptotic process (GO:0042981) capacity
20140508: Bilateria_PTN001491426 lost/modified regulation of apoptotic process (GO:0042981) capacity
20140508: Bilateria_PTN001491415 lost/modified regulation of apoptotic process (GO:0042981) capacity
20140306: Has function cardiac muscle fiber development (GO:0048739) in Bilateria_PTN001491415
20140306: Has function regulation of cytoskeleton organization (GO:0051493) in Bilateria_PTN001491415
20140306: Has function regulation of cell migration (GO:0030334) in Bilateria_PTN001491415
20140306: Has function regulation of apoptotic process (GO:0042981) in Eumetazoa_PTN001121516
20140306: Has function positive regulation of cell migration (GO:0030335) in Euteleostomi_PTN000539684
20140306: Has function smooth muscle contraction (GO:0006939) in Euteleostomi_PTN000539684
20140306: Has function actin filament organization (GO:0007015) in Bilateria_PTN000539674
# Notes
-Annotated MYLK clade (Bilateria_PTN001491415) to regulation of cell migration (GO:0030334) rather than cell motility because the evidence for the Zebrafish paper describes cell migration (athough they use cell motitity in the text as well). 
- Annotated Bilateria_PTN000539674 to actin filament organization (GO:0007015) and myosin light chain kinase activity (GO:0004687) because those two annotations support each other. 


*ISSUES*
- Cannot propagate autophagy: not annotated in the DAPK clade, and the only annotated protein is a fly protein but annotating to a common ancestor would lead to annotating the entire tree. 
- DAPK2 is downstream from TOR (see PMID: 21690574); the GO term 'TOR signaling' does not exactly describe this. 
- Proteins with roles in muscle function (Drosophila sqa; human NEXN) are too distant to be used for annotating ancestors. 

PG 2014-05-08


Annotation inferences using phylogenetic trees

The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).