# molecular_function
20150327: Chordata_PTN001507663 has function RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)
20150327: root_PTN001507608 contributes to sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)
20150327: Bilateria_PTN000577900 has function RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)
20150327: root_PTN001507608 has function RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)
20150327: root_PTN001507608 contributes to sequence-specific DNA binding transcription factor activity (GO:0003700)
20150327: root_PTN001507608 has function sequence-specific DNA binding (GO:0043565)
20150327: root_PTN001507608 has function transcription regulatory region DNA binding (GO:0044212)
# cellular_component
20150327: root_PTN001507608 located in nucleus (GO:0005634)
# biological_process
20150327: Bilateria_PTN001507803 participates in myeloid cell differentiation (GO:0030099)
20150327: Bilateria_PTN001507803 participates in regulation of neurogenesis (GO:0050767)
20150327: Theria <Mammalia>_PTN000148113 participates in positive regulation of gene expression (GO:0010628)
20150327: Theria <Mammalia>_PTN001507751 participates in positive regulation of gene expression (GO:0010628)
20150327: Theria <Mammalia>_PTN001507751 participates in positive regulation of endothelial cell proliferation (GO:0001938)
20150327: Theria <Mammalia>_PTN001507751 participates in positive regulation of cellular component movement (GO:0051272)
20150327: Euteleostomi_PTN000578060 participates in regulation of inflammatory response (GO:0050727)
20150327: Euteleostomi_PTN000578060 participates in type 2 immune response (GO:0042092)
20150327: Euteleostomi_PTN000578060 participates in regulation of cell differentiation (GO:0045595)
20150327: Euteleostomi_PTN000578060 participates in regulation of cell proliferation (GO:0042127)
20150327: Chordata_PTN001507656 participates in negative regulation of cell differentiation (GO:0045596)
20150327: Chordata_PTN001507663 participates in negative regulation of transcription from RNA polymerase II promoter (GO:0000122)
20150327: Chordata_PTN001507663 participates in negative regulation of transcription, DNA-templated (GO:0045892)
20150327: Euteleostomi_PTN000578060 participates in neurogenesis (GO:0022008)
20150327: Euteleostomi_PTN000578396 participates in negative regulation of transcription, DNA-templated (GO:0045892)
20150327: Euteleostomi_PTN000578104 participates in negative regulation of transcription, DNA-templated (GO:0045892)
20150327: Bilateria_PTN001507803 participates in neurogenesis (GO:0022008)
20150327: Bilateria_PTN001507803 participates in negative regulation of transcription from RNA polymerase II promoter (GO:0000122)
20150327: Eumetazoa_PTN001145001 participates in negative regulation of transcription from RNA polymerase II promoter (GO:0000122)
20150327: Eumetazoa_PTN001145001 participates in neurogenesis (GO:0022008)
20150327: Eumetazoa_PTN001145116 participates in neurogenesis (GO:0022008)
20150327: Euteleostomi_PTN000578267 participates in negative regulation of G1/S transition of mitotic cell cycle by negative regulation of transcription from RNA polymerase II promoter (GO:1900477)
20150327: Bilateria_PTN000577900 participates in axon guidance (GO:0007411)
20150327: Bilateria_PTN000577900 participates in negative regulation of transcription, DNA-templated (GO:0045892)
20150327: root_PTN001507608 participates in regulation of transcription from RNA polymerase II promoter (GO:0006357)
# Notes
MAF: Most of the characterized proteins are transcription repressors. However, some are described as activators and many are not characterized, so I did not propagate the negative regulation to the root.


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).