Target categorization

How does ENCODE categorize targets based on GO annotation?

To assign appropriate categories to each human, mouse, fruit fly or worm target, we first check GO annotations of the target's corresponding gene. See the glossary for definitions of each category used by ENCODE. For each GO term annotation, we cross reference each GO term annotation and its parental term with the GO terms in the following table:

ENCODE Label	GO Term ID	GO Term Name
TF	GO:0003700	DNA-binding transcription factor activity
RBP	GO:0003723	RNA binding
RBP	GO:0001070	RNA-binding transcription regulator activity
Cofactor	GO:0008134	transcription factor binding
Cofactor	GO:0003712	transcription coregulator activity
RNAP	GO:0005736	RNA polymerase I complex
RNAP	GO:0016591	RNA polymerase II, holoenzyme
RNAP	GO:0005666	RNA polymerase III complex
Chromatin remodeler	GO:0006325	chromatin organization
Chromatin remodeler	GO:0000118	histone deacetylase complex
Cohesin	GO:0007062	sister chromatid cohesion
DNA replication	GO:0006260	DNA replication
DNA repair	GO:0006281	DNA repair
histone	GO:0000788	nuclear nucleosome
TF**	GO:0003677	DNA binding
TF**	GO:0003682	chromatin binding
TF**	GO:0043167	ion binding
TF**: only used when there is no other data

Next we assign a score to each label based on the annotation evidence of the GO term:

Evidence code	Score
EXP	2
IDA	2
IMP	2
IGI	2
IEP	2
HTP	1
HDA	1
HMP	1
HGI	1
HEP	1
TAS	1
IEA	-1

 

Finally, we summarize labels and scores for the target by combining/summing same labels together. The label(s) having the highest score are used as the category assigned to the target.