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.