Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples

Table 1 Comparison of methods on ENCODE-DREAM challenge test set

Biosample	iPSC	PC-3	Liver	Liver	Liver	Liver	Liver	Liver	Liver
Assay	CTCF	CTCF	EGR1	FOXA1	GABPA	JUND	MAX	REST	TAF1
Method
Yuanfang Guan	0.729	0.600	0.397	0.282	0.353	0.533	0.441	0.319	0.281
dxquang	0.866	0.783	0.274	0.400	0.347	0.260	0.330	0.312	0.264
autosome.ru	0.778	0.486	0.331	0.243	0.342	0.416	0.384	0.264	0.221
J-TEAM	0.812	0.747	0.363	0.462	0.344	0.415	0.377	0.196	0.272
Avocado	0.723	0.791	0.530	0.354	0.396	0.660	0.574	0.477	0.384
Similar biosample	–	–	0.363	0.389	0.226	0.568	0.446	0.408	–
Same biosample	0.741	0.878	0.648	0.716	0.573	0.731	0.622	0.622	0.556
Average activity	0.574	0.735	0.240	0.299	0.253	0.223	0.349	0.124	0.140

The average precision (AP) computed across nine epigenomic experiments in the ENCODE-DREAM challenge test set in chromosome 21. For each track, the score for the best-performing predictive model is in boldface

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