Table 5

Comparison of several computational methods for target gene prediction

ROC AUC


Number of target genes

HIS+PSSM

HIS alone

PSSM alone (FIMO)

Cluster-Buster

MCAST

EEL

Stubb


ABF1

549

0.830

0.736

0.781

0.776

0.676

0.807

0.893

FHL1

207

0.957

0.963

0.827

0.855

0.874

0.852

0.887

FKH1

284

0.656

0.625

0.606

0.680

0.546

0.661

0.725

FKH2

216

0.723

0.694

0.664

0.698

0.566

0.688

0.735

HAP1

215

0.738

0.711

0.635

0.675

0.624

0.676

0.663

RAP1

408

0.865

0.818

0.805

0.752

0.774

0.802

0.811

REB1

278

0.773

0.623

0.774

0.727

0.818

0.765

0.758

SWI4

252

0.831

0.790

0.634

0.680

0.626

0.664

0.651

SWI6

230

0.809

0.768

0.719

0.720

0.629

0.742

0.665

UME6

298

0.854

0.767

0.831

0.774

0.783

0.814

0.815


HIS, histone modification-based method.

Cheng et al. Genome Biology 2011 12:R111   doi:10.1186/gb-2011-12-11-r111

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