If you use COUGER in your research, please cite:

Munteanu A, Ohler U, Gordân R (2014) “COUGER - co-factors associated with uniquely-bound genomic regions.” Nucleic Acids Research, Vol. 12, Web Server issue, W461-W467. doi: 10.1093/nar/gku435

Munteanu A, Gordân R (2013) “Distinguishing between genomic regions bound by paralogous transcription factors.” Research in Computational Molecular Biology 2013 (RECOMB13). 7821:145.

Job details:

Job ID: 5183779317939197157119215
Input format: FASTA format
TF1 name: c-Myc
TF2 name: Mxi1
TF1 input file: K562_Cmyc_not_Mxi1.fa
TF2 input file: K562_Mxi1_not_Cmyc.fa
Limited to: 300 sequences per class
Feature type: PWM data
Command line:
couger -tf1 c-Myc -tf2 Mxi1 -f1 K562_Cmyc_not_Mxi1.fa -f2 K562_Mxi1_not_Cmyc.fa -fa -pwm PWM-UNIPROBE-SELEX-JASPARv -o results/5183779317939197157119215 -l 300
Output link:


The full analysis (including the input files) can be downloaded as a zip file from here.

PLOT c-Myc Mxi1 - Results from 5 runs

(5-fold Cross-Validation; with embedded cross-validation at each step)

Median accuracies (over 5 runs)
Boxplots of accuracy
(over 5 runs)
Feature heatmaps
Accuracies for individual runs
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