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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: 3639631144365536139878187
Input format: FASTA format
TF1 name: E2f4
TF2 name: E2f6
TF1 input file: K562_E2f4_not_E2f6.fa
TF2 input file: K562_E2f6_not_E2f4.fa
Limited to: 300 sequences per class
Feature type: PWM data
Feature set: PWM-UNIPROBE-SELEX-JASPARv
Command line:
couger -tf1 E2f4 -tf2 E2f6 -f1 K562_E2f4_not_E2f6.fa -f2 K562_E2f6_not_E2f4.fa -fa -pwm PWM-UNIPROBE-SELEX-JASPARv -o results/3639631144365536139878187 -l 300
Output link: http://couger.oit.duke.edu/results/3639631144365536139878187

Download:

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



PLOT E2f4 E2f6 - 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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