Table 1

Results of comparisons of each method's performance

Method

<a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M13','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M13">View MathML</a>

<a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M14','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M14">View MathML</a>

<a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M15','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M15">View MathML</a>

<a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M16','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M16">View MathML</a>

<a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M17','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M17">View MathML</a>


1. two-way AIC

0.58578

0.99998

2.721 × 10-5

5.71280

0.10295

2. t-rank/F -test

0.58477

0.99821

7.901 × 10-3

245

4.41521

3. RankProducts

0.58597

0.99717

1.123 × 10-2

312

5.62263

4. SAM

0.58690

0.99983

9.034 × 10-4

96

1.73004

5. U -value (gene side)

0.65665

0.68416

2.085 × 10-1

54.49481

0.98206

6. U -value (experiment side)

0.75034

0.99967

5.325 × 10-4

23.91349

0.43095

7. 2-σ

0.65270

0.99871

5.202 × 10-3

74.96886

1.35103

8. 3-σ

0.65488

0.99990

4.030 × 10-4

17.01730

0.30667


We assess the performance of all methods by calculating <a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M18','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M18">View MathML</a> (average sensitivity of detection of gene pairs in all operons), <a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M19','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M19">View MathML</a> (average specificity of detection of gene pairs in all operons), <a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M20','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M20">View MathML</a> (average p-values of detection of gene pairs in all operons), <a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M21','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M21">View MathML</a> (number of DEGs), and <a onClick="popup('http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M22','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/14/S2/S9/mathml/M22">View MathML</a> (the percentage of DEGs). Threshold of t-rank/F-test, RankProducts and SAM is set to 245, 312 and 96 to match the sensitivity with that of two-way AIC.

Tsuyuzaki et al. BMC Genomics 2013 14(Suppl 2):S9   doi:10.1186/1471-2164-14-S2-S9

Open Data