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Table 2 A comparison of motif finding by the adjacency matrix approach and FANMOD

From: Transcription factor and microRNA-regulated network motifs for cancer and signal transduction networks

approach

motif

AML

Glioma

Melanoma

NSCLC

PC

RCC

Adjacency Matrix

FFL

0 §

0 §

0 §

1

1

1

 

bi-fan

1 §

1 §

1

1

0 §

0 §

FANMOD

FFL

0 §

0 §

0 §

0 (FN)

0 (FN)

0 (FN)

 

bi-fan

1 §

1 §

0 (FN)

0 (FN)

0 §

0 §

 

Non bi-fan

2(2)*

1(1)*

0(0)*

2(2)*

3(3)*

3(1)*

  1. §given a fixed motif size, the italic and underlined fonts denote the results uisng adjacency matrix approach are consistent with those of FANMON, i.e. true positive or true negative events
  2. * the first number denotes the number of identified motifs, the number inside the parenthesis denotes the total number of motif pattern found in the cancer type