Table 1

Overlap between predicted miR-125a target genes and genes significantly altered in GK compared to BN rats in adipose tissue and in liver.

miRanda

PicTar

TargetScan

>1 Algorithm


Predicted miR-125a target genes

975

350

165

152

Number genes tested

536

231

94

114


Overlap

FDR

Overlap

FDR

Overlap

FDR

Overlap

FDR


Liver up-regulated (95 genes)

5

0.074

1

0.63

1

0.33

1

0.40

Liver down-regulated (138 genes)

5

0.248

2

0.43

0

1.00

0

1.00

Adipose up-regulated (477 genes)

21

0.006

5

0.57

1

0.87

3

0.46

Adipose down-regulated (598 genes)

22

0.036

7

0.44

1

0.92

0

1.00


The number of predicted miR-125a target genes found among the significantly up- and down-regulated genes in each tissue is shown for each algorithm and for the subset of targets predicted by more than one algorithm. In each case, the significance of the overlap (estimated false discovery rate) is calculated as the proportion of 10,000 random sets of non-miR-125 target genes of the same size showing equal or greater overlap.

Herrera et al. BMC Medical Genomics 2009 2:54   doi:10.1186/1755-8794-2-54

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