4. miRNA target gene list
Gene8
Gene7
Gene6
Gene5
Gene4
Gene3
Gene2
Gene1
simple seed match
(Virtual)
miRNA1 ○×○○○○××
miRNA2 ○×○○××○○
Prediction miRNA3 ×○○×○○××
miRNA4 ○○○×○○××
VS
Human lung cancer
Murine medulloblastoma
gene1 Murine ES cell
gene2 miRNA1
Real
gene3
4
5. Control Treated
Gather the information of miRNA targets
Compare the expressions of targets for each
miRNAs (see Next Slides)
Calculate False Discovery Rate
Generate ranking
5
6. MiRaG
miRNA Targets E Down Pvalue FDR
miRa 54 3 0.5 0.4
miRb 120 54 0.0001 0.005
miRc 36 1 0.5 0.7
... ... ... ... ...
miRX 60 18 0.001 0.007
Reject miRa & c because the FDR > 0.05
Filtrate with miRNA expression profiles
Ranking 6
15. selected by
miRNA miRNA expression / MiRaGE
miRNA P30<MB
1 mmu-miR-25 1 1
target gene P30>MB
2 m m u-m iR-466i-5p 1 1
3 mmu-miR-92a 0.75 1
4 mmu-miR-19a 1 0.69 miR17~92 cluster family
5 mmu-miR-19b 1 0.69 members are ranked in top 5
members
6 m m u-m iR-3082-5p 1 0.56 by combination of MiRaGE
7 m m u-m iR-130a 1 0.5 methods and miRNA
8 m m u-m iR-130b 1 0.5 expression profiling.
9 m m u-m iR-15b 1 0.5
10 m m u-m iR-2861 1 0.5
11 m m u-m iR-3096-5p 1 0.5
12 m m u-m iR-32 0.5 1
13 m m u-m iR-322 1 0.5
14 m m u-m iR-721 1 0.5
15 m m u-m iR-149* 0.5 0.88
16 m m u-m iR-3081* 1 0.38
17 m m u-m iR-574-5p 1 0.31
18 m m u-m iR-669n 0.5 0.81 suggested contribution to
15
19 m m u-m iR-1187 1 0.25
cancer formation
16. selected by
miRNA P30>MB
miRNA miRNA expression / MiRaGE
m m u-m iR-100 1 1
target gene P30<MB
m m u-m iR-126-3p 1 1
mmu-miR-29c 1 1 Some of the neuron
mmu-miR-376a 1 1 specific miRNAs and
specific miRNA
m m u-m iR-451 1 1 tumorsuppressive
m m u-m iR-99b 1 1 miRNAs seem to contribute
miRNAs
m m u-m iR-136* 1 0.9375
to the gene expression
m m u-m iR-299* 0.75 1
profiles of P30.
mmu-miR-26a 1 0.5
mmu-miR-26b 1 0.5
mmu-miR-29a 0.5 1
mmu-miR-7a-1* 1 0.5
m m u-m iR-3107 1 0.4375
m m u-m iR-340-5p 1 0.3125
m m u-m iR-369-5p 1 0.3125
mmu-let-7a 1 0.25
tumorsuppressive miRNAs
mmu-let-7e 1 0.25
mmu-let-7g 1 0.25 neuronspecific miRNAs
16
mmu-let-7i 1 0.25
17. selected by
miRNA miRNA expression / MiRaGE
miRNA P30<P6
1 mmu-miR-106b 1.00 1.00
target gene P30>P6
2 m m u-m iR-130a 1.00 1.00
3 m m u-m iR-130b 1.00 1.00
4 m m u-m iR-15b 1.00 1.00 miR17~92, mir106b
5 mmu-miR-17 1.00 1.00 25,mir106a363
6 mmu-miR-20a 1.00 1.00 cluster family members are
7 mmu-miR-20b 1.00 1.00 ranked in top 5 by
8 m m u-m iR-301b 1.00 1.00 combination of MiRaGE
9 m m u-m iR-322 1.00 1.00 methods and miRNA
10 m m u-m iR-721 1.00 1.00 expression profiling.
11 mmu-miR-93 1.00 1.00
12 m m u-m iR-542-3p 1.00 0.94
13 m m u-m iR-3081* 1.00 0.88
14 m m u-m iR-335-3p 1.00 0.88
15 m m u-m iR-199a-5p 1.00 0.81
16 m m u-m iR-199b* 1.00 0.81
17 mmu-miR-19a 1.00 0.81
17
18 mmu-miR-1 9 b 1.00 0.81
18. selected by
miRNA miRNA expression / MiRaGE miRNA P30>P6
m m u-m iR-29c 1.00 1.00 target gene P30<P6
mmu-miR-376a 1.00 1.00
m m u-m iR-451 1.00 1.00
Some of the neuron
mmu-let-7b 1.00 0.94
specific miRNAs and
specific miRNA
mmu-let-7e 1.00 0.94
tumorsuppressive
mmu-let-7g 1.00 0.94
miRNAs seem to contribute
miRNAs
mmu-let-7i 1.00 0.94
m m u-m iR-98 1.00 0.94
to the gene expression
profiles of P30.
m m u-m iR-126-3p 0.75 1.00
m m u-m iR-299* 0.75 1.00
m m u-m iR-29a 0.75 1.00
mmu-let-7a 0.75 0.94
m m u-m iR-3070b-3p 1.00 0.69
m m u-m iR-138 1.00 0.63
m m u-m iR-3107 1.00 0.56
m m u-m iR-181a-1* 0.50 1.00 tumorsuppressive miRNAs
mmu-let-7d 0.50 0.94
neuronspecific miRNAs
18
m m u-m iR-1937b 0.25 1.00
22. m iRNAs
m m u-m iR-200b
ratio
1.00
miRNA ES> Neuronal Cell
>
m m u-m iR-200c (+) 1.00 target gene ES< Neuronal Cell
<
m m u-m iR-23a 1.00
m m u-m iR-23b 1.00
mmu-miR-291a-3p 1.00
mmu-miR-429 1.00
mmu-miR-294 0.98
mmu-miR-295 0.98
m m u-m iR-302a (+) 0.98
m m u-m iR-302b (+) 0.97
m m u-m iR-302d (+) 0.97
m m u-m iR-199a-5p 0.94
m m u-m iR-141 0.69
m m u-m iR-200a 0.69
m m u-m iR-409-3p 0.67
m m u-m iR-369-3p (+) 0.36
m m u-m iR-96 0.11
m m u-m iR-674 0.08
Mallanna, S.K., and Rizzino., A.(2010)
m m u-m iR-467b 0.06