ICIC2011

1. MiRaGE: Inference of gene expression
regulation via microRNA transfection II
Y­h. Taguchi/Dept.Phys.,Chuo Univ.
Jun Yasuda /School Med.,Tohoku Uinv.

2. MiRaGE:
MiRNA Ranking by Gene Expression
What is miRNA?
non­coding RNAs which bind to mRNAs
and cleavage them or disturb translation.

3. Regulation of gene expression via miRNA
Computer oriented prediction
(uncertain)
Target genes genome
microRNA mRNA
microRNA mRNA 3

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
gene1
gene2
miRNA1
Real
gene3
4

5. Concepts of MiRaGE method
Control Treated
All of
miRNAs' Gene
target Expression
Gather the information of miRNAs' targets
Compare the expressions of targets for each
miRNAs and check significance (see Next Slides)
Calculate False Discovery Rate
5
Generate ranking of each miRNA

6. Computation of significance
miRNA Targets Down P­value FDR
miR­a 54 3 0.5 0.4
1st miR­b 120 54 0.0001 0.005
miR­c 36 1 0.5 0.7
... ... ... ... ...
2nd miR­X 60 18 0.001 0.007
Reject miR­a & c because the FDR > 0.05
Ranking 6

7. Application
Inference of transfection of miRNA to human
lung cancer cell

8. Gene expression by
Array: Agilent
at
One and three days
after transfection of
Mir­107, mir­185, and let­7a.
log(xg[miRNA]) vs log(xg[Control])
xg: gene expression
Target gene list: simple seed match
ICIC2011, LNBI in press. (2011/8/11­14)

9. Transfected miRNA
mir­107 mir­185 let­7a
time replicate 1 replicate 2 replicate 1 replicate 2 replicate 1 replicate 2
day1 1[1st] 1[1st] 7[1st] 9[1st] 2[1st] 2[1st]
day3 1[1st] 0[­­­] 0[1st] 0[­­­] 1[1st] 1[1st]
Numbers of significant miRNAs.
The ranks of transfected micriRNAs are shown in
square brackets.
Transfected miRNAs are
correctly identified by MiRaGE
method.

10. Conclusion
MiRaGE method can correctly infer
regulation of miRNA vis target mRNA
expression.
The application is now planed...

11. Web Server
http://granular.com/MiRaGE/
now available
Data base
http://granular.com/MiRaGEDB/
Collection of results by MiRaGE to GEO
(Gene expression Omnibus)
coming soon...