Pathway Finding by Reverse Engineering Based on Simulation

1

Pathway Finding by Reverse Engineering Based on

Simulation

C.Y. TangDepartment of Computer

ScienceNTHU

2

Reverse Engineering (Computer Aided

Engineering)

VLSI CADCommunication ProtocolBio-X ?

3

Protocol ImplementationCorret Spec. & Documentation

coding & debugging

test generation

code generation

pass?

Diagnostics

Error Reports

Product

Interoperability Testing

Program code test suite

Conformance Testing

test env. Yes

No

YesNo

Standard

Error Reports

Validation Model

SDLFormal Spec.

Read & Formal Specify

add assertions

Validate

pass?

4

Key IssuesFormal SpecificationRelationship Exploring

5

Bolouri, H., and Davidson, E. H. (2002). Modeling DNA sequence-based cis-regulatory gene networks. Dev. Biol. 246, 2–13. Brown, C. T., Rust, A. G., Clarke, P. J. C., Pan, Z., Schilstra, M. J., De Buysscher, T., Griffin, G., Wold, B. J., Cameron, R. A., Davidson, E. H., and Bolouri, H. (2002). New computational approaches for analysis of cis-regulatory networks. Dev. Biol. 246, 86–102.

Davidson, E. H., Rast, J. P., Oliveri, P., Ransick A., Calestani, C., Yuh, C.-H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., Otim, O., Brown, C. T., Livi, C. B., Lee, P. Y., Revilla, R., Schilstra, M. J., Clarkes, P. J. C., Rust, A. G., Pan, Z., Arnone, M. I., Rowen, L., Cameron, R. A., McClay, D. R., Hood, L., and Bolouri, H. (2002). A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev. Biol. 246, 162–190. Yuh, C.-H., Brown, C. T., Livi, C. B., Rowen, L., Clarke, P. J. C., and Davidson, E. H. (2002). Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin. Dev. Biol. 246, 148–161. 

Construction of cis-regulatory gene networks (update continuously at http://www.its.caltech.edu/~mirsky/endomes.htm)

Purpose:

To understand how various genes are expressed under the regulation of cis-regulatory elements during the developmental period of sea urchin embryos

6

Purple sea urchin (Strongylocentrotus purpuratus)

and white sea urchin (Lytechinus variegatus)

http://www.divebums.com/FishID/Pages/sea_urchin_purple.html  

http://digimorph.org/specimens/Strongylocentrotus_purpuratus/

7

Cells at different location have different fates in embryogenesis

8

cis-Regulation

trans-Regulation

9

A network exists in the cis-regulatory elements

with some logical rules

10

11

Constructing Relationshipsof Networks from

Expression and Perturbation Data

Developing a computational platform which can inference networks automatically by e

xperiment data

12

What is network ?Network is commonly in organism. e.g. gene regulatory network, pathway, neuron network…etc.Abstractly, network can defined as combinations of a group nodes and edges.

13

Our approachMining the relationship between nodes from expression curve and perturbation matrix.Inference networks by the relationships we found.

14

Expression curvenode A

node B Alignment

Bioinformatics 2003 19: 905-912

Scoring

Score

Relationship of A & B

15

Perturbation matrix

0

1

1

1

D

1

0

1

1

C

0

1

0

1

B

0

0

0

0

A

1

1

1

1

WT

D

C

B

A A BCD

AAB D

A

B

C

D

16

Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Met

abolic Network

SCIENCE VOL 292:929-934, MAY 4, 2001

Trey Ideker, Vesteinn Thorsson, Jeffrey A. Ranish, Rowan Christmas, Jeremy Buhler, Jimmy K. Eng, Roger Bumgarner,

David R. Goodlett, Ruedi Aebersold, Leroy Hood

17

18

19

Perturbation Matrix（mRNA Level）

mR

NA

加 Galactose 不加 Galactose

WT

A

B

C

A

B

A

C

B

C

A

BC

WT

A

B

C

A

B

A

C

B

C

A

BC

A

B

C

數量變化

20

Reverse Engineering Strategy

Hypothesis

Simulation Models

Candidate Set

Match

實際 Microarray 輸出結果

Believe it or not是否唯一吻合

重新假設

再作 Distinguishable 實驗

是

否

否

是

21

A

B

C

A

B

C

A

B

C

A

B

C

A

B

C

A

BC

A

BC

A

BC

A

BC

a b c d e

A

B

C

g

s t u v

Possible ModelsA

B

C

f

A

BC

A

BCp

A

BCq r

22

A(GAL4)

B(GAL80)

C(GAL3)

D(Galactose)

Gala

ctose

調控機制核心

23

A System of Cellular Pathway

化學連鎖反應

調控機制核心 Regulation Gene

Metabolic Flow

Structure Gene

化學物質

24

化學連鎖反應（ Metabolic Flow ）

Mutate structure genes and then we will find a Acyclic Directed Graph(ADG).

Mutate structure genes and then we will find a Acyclic Directed Graph(ADG).

25

A Pathway with Cycle(1/2)

1 2 3 4 5

On/Off Switch

A B C

E

D

？

26

A Pathway with Cycle(2/2)

1 2 3 4 5

On/Off Switch

B C

E

D

Observed

A

27

Raw Data

Mining information

HypothesisModeling

Experimental Simulator

Simulation Result

Match

Verification by other biologists

New Biological study

New Biological Experiments

Experiment results

Revise hypothesis by biologists

Error Report

Significant Information

Confirm

Error Report

Biological Study

N

Y

N

Y