Download Applns of Graph-Based Data Mining to Biological Ntwks - C. You [thesis] (2005) WW PDF

TitleApplns of Graph-Based Data Mining to Biological Ntwks - C. You [thesis] (2005) WW
TagsMedical
LanguageEnglish
File Size1.2 MB
Total Pages96
Document Text Contents
Page 1

APPLICATION OF GRAPH BASED DATA MINING

TO BIOLOGICAL NETWORKS

by

CHANG HUN YOU

Presented to the Faculty of the Graduate School of

The University of Texas at Arlington in Partial Fulfillment

of the Requirements

for the Degree of

MASTER OF SCIENCE IN COMPUTER SCIENCE

THE UNIVERSITY OF TEXAS AT ARLINGTON

December 2005

Page 2

UMI Number: 1430664

1430664

2006

Copyright 2005 by

You, Chang hun

UMI Microform

Copyright
All rights reserved. This microform edition is protected against
unauthorized copying under Title 17, United States Code.

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by ProQuest Information and Learning Company.

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Table 4.2. Subtype node value and Subvalue node value of the Relation element [3]

Subtype value Subvalue value ECrel PPrel GErel
compound link to Entry for compound ∗ ∗
hidden compound link to Entry for hidden compound ∗
activation −− > ∗
inhibition −− | ∗
expression −− > ∗
repression −− | ∗
indirect effect .. > ∗ ∗
state change ... ∗
binding/association −−− ∗
dissociation − + − ∗
phosphorylation +p ∗
dephosphorylation −p ∗
glycosylation +g ∗
ubiquitination +u ∗
methylation +m ∗

not available. Map which is the Id of the map entry is specified if this entry appears in

another pathway map [3].

Relation is relationship between protein, gene, compound and map. Relation node

is a central node of relation part. Each Relation node has several attributes. First, two

attributes explain basic properties of the relation such as Type and Subtype. Type at-

tribute may have ECrel, PPrel, GErel, PCrel and maplink as an attribute value. Subtype

attribute may have several values as mentioned in Table 4.2. The Subtype value may

have link or its own value to give additional information of the relation. At Table 4.2.

first two rows of the Subtype have a link to another Entry. Other values of Subtype are

specific information dependent on the Type value of the relation. Second, the relation has

two or more Entry elements (protein, gene, compound or map) as its child elements. Re-

lation entry explains the relationships between these objects by using type and subtype

[3].

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Reaction represents a chemical reaction between one or more substrate and one

or more product catalyzed by one or more enzyme. Each Reaction has two or more main

entries like a substrate and a product. The other two attributes, type and name, describe

properties of the reaction. By a semantics of biochemistry, the enzyme is not included

as an attribute to Reaction entry. The enzyme entry has a pointer to Reaction entry to

catalyze as explained above [3].

4.7 Summary

This chapter described the domain of this research. Some important biochemical

concepts are explained for background of this research. Systems biology are introduced for

post-genomic bioinformatics research. As one of the approaches of Systems biology, the

study of biological networks is introduced with some examples of computational analysis.

Biological network databases are represented as the result of the traditional bioinformat-

ics research and the resource of the future work. Finally, the KEGG database which is

the most comprehensive archive of the biological network is introduced as the resource

of this research with its own distributed format, KGML. In the next chapter, we will

describe the graph representation of the KEGG biological network and the application

of the graph-based data mining as the main approach of this research.

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[75] (2003) Extensible markup language (xml). [Online]. Available:

http://www.w3.org/XML/

[76] (2004, Apr.) Document object model (dom) level 3 core specification. [Online].

Available: http://www.w3.org/TR/2004/REC-DOM-Level-3-Core-20040407/

[77] McLaughlin, Foundations of Systems Biology. O’Reilly, 2001.

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BIOGRAPHICAL STATEMENT

Chang hun You was born in Seoul, Korea in 1976. He received B.A. in Agricultural

Biology from The Korea University in 2002. He began his study toward the M.S. degree

in the department of Computer Science and Engineering at The University of Texas at

Arlington in August 2003. His research interests focus on data mining and bioinformatics.

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