Toward automatically drawn metabolic pathway atlas with peripheral node abstraction algorithm
Sponsored Links
This presentation is the property of its rightful owner.
1 / 19

Toward Automatically Drawn Metabolic Pathway Atlas with Peripheral Node Abstraction Algorithm PowerPoint PPT Presentation


  • 47 Views
  • Uploaded on
  • Presentation posted in: General

Toward Automatically Drawn Metabolic Pathway Atlas with Peripheral Node Abstraction Algorithm. Myungha Jang, Arang Rhie , and Hyun- Seok Park * Bioinformatics Laboratory, School of Engineering Ewha Womans University Seoul, Korea. IEEE BIBM, 18-21 Dec 2010, Hong Kong.

Download Presentation

Toward Automatically Drawn Metabolic Pathway Atlas with Peripheral Node Abstraction Algorithm

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


Toward Automatically Drawn Metabolic Pathway Atlas with Peripheral Node Abstraction Algorithm

Myungha Jang, ArangRhie, and Hyun-Seok Park*

Bioinformatics Laboratory, School of Engineering

EwhaWomans University

Seoul, Korea

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


Table of Contents

Introduction

Topological Nature of Metabolic Networks at Peripheral Nodes

Node Abstraction Featured Scale-free Algorithm

Experimental Results

Discussion and Future Work

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


I. INTRODUCTION

Automatic graph layout algorithms in systems biology

  • Abstract graph structure ⇒ visual representation

  • Graphical diagrams are intuitively helpful to understand biochemical reaction networks

    • - Node : compound, Edge : reactions

  • Optimal solutions : NP-hard problems

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


I. INTRODUCTION

Focusing on Global Metabolic Pathway

  • A complete metabolic network indicates all the metabolic potential and capacity.

  • The shift of research focus: single pathways to multiple pathways.

  • Visualization serves an important role in understanding large scale metabolic network.

  • KEGGAtlas(http://www.genome.ad.jp/kegg), 2008

  • Terms : Global (metabolic) pathway, Multiple pathway, Atlas

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


I. INTRODUCTION

Our Efforts Toward Automatic Global Layout

  • Not enough to deal with the global pathway!

  • How can we obtain a complete view?

  • No attempts for automatic visualization for Atlas

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


I. INTRODUCTION

How To Deal With Large-scale Metabolic Pathway?

  • Related work: KEGG Atlas

  • The map integration process is carried out manually by curators.

  • Based on curator’s experience

  • However, that metabolic networks are dynamic in nature should not be disregarded  Systematic approach is necessary

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


INTRODUCTION

How To Deal With Large-scale Metabolic Pathway? (con’d)

  • Our Strategy

  • We provide a novel algorithmic approach in drawing multiple metabolic pathways by considering two properties:

  • 1. Automatic abstraction criteria: by analyzing a topological nature of metabolic networks based on the graphical property of relation distance, linear reactions were abstracted as a unit reaction.

  • 2. the consistency of highly connected nodes


II. Topological Nature of Metabolic Networks at Peripheral Nodes

  • We obtained 255 map data by parsing KEGG XML (KGML) documents of version 0.6 using our KGML Parser.

+

KGML

Two terms were defined:

1. Relation degree

the number of edges branching from a node

2. Relation distance

a factor to measure the length between any two compounds encompassing nodes which all have relation degrees less than or equal to p (p = 2)

  • A dedicated analysis on peripheral nodes with low connectivity was performed.

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


II. Topological Nature of Metabolic Networks at Peripheral Nodes

Relation Distance Term Clarification

  • Definition: The length between any two compounds encompassing nodes which all have relation degrees equal to p

  • Here, p = 2

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


II. Topological Nature of Metabolic Networks at Peripheral Nodes

Relation Distance Example in Map

RD(C01290, C00369) = 7

  • cpd:C01291

  • cpd:C01290

  • cpd:C16466

  • cpd:C16475

  • cpd:C16468

  • cpd:C16470

  • cpd:C16471

  • cpd:C16469

  • cpd:C00369

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


III. Node Abstraction Featured Scale-free Algorithm

Basic Motivation

  • Observation: 66.83% of the total compounds within the complete metabolic pathways were of low connectivity, with less than relation degree of 3.

  • The number of compounds with higher relation degree, i.e. more than 6 edges, was much less.

Abstracting Compounds With Linear Interaction

Layout Components according to High Connectivity

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


III. Node Abstraction Featured Scale-free Algorithm

A. Abstracting Compounds With Linear Interaction

  • We abstracted and hid all those compounds that appear within these linear interactions.

  • This approach could be called “chain reduction”(M. Chimaniet al)

  • All green compounds in the figure will be hidden in the graph layout according to this approach.

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


III. Node Abstraction Featured Scale-free Algorithm

B. Layout Components according to High Connectivity

  • Highly Connected Nodes: Nodes with relation degree bigger than 6

  • LayoutHighConnectedNode()Algorithm Steps

  • Find a highly Connected node Nd

  • Each component connected to Nd is decomposed into sub-graph

  • Each decomposed sub-graph is treated as a super node to apply the spring-embedding algorithm

  • Input : Metabolic Pathway Graph

  • Output : coordinates of each node

  • voidLayoutPathway(Pathway graph)

  • {

  • IF highly connected nodes (Nd) exist in graph

  • LayoutHighlyConnectedNode(graph, Nd);

  • ELSEIF any cycle(Nc) exists in graph

  • AND size of cycle ≥ 6

  • LayoutCircular(graph, Nc);

  • ELSELayoutHierarchic(graph);

  • }

6

3

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


IV. Experimental results

  • Experiments : To compare compression rate of compounds, we obtained the number of abstracted compounds and edge crossings by applying two different layout algorithms:

  • Result 1

  • Node compression rate performance

  • Scope

  • 1. 84 single metabolic pathways

  • 2. 8 major categorized metabolic pathways

  • 3. the global pathway

  • Result 2

  • The number of edge crossing comparison between by

  • 1. Conventional algorithm

  • 2. Our Node abstraction featured scale-free layout algorithm

Categorized pathways

Global

pathway

single pathways

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


III. Experimental results

Peripheral path as supplementary nodes

Result 1B

The Number of Nodes Before and After Applying Node Abstraction

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


III. Experimental results

Peripheral path as super edges

Result 1A

Original Network Abstracted Network

Results drawn with Cytoscape, using conventional spring embedding

The red-colored edges represent the abstracted edges. (abstraction rate : 70%)

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


III. Experimental results

Result 2 : Edge Crossing Reduction

  • In single metabolic pathways, the node abstraction featured algorithm reduced edge crossings by 63.31%.

  • In a global metabolic pathway, the number of edge crossings has reached a reduction of 58.08% in total.

  • Our proposed algorithm with node abstraction resulted in 86,067 edge crossings, whereas the one without node abstraction resulted in 205,316 edge crossings.

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


IV. Discussion

  • Two approaches were used:

  • 1. Abstracting compound pairs according to a consistent criteria

  • 2. Layout components according to high connectivity

  • Our experimental results show that node abstraction feature reduced the number of compounds by approximately 23% in global pathway.

  • Further discussion is necessary regarding enzyme reactions

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


IV. Why is our work important?

  • The first systematic approach for Atlas visualization focusing on peripheral nodes

  • Fundamental to building a hierarchical structure of Atlas

  • Our approach is flexible upon pathway database change that frequently updates

  • It is a crucial preliminary step toward automatically drawn metabolic pathway

  • Future research on individual biological meaning of each peripheral nodes and abstracted path

IEEE BIBM, 18-21 Dec 2010, Hong Kong

EwhaWomans University


  • Login