Investigating the structure of integrated biological networks: Master's thesis

Erno Lindfors

Research output: ThesisMaster's thesisTheses

Abstract

The current biological data is very diverse. It is located in different databases and it is presented in different ways. There are several biological databases with good visualization tools. However, there are very few tools that are able to retrieve data across multiple databases. It is thus very difficult to get a clear and overall picture of the complicated biological data. In this thesis we develop a Java application that is able to retrieve data from several biological databases. Based on the latest research it is assumed that a hierarchical modularity is present in metabolic networks. This fact has a very important role in the robustness arid error-tolerance of metabolic networks. However, it is unknown how this structure changes when we combine such networks with other types of biological interactions. We use the Sammon's mapping projection algorithm to investigate the structure of biological networks in Saccharomyces cerevisiae. First, we cluster metabolic pathways. Next, we combine metabolic pathways with protein-protein interaction networks. In high hierarchy levels there occur very strong mergers. In lower hierarchy levels the mergers are considerably weaker. Between high and low hierarchy levels there do not occur any mergers.
Original languageEnglish
QualificationMaster Degree
Awarding Institution
  • Helsinki University of Technology
Place of PublicationEspoo
Publisher
Publication statusPublished - 2005
MoE publication typeG2 Master's thesis, polytechnic Master's thesis

Fingerprint

Proteins
Yeast
Visualization
Metabolic Networks and Pathways

Keywords

  • data visualizing and clustering
  • robustness
  • network topologies
  • bioinformatics
  • tiedon visualisointi ja klusterointi
  • robustisuus
  • verkkotopologiat
  • bioinformatiikka

Cite this

Lindfors, E. (2005). Investigating the structure of integrated biological networks: Master's thesis. Espoo: Helsinki University of Technology.
Lindfors, Erno. / Investigating the structure of integrated biological networks : Master's thesis. Espoo : Helsinki University of Technology, 2005. 77 p.
@phdthesis{49f64c166a544e8b80720ead35a4265c,
title = "Investigating the structure of integrated biological networks: Master's thesis",
abstract = "The current biological data is very diverse. It is located in different databases and it is presented in different ways. There are several biological databases with good visualization tools. However, there are very few tools that are able to retrieve data across multiple databases. It is thus very difficult to get a clear and overall picture of the complicated biological data. In this thesis we develop a Java application that is able to retrieve data from several biological databases. Based on the latest research it is assumed that a hierarchical modularity is present in metabolic networks. This fact has a very important role in the robustness arid error-tolerance of metabolic networks. However, it is unknown how this structure changes when we combine such networks with other types of biological interactions. We use the Sammon's mapping projection algorithm to investigate the structure of biological networks in Saccharomyces cerevisiae. First, we cluster metabolic pathways. Next, we combine metabolic pathways with protein-protein interaction networks. In high hierarchy levels there occur very strong mergers. In lower hierarchy levels the mergers are considerably weaker. Between high and low hierarchy levels there do not occur any mergers.",
keywords = "data visualizing and clustering, robustness, network topologies, bioinformatics, tiedon visualisointi ja klusterointi, robustisuus, verkkotopologiat, bioinformatiikka",
author = "Erno Lindfors",
note = "CA: BEL diplomity{\"o} Helsinki University of Technology. Department of Electrical and Communications Engineering",
year = "2005",
language = "English",
publisher = "Helsinki University of Technology",
address = "Finland",
school = "Helsinki University of Technology",

}

Lindfors, E 2005, 'Investigating the structure of integrated biological networks: Master's thesis', Master Degree, Helsinki University of Technology, Espoo.

Investigating the structure of integrated biological networks : Master's thesis. / Lindfors, Erno.

Espoo : Helsinki University of Technology, 2005. 77 p.

Research output: ThesisMaster's thesisTheses

TY - THES

T1 - Investigating the structure of integrated biological networks

T2 - Master's thesis

AU - Lindfors, Erno

N1 - CA: BEL diplomityö Helsinki University of Technology. Department of Electrical and Communications Engineering

PY - 2005

Y1 - 2005

N2 - The current biological data is very diverse. It is located in different databases and it is presented in different ways. There are several biological databases with good visualization tools. However, there are very few tools that are able to retrieve data across multiple databases. It is thus very difficult to get a clear and overall picture of the complicated biological data. In this thesis we develop a Java application that is able to retrieve data from several biological databases. Based on the latest research it is assumed that a hierarchical modularity is present in metabolic networks. This fact has a very important role in the robustness arid error-tolerance of metabolic networks. However, it is unknown how this structure changes when we combine such networks with other types of biological interactions. We use the Sammon's mapping projection algorithm to investigate the structure of biological networks in Saccharomyces cerevisiae. First, we cluster metabolic pathways. Next, we combine metabolic pathways with protein-protein interaction networks. In high hierarchy levels there occur very strong mergers. In lower hierarchy levels the mergers are considerably weaker. Between high and low hierarchy levels there do not occur any mergers.

AB - The current biological data is very diverse. It is located in different databases and it is presented in different ways. There are several biological databases with good visualization tools. However, there are very few tools that are able to retrieve data across multiple databases. It is thus very difficult to get a clear and overall picture of the complicated biological data. In this thesis we develop a Java application that is able to retrieve data from several biological databases. Based on the latest research it is assumed that a hierarchical modularity is present in metabolic networks. This fact has a very important role in the robustness arid error-tolerance of metabolic networks. However, it is unknown how this structure changes when we combine such networks with other types of biological interactions. We use the Sammon's mapping projection algorithm to investigate the structure of biological networks in Saccharomyces cerevisiae. First, we cluster metabolic pathways. Next, we combine metabolic pathways with protein-protein interaction networks. In high hierarchy levels there occur very strong mergers. In lower hierarchy levels the mergers are considerably weaker. Between high and low hierarchy levels there do not occur any mergers.

KW - data visualizing and clustering

KW - robustness

KW - network topologies

KW - bioinformatics

KW - tiedon visualisointi ja klusterointi

KW - robustisuus

KW - verkkotopologiat

KW - bioinformatiikka

M3 - Master's thesis

PB - Helsinki University of Technology

CY - Espoo

ER -

Lindfors E. Investigating the structure of integrated biological networks: Master's thesis. Espoo: Helsinki University of Technology, 2005. 77 p.