his.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
A method for extracting pathways from Scansite-predicted protein-protein interactions
University of Skövde, School of Humanities and Informatics.
2006 (English)Independent thesis Advanced level (degree of Master (One Year))Student thesis
Abstract [en]

Protein interaction is an important mechanism for cellular functionality. Predicting protein interactions is available in many cases as computational methods in publicly available resources (for example Scansite). These predictions can be further combined with other information sources to generate hypothetical pathways. However, when using computational methods for building pathways, the process may become time consuming, as it requires multiple iterations and consolidating data from different sources. We have tested whether it is possible to generate graphs of protein-protein interaction by using only domain-motif interaction data and the degree to which it is possible to automate this process by developing a program that is able to aggregate, under user guidance, query results from different information sources. The data sources used are Scansite and SwissProt. Visualisation of the graphs is done with an external program freely available for academic purposes, Osprey. The graphs obtained by running the software show that although it is possible to combine publicly available data and theoretical protein-protein interaction predictions from Scansite, further efforts are needed to increase the biological plausibility of these collections of data. It is possible, however, to reduce the dimensionality of the obtained graphs by focusing the searches on a certain tissue of interest.

Place, publisher, year, edition, pages
Skövde: Institutionen för kommunikation och information , 2006. , 39 p.
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:his:diva-34OAI: oai:DiVA.org:his-34DiVA: diva2:2705
Presentation
(English)
Uppsok
Physics, Chemistry, Mathematics
Supervisors
Examiners
Available from: 2006-11-06 Created: 2006-11-06 Last updated: 2010-02-09

Open Access in DiVA

fulltext(822 kB)417 downloads
File information
File name FULLTEXT01.pdfFile size 822 kBChecksum SHA-1
251c6a2ceeabf15c8af0a3fa923e0a0e6cb8f5aa375e042546aba3bd602d54655fedb91a
Type fulltextMimetype application/pdf

By organisation
School of Humanities and Informatics
Bioinformatics (Computational Biology)

Search outside of DiVA

GoogleGoogle Scholar
Total: 417 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Total: 270 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf