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Knowledge Based Gene Set analysis (KB-GSA): A novel method for gene expression analysis
University of Skövde, School of Life Sciences.
2010 (English)Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
Abstract [en]

Microarray technology allows measurement of the expression levels of thousand of genes simultaneously. Several gene set analysis (GSA) methods are widely used for extracting useful information from microarrays, for example identifying differentially expressed pathways associated with a particular biological process or disease phenotype. Though GSA methods like Gene Set Enrichment Analysis (GSEA) are widely used for pathway analysis, these methods are solely based on statistics. Such methods can be awkward to use if knowledge of specific pathways involved in particular biological processes are the aim of the study. Here we present a novel method (Knowledge Based Gene Set Analysis: KB-GSA) which integrates knowledge about user-selected pathways that are known to be involved in specific biological processes. The method generates an easy to understand graphical visualization of the changes in expression of the genes, complemented with some common statistics about the pathway of particular interest.

Place, publisher, year, edition, pages
2010. , 18 p.
Keyword [en]
Gene set analysis, functional enrichment analysis
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:his:diva-4352OAI: oai:DiVA.org:his-4352DiVA: diva2:346101
Presentation
(English)
Uppsok
Medicine
Supervisors
Examiners
Available from: 2010-09-01 Created: 2010-08-30 Last updated: 2010-09-01Bibliographically approved

Open Access in DiVA

fulltext(344 kB)372 downloads
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Jadhav, Trishul
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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