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Disease modules identification in heterogenous diseases with WGCNA method
University of Skövde, School of Bioscience. (Bioinformatics)
2019 (English)Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

The widely collected and analyzed genetic data help in understanding the underlying mechanisms of heterogeneous diseases. Cellular components interact in a network fashion where genes are nodes and edges are the interactions. The failure in individual genes lead to dys-regulation of sub-groups of genes which causes a disease phenotype, and this dys-functional region is called a disease module. Disease module identification in complex diseases such as asthma and cancer is a huge challenge. Despite the development of numerous sophisticated methods there is a still no gold standard. In this study we apply different parameter settings to test the performance of a widely used method for disease module detection in multi-omics data called Weighted Gene Co-expression Network Analysis (WGCNA). A systematic approach is used to identify disease modules in asthma and arthritis diseases. The accuracy of obtained modules is validated by a pathway scoring algorithm (PASCAL) and GWAS SNP enrichment. Our results differ between the tested data sets and therefore we cannot conclude with recommendations for an optimal setting that could perform best for multiple data sets using this method.

Place, publisher, year, edition, pages
2019. , p. 52
Keywords [en]
disease module, WGCNA, parameter settings
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:his:diva-16692OAI: oai:DiVA.org:his-16692DiVA, id: diva2:1295665
Subject / course
Bioinformatics
Educational program
Bioinformatics - Master’s Programme
Supervisors
Examiners
Available from: 2019-03-26 Created: 2019-03-12 Last updated: 2019-03-26Bibliographically approved

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School of Bioscience
Bioinformatics and Systems Biology

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CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • 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