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A method for identification of putatively co-regulated genes
University of Skövde, Department of Computer Science.
2002 (English)Independent thesis Advanced level (degree of Master (One Year))Student thesis
Abstract [en]

The genomes of several organisms have been sequenced and the need for methods to analyse the data is growing. In this project a method is described that tries to identify co-regulated genes. The method identifies transcription factor binding sites, documented in TRANSFAC, in the non-coding regions of genes. The algorithm counts the number of common binding sites and the number of unique binding sites for each pair of genes and decides if the genes are co-regulated. The result of the method is compared with the correlation between the gene expression patterns of the genes. The method is tested on 21 gene pairs from the genome of Saccharomyces cerevisiae. The algorithm first identified binding sites from all organisms. The accuracy of the program was very low in this case. When the algorithm was modified to only identify binding sites found in plants the accuracy was much improved, from 52% to 76% correct predictions.

Place, publisher, year, edition, pages
Skövde: Institutionen för datavetenskap , 2002. , 72 p.
Keyword [en]
Co-regulated genes, binding site, TRANSFAC, gene expression
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:his:diva-705OAI: oai:DiVA.org:his-705DiVA: diva2:3105
Presentation
(English)
Uppsok
fysik/kemi/matematik
Supervisors
Available from: 2008-02-04 Created: 2008-02-04 Last updated: 2009-05-06

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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