oru.sePublikationer
Ändra sökning
RefereraExporteraLänk till posten
Permanent länk

Direktlänk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Effects of threshold choice on the results of gene expression profiling, using microarray analysis, in a model feeding experiment with rat
Research Group Functional Genomics.
Research Unit Genetics and Biometrics.
Research Unit Genetics and Biometrics.ORCID-id: 0000-0002-7173-5579
Institute of Veterinary Anatomy, Department of Veterinary Medicine, Free University of Berlin, Berlin, Germany.
Visa övriga samt affilieringar
2009 (Engelska)Ingår i: Archiv für Tierzucht, ISSN 0003-9438, Vol. 52, nr 1, s. 65-78Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Global gene expression studies using microarray technology are widely employed to identify biological processes which are influenced by a treatment e.g. a specific diet. Affected processes are characterized by a significant enrichment of differentially expressed genes (functional annotation analysis). However, different choices of statistical thresholds to select candidates for differential expression will alter the resulting candidates list. This study was conducted to investigate the effect of applying a False Discovery Rate (FDR) correction and different fold change thresholds in statistical analysis of microarray data on diet-affected biological processes based on a significantly increased proportion of differentially expressed genes. In a model feeding experiment with rats fed genetically modified food additives, animals received a supplement of either lyophilized inactivated recombinant VP60 baculovirus (rBV-VP60) or lyophilized inactivated wild type baculovirus (wtBV). Comparative expression profiling was done in spleen, liver and small intestine mucosa. We demonstrated the extent to which threshold choice can affect the biological processes identified as significantly regulated and thus the conclusion drawn from the microarray data. In our study, the combined application of a moderate fold change threshold (FC≥1.5) and a stringent FDR threshold (q≤0.05) exhibited high reliability of biological processes identified as differentially regulated. The application of a stringent FDR threshold of q≤0.05 seems to be an essential prerequisite to reduce considerably the number of false positives. Microarray results of selected differentially expressed molecules were validated successfully by using real-time RT-PCR.

Ort, förlag, år, upplaga, sidor
Dummerstorf, Germany: Research Institute for the Biology of Farm Animals (FBN) , 2009. Vol. 52, nr 1, s. 65-78
Nyckelord [en]
Biological process; False discovery rate; Fold change threshold; Microarray expression profiling
Nationell ämneskategori
Bioinformatik och systembiologi
Identifikatorer
URN: urn:nbn:se:oru:diva-40733ISI: 000263312600008Scopus ID: 2-s2.0-61649098016OAI: oai:DiVA.org:oru-40733DiVA, id: diva2:778566
Tillgänglig från: 2015-01-11 Skapad: 2015-01-11 Senast uppdaterad: 2017-10-17Bibliografiskt granskad

Open Access i DiVA

fulltext(200 kB)675 nedladdningar
Filinformation
Filnamn FULLTEXT01.pdfFilstorlek 200 kBChecksumma SHA-512
dd04856a3bb6556c82585e8fb0822e3bbf584d532e82637d55f355155a66ee11279aa3ba9a8f4eb4f4db6638e9e937db952ee342358a67eb011f5702aa53adf0
Typ fulltextMimetyp application/pdf

Scopus

Personposter BETA

Repsilber, Dirk

Sök vidare i DiVA

Av författaren/redaktören
Repsilber, Dirk
Bioinformatik och systembiologi

Sök vidare utanför DiVA

GoogleGoogle Scholar
Totalt: 675 nedladdningar
Antalet nedladdningar är summan av nedladdningar för alla fulltexter. Det kan inkludera t.ex tidigare versioner som nu inte längre är tillgängliga.

urn-nbn

Altmetricpoäng

urn-nbn
Totalt: 472 träffar
RefereraExporteraLänk till posten
Permanent länk

Direktlänk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf