A method for detection of differential gene expression in the presence of inter-individual variability in response

David M Rocke, Zelanna Goldberg, Chad Schweitert, Alison Santana

Research output: Contribution to journalArticle

16 Scopus citations

Abstract

Motivation: Many stimuli to biological systems result in transcriptional responses that vary across the individual organism either in type or in timing. This creates substantial difficulties in detecting these responses. This is especially the case when the data for any one individual are limited and when the number of genes, probes or probe sets is large. Results: We have developed a procedure that allows for sensitive detection of transcriptional responses that differ between individuals in type or in timing. This consists of four steps: one is to identify a group of genes, probes or probe sets that detect genes that belong to a molecular class or to a common pathway. The second is to conduct a statistical test of the hypothesis that the gene is differentially expressed for each individual and for each gene in the set. The third is to examine the collection of these statistics to see if there is a detectable signal in the aggregate of them. The final step is to assess the significance of this by resampling to avoid correlational bias.

Original languageEnglish (US)
Pages (from-to)3990-3992
Number of pages3
JournalBioinformatics
Volume21
Issue number21
DOIs
StatePublished - Nov 2005

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

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