Superposition of transcriptional behaviors determines gene state

Sol Efroni, Liran Carmel, Carl G. Schaefer, Kenneth Buetow

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

We introduce a novel technique to determine the expression state of a gene from quantitative information measuring its expression. Adopting a productive abstraction from current thinking in molecular biology, we consider two expression states for a gene - Up or Down. We determine this state by using a statistical model that assumes the data behaves as a combination of two biological distributions. Given a cohort of hybridizations, our algorithm predicts, for the single reading, the probability of each gene's being in an Up or a Down state in each hybridization. Using a series of publicly available gene expression data sets, we demonstrate that our algorithm outperforms the prevalent algorithm. We also show that our algorithm can be used in conjunction with expression adjustment techniques to produce a more biologically sound gene-state call. The technique we present here enables a routine update, where the continuously evolving expression level adjustments feed into gene-state calculations. The technique can be applied in almost any multi-sample gene expression experiment, and holds equal promise for protein abundance experiments.

Original languageEnglish (US)
Article numbere2901
JournalPLoS One
Volume3
Issue number8
DOIs
StatePublished - Aug 6 2008
Externally publishedYes

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Genes
genes
Gene expression
hybridization
Gene Expression
gene expression
Molecular biology
Statistical Models
statistical models
methodology
molecular biology
Reading
Molecular Biology
Experiments
Acoustic waves
Proteins
proteins
sampling

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Superposition of transcriptional behaviors determines gene state. / Efroni, Sol; Carmel, Liran; Schaefer, Carl G.; Buetow, Kenneth.

In: PLoS One, Vol. 3, No. 8, e2901, 06.08.2008.

Research output: Contribution to journalArticle

Efroni, Sol ; Carmel, Liran ; Schaefer, Carl G. ; Buetow, Kenneth. / Superposition of transcriptional behaviors determines gene state. In: PLoS One. 2008 ; Vol. 3, No. 8.
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