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Related Experiment Videos

Cis sequence effects on gene expression.

Andrew W Bergen1, Andrea Baccarelli, Timothy K McDaniel

  • 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA. andrew.bergen@sri.com

BMC Genomics
|August 31, 2007
PubMed
Summary
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Approximately 25% of genes show significant cis sequence effects, influencing gene expression. This finding, consistent across studies, highlights the role of sequence variation in gene regulation.

Area of Science:

  • Genetics
  • Genomics
  • Molecular Biology

Background:

  • Investigated the independent study of sequence and transcriptional variability.
  • Introduced genetical genomics for joint analysis of sequence and gene expression variation.
  • Focused on cis sequence effects on gene expression in cancer-related genes within lymphoblastoid cell lines.

Purpose of the Study:

  • To estimate the proportion of genes with cis sequence effects.
  • To determine the proportion of gene expression variation explained by cis sequence effects.
  • To compare findings with existing literature using three analytical approaches.

Main Methods:

  • Generated gene expression profiling data for 697 candidate genes in 30 lymphoblastoid cell lines.
  • Utilized available resequencing data for 552 candidate genes.

Related Experiment Videos

  • Employed two additive models and the Templeton Tree Scanning approach to assess SNP, gene, and diplotype associations with gene expression.

    • Main Results:

    • Identified 30 candidate genes with sufficient variance in both expression and sequence data.
    • Found statistically significant associations (p < 0.05) between SNPs/diplotypes and gene expression at eight candidate genes.
    • Achieved 80-85% concordance with literature data for genes exhibiting or not exhibiting significant cis sequence effects.

    Conclusions:

    • Concluded that approximately one in four genes exhibits significant cis sequence effects.
    • Determined that cis sequence variation accounts for about 30% of gene expression variation in these genes.
    • Confirmed that findings are largely supported by diverse, previously published experimental approaches.