A method for finding putative causes of gene expression variation

Research output: Chapter in Book/Report/Conference proceedingPaper in conference proceeding


The majority of microarray studies evaluate gene ex-
pression differences between various specimens or con-
ditions. However, the causes of this variability often re-
main unknown. Our aim is to identify underlying causes
of these patterns, a process that would eventually enable
a mechanistic understanding of the deregulation of gene
expression in cancer. The procedure consists of three
phases: pre-processing, data integration and statistical
analysis. We have applied the strategy to identify genes
that are overexpressed due to amplification in breast
cancer. The data were obtained from 14 breast cancer
cell lines, which were subjected to cDNA microarray
based copy number and expression experiments. The re-
sult of the analysis was a list that consisted of 92 genes.
This set includes several genes that are known to be both
overexpressed and amplified in breast cancer. The com-
plete study was published in Journal of the Franklin In-
stitute 2004, and in this paper we focus on the main
issues of the study.


  • Reija Autio
  • Sampsa Hautaniemi
  • Markus Ringnér
  • Päivikki Kauraniemi
  • Henrik Edgren
  • Olli Yli-Harja
  • Jaakko Astola
  • Anne Kallioniemi
  • Olli-Pekka Kallioniemi
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Biophysics
Original languageEnglish
Title of host publication2nd TICSP Workshop on Computational Systems Biology, WCSB 2004
Subtitle of host publicationSilja Opera, Helsinki-St. Petersburg, June 14 - 16, 2004
EditorsTommi Aho, Harri Lähdesmäki, Olli Yli-Harja
PublisherTampere University of Technology
Number of pages2
ISBN (Print)952-15-1204-0
Publication statusPublished - 2004
Publication categoryResearch
Event2nd TICSP Workshop on Computational Systems Biology, WCSB'2004 - Silja Opera, Helsinki-St. Petersburg
Duration: 2004 Jun 142004 Jun 16

Publication series

NameTICSP Series
PublisherTampere University of Technology
ISSN (Print)1456-2774


Conference2nd TICSP Workshop on Computational Systems Biology, WCSB'2004

Total downloads

No data available