A method for finding putative causes of gene expression variation

Reija Autio; Sampsa Hautaniemi; Markus Ringnér; Päivikki Kauraniemi; Henrik Edgren; Olli Yli-Harja; Jaakko Astola; Anne Kallioniemi; Olli-Pekka Kallioniemi

A method for finding putative causes of gene expression variation

Reija Autio, Sampsa Hautaniemi, Markus Ringnér, Päivikki Kauraniemi, Henrik Edgren, Olli Yli-Harja, Jaakko Astola, Anne Kallioniemi, Olli-Pekka Kallioniemi

Research output: Chapter in Book/Report/Conference proceeding › Paper in conference proceeding

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Abstract

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.

Original language	English
Title of host publication	2nd TICSP Workshop on Computational Systems Biology, WCSB 2004
Subtitle of host publication	Silja Opera, Helsinki-St. Petersburg, June 14 - 16, 2004
Editors	Tommi Aho, Harri Lähdesmäki, Olli Yli-Harja
Publisher	Tampere University of Technology
Pages	29-30
ISBN (Print)	952-15-1204-0
Publication status	Published - 2004
Event	2nd TICSP Workshop on Computational Systems Biology, WCSB'2004 - Silja Opera, Helsinki-St. Petersburg Duration: 2004 Jun 14 → 2004 Jun 16

Publication series

Name	TICSP Series
Publisher	Tampere University of Technology
Volume	24
ISSN (Print)	1456-2774

Conference

Conference	2nd TICSP Workshop on Computational Systems Biology, WCSB'2004
Period	2004/06/14 → 2004/06/16

Subject classification (UKÄ)

Bioinformatics and Systems Biology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Autio, R., Hautaniemi, S., Ringnér, M., Kauraniemi, P., Edgren, H., Yli-Harja, O., Astola, J., Kallioniemi, A., & Kallioniemi, O.-P. (2004). A method for finding putative causes of gene expression variation. In T. Aho, H. Lähdesmäki, & O. Yli-Harja (Eds.), 2nd TICSP Workshop on Computational Systems Biology, WCSB 2004: Silja Opera, Helsinki-St. Petersburg, June 14 - 16, 2004 (pp. 29-30). (TICSP Series ; Vol. 24). Tampere University of Technology.

Autio, Reija ; Hautaniemi, Sampsa ; Ringnér, Markus et al. / A method for finding putative causes of gene expression variation. 2nd TICSP Workshop on Computational Systems Biology, WCSB 2004: Silja Opera, Helsinki-St. Petersburg, June 14 - 16, 2004. editor / Tommi Aho ; Harri Lähdesmäki ; Olli Yli-Harja. Tampere University of Technology, 2004. pp. 29-30 (TICSP Series ).

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title = "A method for finding putative causes of gene expression variation",

abstract = "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.",

author = "Reija Autio and Sampsa Hautaniemi and Markus Ringn{\'e}r and P{\"a}ivikki Kauraniemi and Henrik Edgren and Olli Yli-Harja and Jaakko Astola and Anne Kallioniemi and Olli-Pekka Kallioniemi",

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language = "English",

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editor = "Tommi Aho and Harri L{\"a}hdesm{\"a}ki and Olli Yli-Harja",

booktitle = "2nd TICSP Workshop on Computational Systems Biology, WCSB 2004",

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Autio, R, Hautaniemi, S, Ringnér, M, Kauraniemi, P, Edgren, H, Yli-Harja, O, Astola, J, Kallioniemi, A & Kallioniemi, O-P 2004, A method for finding putative causes of gene expression variation. in T Aho, H Lähdesmäki & O Yli-Harja (eds), 2nd TICSP Workshop on Computational Systems Biology, WCSB 2004: Silja Opera, Helsinki-St. Petersburg, June 14 - 16, 2004. TICSP Series , vol. 24, Tampere University of Technology, pp. 29-30, 2nd TICSP Workshop on Computational Systems Biology, WCSB'2004, 2004/06/14.

A method for finding putative causes of gene expression variation. / Autio, Reija; Hautaniemi, Sampsa; Ringnér, Markus et al.
2nd TICSP Workshop on Computational Systems Biology, WCSB 2004: Silja Opera, Helsinki-St. Petersburg, June 14 - 16, 2004. ed. / Tommi Aho; Harri Lähdesmäki; Olli Yli-Harja. Tampere University of Technology, 2004. p. 29-30 (TICSP Series ; Vol. 24).

Research output: Chapter in Book/Report/Conference proceeding › Paper in conference proceeding

TY - GEN

T1 - A method for finding putative causes of gene expression variation

AU - Autio, Reija

AU - Hautaniemi, Sampsa

AU - Ringnér, Markus

AU - Kauraniemi, Päivikki

AU - Edgren, Henrik

AU - Yli-Harja, Olli

AU - Astola, Jaakko

AU - Kallioniemi, Anne

AU - Kallioniemi, Olli-Pekka

PY - 2004

Y1 - 2004

N2 - 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.

AB - 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.

M3 - Paper in conference proceeding

SN - 952-15-1204-0

T3 - TICSP Series

SP - 29

EP - 30

BT - 2nd TICSP Workshop on Computational Systems Biology, WCSB 2004

A2 - Aho, Tommi

A2 - Lähdesmäki, Harri

A2 - Yli-Harja, Olli

PB - Tampere University of Technology

T2 - 2nd TICSP Workshop on Computational Systems Biology, WCSB'2004

Y2 - 14 June 2004 through 16 June 2004

ER -

Autio R, Hautaniemi S, Ringnér M, Kauraniemi P, Edgren H, Yli-Harja O et al. A method for finding putative causes of gene expression variation. In Aho T, Lähdesmäki H, Yli-Harja O, editors, 2nd TICSP Workshop on Computational Systems Biology, WCSB 2004: Silja Opera, Helsinki-St. Petersburg, June 14 - 16, 2004. Tampere University of Technology. 2004. p. 29-30. (TICSP Series ).

A method for finding putative causes of gene expression variation

Abstract

Publication series

Conference

Subject classification (UKÄ)

UN SDGs

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Cite this