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A framework for list representation, enabling list stabilization through incorporation of gene exchangeabilities.

Soneson, Charlotte LU and Fontes, Magnus LU (2012) In Biostatistics 13. p.129-141
Abstract
Analysis of multivariate data sets from, for example, microarray studies frequently results in lists of genes which are associated with some response of interest. The biological interpretation is often complicated by the statistical instability of the obtained gene lists, which may partly be due to the functional redundancy among genes, implying that multiple genes can play exchangeable roles in the cell. In this paper, we use the concept of exchangeability of random variables to model this functional redundancy and thereby account for the instability. We present a flexible framework to incorporate the exchangeability into the representation of lists. The proposed framework supports straightforward comparison between any 2 lists. It can... (More)
Analysis of multivariate data sets from, for example, microarray studies frequently results in lists of genes which are associated with some response of interest. The biological interpretation is often complicated by the statistical instability of the obtained gene lists, which may partly be due to the functional redundancy among genes, implying that multiple genes can play exchangeable roles in the cell. In this paper, we use the concept of exchangeability of random variables to model this functional redundancy and thereby account for the instability. We present a flexible framework to incorporate the exchangeability into the representation of lists. The proposed framework supports straightforward comparison between any 2 lists. It can also be used to generate new more stable gene rankings incorporating more information from the experimental data. Using 2 microarray data sets, we show that the proposed method provides more robust gene rankings than existing methods with respect to sampling variations, without compromising the biological significance of the rankings. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Biostatistics
volume
13
pages
129 - 141
publisher
Oxford University Press
external identifiers
  • wos:000298192300011
  • pmid:21908866
  • scopus:83755220000
ISSN
1468-4357
DOI
10.1093/biostatistics/kxr023
language
English
LU publication?
yes
id
63633086-b4d4-4496-b421-235e4ae8586a (old id 2168985)
date added to LUP
2011-09-30 09:40:33
date last changed
2017-04-16 03:17:53
@article{63633086-b4d4-4496-b421-235e4ae8586a,
  abstract     = {Analysis of multivariate data sets from, for example, microarray studies frequently results in lists of genes which are associated with some response of interest. The biological interpretation is often complicated by the statistical instability of the obtained gene lists, which may partly be due to the functional redundancy among genes, implying that multiple genes can play exchangeable roles in the cell. In this paper, we use the concept of exchangeability of random variables to model this functional redundancy and thereby account for the instability. We present a flexible framework to incorporate the exchangeability into the representation of lists. The proposed framework supports straightforward comparison between any 2 lists. It can also be used to generate new more stable gene rankings incorporating more information from the experimental data. Using 2 microarray data sets, we show that the proposed method provides more robust gene rankings than existing methods with respect to sampling variations, without compromising the biological significance of the rankings.},
  author       = {Soneson, Charlotte and Fontes, Magnus},
  issn         = {1468-4357},
  language     = {eng},
  pages        = {129--141},
  publisher    = {Oxford University Press},
  series       = {Biostatistics},
  title        = {A framework for list representation, enabling list stabilization through incorporation of gene exchangeabilities.},
  url          = {http://dx.doi.org/10.1093/biostatistics/kxr023},
  volume       = {13},
  year         = {2012},
}