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Multimodel Pathway Enrichment Methods for Functional Evaluation of Expression Regulation.

Kirik, Ufuk LU ; Cifani, Paolo LU ; Albrekt, Ann-Sofie LU ; Lindstedt, Malin LU ; Heyden, Anders LU and Levander, Fredrik LU (2012) In Journal of Proteome Research 11(5). p.2955-2967
Abstract
Functional analysis of quantitative expression data is becoming common practice within the proteomics and transcriptomics fields; however, a gold standard for this type of analysis has yet not emerged. To grasp the systemic changes in biological systems, efficient and robust methods are needed for data analysis following expression regulation experiments. We discuss several conceptual and practical challenges potentially hindering the emergence of such methods and present a novel method, called FEvER, that utilizes two enrichment models in parallel. We also present analysis of three disparate differential expression data sets using our method and compare our results to other established methods. With many useful features such as pathway... (More)
Functional analysis of quantitative expression data is becoming common practice within the proteomics and transcriptomics fields; however, a gold standard for this type of analysis has yet not emerged. To grasp the systemic changes in biological systems, efficient and robust methods are needed for data analysis following expression regulation experiments. We discuss several conceptual and practical challenges potentially hindering the emergence of such methods and present a novel method, called FEvER, that utilizes two enrichment models in parallel. We also present analysis of three disparate differential expression data sets using our method and compare our results to other established methods. With many useful features such as pathway hierarchy overview, we believe the FEvER method and its software implementation will provide a useful tool for peers in the field of proteomics. Furthermore, we show that the method is also applicable to other types of expression data. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Proteome Research
volume
11
issue
5
pages
2955 - 2967
publisher
The American Chemical Society
external identifiers
  • pmid:22471554
  • wos:000303492100028
  • scopus:84860639311
ISSN
1535-3893
DOI
10.1021/pr300038b
project
CREATE Health
language
English
LU publication?
yes
id
1efe49bc-4ecb-496a-ba86-018c18eec466 (old id 2519856)
date added to LUP
2012-05-09 13:06:19
date last changed
2017-01-01 04:17:17
@article{1efe49bc-4ecb-496a-ba86-018c18eec466,
  abstract     = {Functional analysis of quantitative expression data is becoming common practice within the proteomics and transcriptomics fields; however, a gold standard for this type of analysis has yet not emerged. To grasp the systemic changes in biological systems, efficient and robust methods are needed for data analysis following expression regulation experiments. We discuss several conceptual and practical challenges potentially hindering the emergence of such methods and present a novel method, called FEvER, that utilizes two enrichment models in parallel. We also present analysis of three disparate differential expression data sets using our method and compare our results to other established methods. With many useful features such as pathway hierarchy overview, we believe the FEvER method and its software implementation will provide a useful tool for peers in the field of proteomics. Furthermore, we show that the method is also applicable to other types of expression data.},
  author       = {Kirik, Ufuk and Cifani, Paolo and Albrekt, Ann-Sofie and Lindstedt, Malin and Heyden, Anders and Levander, Fredrik},
  issn         = {1535-3893},
  language     = {eng},
  number       = {5},
  pages        = {2955--2967},
  publisher    = {The American Chemical Society},
  series       = {Journal of Proteome Research},
  title        = {Multimodel Pathway Enrichment Methods for Functional Evaluation of Expression Regulation.},
  url          = {http://dx.doi.org/10.1021/pr300038b},
  volume       = {11},
  year         = {2012},
}