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:
https://lup.lub.lu.se/record/2519856
- author
- Kirik, Ufuk
LU
; Cifani, Paolo
LU
; Albrekt, Ann-Sofie
LU
; Lindstedt, Malin
LU
; Heyden, Anders
LU
and Levander, Fredrik
LU
- organization
- publishing date
- 2012
- 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 (ACS)
- external identifiers
-
- pmid:22471554
- wos:000303492100028
- scopus:84860639311
- pmid:22471554
- ISSN
- 1535-3893
- DOI
- 10.1021/pr300038b
- language
- English
- LU publication?
- yes
- id
- 1efe49bc-4ecb-496a-ba86-018c18eec466 (old id 2519856)
- date added to LUP
- 2016-04-01 11:14:48
- date last changed
- 2023-08-31 21:36:15
@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 (ACS)}},
series = {{Journal of Proteome Research}},
title = {{Multimodel Pathway Enrichment Methods for Functional Evaluation of Expression Regulation.}},
url = {{http://dx.doi.org/10.1021/pr300038b}},
doi = {{10.1021/pr300038b}},
volume = {{11}},
year = {{2012}},
}