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On the statistical analysis of the GS-NS0 cell proteome: Imputation, clustering and variability testing

Ahmad, Norhaiza, Zhang, Jian, Brown, Philip J., James, David C., Birch, John R., Racher, Andrew J., Smales, Christopher Mark (2006) On the statistical analysis of the GS-NS0 cell proteome: Imputation, clustering and variability testing. Biochimica Et Biophysica Acta-Proteins and Proteomics, 1764 (7). pp. 1179-1187. ISSN 1570-9639. (doi:10.1016/j.bbapap.2006.05.002) (The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided) (KAR id:6224)

The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided.
Official URL:
http://dx.doi.org/10.1016/j.bbapap.2006.05.002

Abstract

We have undertaken two-dimensional gel electrophoresis proteomic profiling on a series of cell lines with different recombinant antibody production rates. Due to the nature of gel-based experiments not all protein spots are detected across all samples in an experiment, and hence datasets are invariably incomplete. New approaches are therefore required for the analysis of such graduated datasets. We approached this problem in two ways. Firstly, we applied a missing value imputation technique to calculate missing data points. Secondly, we combined a singular value decomposition based hierarchical clustering with the expression variability test to identify protein spots whose expression correlates with increased antibody production. The results have shown that while imputation of missing data was a useful method to improve the statistical analysis of such data sets, this was of limited use in differentiating between the samples investigated, and highlighted a small number of candidate proteins for further investigation.

Item Type: Article
DOI/Identification number: 10.1016/j.bbapap.2006.05.002
Uncontrolled keywords: 2D-PAGE; proteomic profiling; NS0 cells; imputed values; hierarchical clustering; rank correlation
Subjects: Q Science
Divisions: Divisions > Division of Natural Sciences > Biosciences
Divisions > Division of Computing, Engineering and Mathematical Sciences > School of Mathematics, Statistics and Actuarial Science
Depositing User: Mark Smales
Date Deposited: 03 Sep 2008 07:07 UTC
Last Modified: 16 Nov 2021 09:44 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/6224 (The current URI for this page, for reference purposes)

University of Kent Author Information

Zhang, Jian.

Creator's ORCID: https://orcid.org/0000-0001-8405-2323
CReDIT Contributor Roles:

Brown, Philip J..

Creator's ORCID:
CReDIT Contributor Roles:

James, David C..

Creator's ORCID:
CReDIT Contributor Roles:

Smales, Christopher Mark.

Creator's ORCID: https://orcid.org/0000-0002-2762-4724
CReDIT Contributor Roles:
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