Interlaboratory and Interplatform Comparison of Microarray Gene Expression Analysis of HepG2 Cells Exposed to Benzo(a)pyrene.

2.50
Hdl Handle:
http://hdl.handle.net/10146/76776
Title:
Interlaboratory and Interplatform Comparison of Microarray Gene Expression Analysis of HepG2 Cells Exposed to Benzo(a)pyrene.
Authors:
Hockley, Sarah L.; Mathijs, Karen; Staal, Yvonne C.M.; Brewer, Daniel; Giddings, Ian; van Delft, Joost H.M.; Phillips, David H.
Abstract:
Abstract Microarray technology is being used increasingly to study gene expression of biological systems on a large scale. Both interlaboratory and interplatform differences are known to contribute to variability in microarray data. In this study we have investigated data from different platforms and laboratories on the transcriptomic profile of HepG2 cells exposed to benzo(a)pyrene (BaP). RNA samples generated in two different laboratories were analyzed using both Agilent oligonucleotide microarrays and Cancer Research UK (CR-UK) cDNA microarrays. Comparability of the expression profiles was assessed at various levels including correlation and overlap between the data, clustering of the data and affected biological processes. Overlap and correlation occurred, but it was not possible to deduce whether choice of platform or interlaboratory differences contributed more to the data variation. Principal component analysis (PCA) and hierarchical clustering of the expression profiles indicated that the data were most clearly defined by duration of exposure to BaP, suggesting that laboratory and platform variability does not mask the biological effects. Real-time quantitative PCR was used to validate the two array platforms and indicated that false negatives, rather than false positives, are obtained with both systems. All together these results suggest that data from similar biological experiments analyzed on different microarray platforms can be combined to give a more complete transcriptomic profile. Each platform gives a slight variation in the BaP-gene expression response and, although it cannot be stated which is more correct, combining the two data sets is more informative than considering them individually.
Citation:
OMICS 2009, 13 (2):115-125
Journal:
Omics : a journal of integrative biology
Issue Date:
Apr-2009
URI:
http://hdl.handle.net/10146/76776
DOI:
10.1089/omi.2008.0060
PubMed ID:
19245359
Additional Links:
http://www.liebertonline.com/doi/abs/10.1089/omi.2008.0060
Type:
Article
Language:
en
ISSN:
1557-8100
Appears in Collections:
Articles

Full metadata record

DC FieldValue Language
dc.contributor.authorHockley, Sarah L.-
dc.contributor.authorMathijs, Karen-
dc.contributor.authorStaal, Yvonne C.M.-
dc.contributor.authorBrewer, Daniel-
dc.contributor.authorGiddings, Ian-
dc.contributor.authorvan Delft, Joost H.M.-
dc.contributor.authorPhillips, David H.-
dc.date.accessioned2009-08-10T09:02:19Z-
dc.date.available2009-08-10T09:02:19Z-
dc.date.issued2009-04-
dc.identifier.citationOMICS 2009, 13 (2):115-125en
dc.identifier.issn1557-8100-
dc.identifier.pmid19245359-
dc.identifier.doi10.1089/omi.2008.0060-
dc.identifier.urihttp://hdl.handle.net/10146/76776-
dc.description.abstractAbstract Microarray technology is being used increasingly to study gene expression of biological systems on a large scale. Both interlaboratory and interplatform differences are known to contribute to variability in microarray data. In this study we have investigated data from different platforms and laboratories on the transcriptomic profile of HepG2 cells exposed to benzo(a)pyrene (BaP). RNA samples generated in two different laboratories were analyzed using both Agilent oligonucleotide microarrays and Cancer Research UK (CR-UK) cDNA microarrays. Comparability of the expression profiles was assessed at various levels including correlation and overlap between the data, clustering of the data and affected biological processes. Overlap and correlation occurred, but it was not possible to deduce whether choice of platform or interlaboratory differences contributed more to the data variation. Principal component analysis (PCA) and hierarchical clustering of the expression profiles indicated that the data were most clearly defined by duration of exposure to BaP, suggesting that laboratory and platform variability does not mask the biological effects. Real-time quantitative PCR was used to validate the two array platforms and indicated that false negatives, rather than false positives, are obtained with both systems. All together these results suggest that data from similar biological experiments analyzed on different microarray platforms can be combined to give a more complete transcriptomic profile. Each platform gives a slight variation in the BaP-gene expression response and, although it cannot be stated which is more correct, combining the two data sets is more informative than considering them individually.en
dc.language.isoenen
dc.relation.urlhttp://www.liebertonline.com/doi/abs/10.1089/omi.2008.0060en
dc.subject.meshBenzo(a)pyreneen
dc.subject.meshCell Line, Tumoren
dc.subject.meshGene Expression Profilingen
dc.subject.meshHumansen
dc.subject.meshNucleic Acid Hybridizationen
dc.subject.meshOligonucleotide Array Sequence Analysisen
dc.titleInterlaboratory and Interplatform Comparison of Microarray Gene Expression Analysis of HepG2 Cells Exposed to Benzo(a)pyrene.en
dc.typeArticleen
dc.identifier.journalOmics : a journal of integrative biologyen
All Items in ECNIS-NIOM are protected by copyright, with all rights reserved, unless otherwise indicated.