Interlaboratory and Interplatform Comparison of Microarray Gene Expression Analysis of HepG2 Cells Exposed to Benzo(a)pyrene.
Cast your vote
You can rate an item by clicking the amount of stars they wish to award to this item.
When enough users have cast their vote on this item, the average rating will also be shown.
Your vote was cast
Thank you for your feedback
Thank you for your feedback
AuthorsHockley, Sarah L.
Staal, Yvonne C.M.
van Delft, Joost H.M.
Phillips, David H.
MetadataShow full item record
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.
CitationOMICS 2009, 13 (2):115-125
- Transcriptional signatures of normal human mammary epithelial cells in response to benzo[a]pyrene exposure: a comparison of three microarray platforms.
- Authors: Gwinn MR, Keshava C, Olivero OA, Humsi JA, Poirier MC, Weston A
- Issue date: 2005 Winter
- Time- and concentration-dependent changes in gene expression induced by benzo(a)pyrene in two human cell lines, MCF-7 and HepG2.
- Authors: Hockley SL, Arlt VM, Brewer D, Giddings I, Phillips DH
- Issue date: 2006 Oct 16
- Identification through microarray gene expression analysis of cellular responses to benzo(a)pyrene and its diol-epoxide that are dependent or independent of p53.
- Authors: Hockley SL, Arlt VM, Jahnke G, Hartwig A, Giddings I, Phillips DH
- Issue date: 2008 Jan
- Benzo[a]pyrene and glycine N-methyltransferse interactions: gene expression profiles of the liver detoxification pathway.
- Authors: Lee CM, Chen SY, Lee YC, Huang CY, Chen YM
- Issue date: 2006 Jul 15
- Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays.
- Authors: Wang Y, Barbacioru C, Hyland F, Xiao W, Hunkapiller KL, Blake J, Chan F, Gonzalez C, Zhang L, Samaha RR
- Issue date: 2006 Mar 21