ArticleBMC cancer2005
Application of Affymetrix array and Massively Parallel Signature Sequencing for identification of genes involved in prostate cancer progression.
Article in BMC cancer, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
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34 citing papers in PubMed, 1 synthesis or guideline pooled it, 71 citations in OpenAlex.
- A meta-analysis of kidney microarray datasets: investigation of cytokine gene detection and correlation with rt-PCR and detection thresholds.BMC genomics · 2007Pooled it
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- Cancer-secreted AGR2 induces programmed cell death in normal cells.Oncotarget · 2016Article
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- Elisidepsin Interacts Directly with Glycosylceramides in the Plasma Membrane of Tumor Cells to Induce Necrotic Cell Death.PloS one · 2015Article
- Comparative genomic and transcriptomic analyses of LNCaP and C4-2B prostate cancer cell lines.PloS one · 2014Article
- Ceramide glycosylation catalyzed by glucosylceramide synthase and cancer drug resistance.Advances in cancer research · 2013Review
- DNA methylation in promoter region as biomarkers in prostate cancer.Methods in molecular biology (Clifton, N.J.) · 2012Article
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- Aberrant DNA methylation and prostate cancer.Current genomics · 2011Article
- Lineage relationship of prostate cancer cell types based on gene expression.BMC medical genomics · 2011Article
- Androgen receptor signaling in prostate cancer development and progression.Journal of carcinogenesis · 2011Article
- Promoter hypermethylation in prostate cancer.Cancer control : journal of the Moffitt Cancer Center · 2010Review
- Ceramide galactosyltransferase (UGT8) is a molecular marker of breast cancer malignancy and lung metastases.British journal of cancer · 2010Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundAffymetrix GeneChip Array and Massively Parallel Signature Sequencing (MPSS) are two high throughput methodologies used to profile transcriptomes. Each method has certain strengths and weaknesses; however, no comparison has been made between the data derived from Affymetrix arrays and MPSS. In this study, two lineage-related prostate cancer cell lines, LNCaP and C4-2, were used for transcriptome analysis with the aim of identifying genes associated with prostate cancer progression.
methodsAffymetrix GeneChip array and MPSS analyses were performed. Data was analyzed with GeneSpring 6.2 and in-house perl scripts. Expression array results were verified with RT-PCR.
resultsComparison of the data revealed that both technologies detected genes the other did not. In LNCaP, 3,180 genes were only detected by Affymetrix and 1,169 genes were only detected by MPSS. Similarly, in C4-2, 4,121 genes were only detected by Affymetrix and 1,014 genes were only detected by MPSS. Analysis of the combined transcriptomes identified 66 genes unique to LNCaP cells and 33 genes unique to C4-2 cells. Expression analysis of these genes in prostate cancer specimens showed CA1 to be highly expressed in bone metastasis but not expressed in primary tumor and EPHA7 to be expressed in normal prostate and primary tumor but not bone metastasis.
conclusionOur data indicates that transcriptome profiling with a single methodology will not fully assess the expression of all genes in a cell line. A combination of transcription profiling technologies such as DNA array and MPSS provides a more robust means to assess the expression profile of an RNA sample. Finally, genes that were differentially expressed in cell lines were also differentially expressed in primary prostate cancer and its metastases.
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