ArticleBMC genomics2005
Comparison of array-based comparative genomic hybridization with gene expression-based regional expression biases to identify genetic abnormalities in hepatocellular carcinoma.
Article in BMC genomics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Pancancer Analysis of the Oncogenic and Prognostic Role ofInternational journal of molecular sciences · 2022Article
- Rapid and accurate detection ofOncotarget · 2017Article
- Non-invasive Analysis of Genomic Copy Number Variation in Patients with Hepatocellular Carcinoma by Next Generation DNA Sequencing.Journal of Cancer · 2015Article
- Identification of drivers from cancer genome diversity in hepatocellular carcinoma.International journal of molecular sciences · 2014Review
- RNA sequencing reveals upregulation of RUNX1-RUNX1T1 gene signatures in clear cell renal cell carcinoma.BioMed research international · 2014Article
- Low expression of the putative tumour suppressor spinophilin is associated with higher proliferative activity and poor prognosis in patients with hepatocellular carcinoma.British journal of cancer · 2013Article
- Liverome: a curated database of liver cancer-related gene signatures with self-contained context information.BMC genomics · 2011Article
- Chromosomal amplification of leucine-rich repeat kinase-2 (LRRK2) is required for oncogenic MET signaling in papillary renal and thyroid carcinomas.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Birt-Hogg-Dubé renal tumors are genetically distinct from other renal neoplasias and are associated with up-regulation of mitochondrial gene expression.BMC medical genomics · 2010Article
- Comparative gene expression profiling analysis of urothelial carcinoma of the renal pelvis and bladder.BMC medical genomics · 2010Article
- Proteomic changes resulting from gene copy number variations in cancer cells.PLoS genetics · 2010Article
- A Comprehensive Study of Progressive Cytogenetic Alterations in Clear Cell Renal Cell Carcinoma and a New Model for ccRCC Tumorigenesis and Progression.Advances in bioinformatics · 2010Article
- Somatic pairing of chromosome 19 in renal oncocytoma is associated with deregulated EGLN2-mediated [corrected] oxygen-sensing response.PLoS genetics · 2008Article
- An improved method for detecting and delineating genomic regions with altered gene expression in cancer.Genome biology · 2008Article
- SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets.BMC bioinformatics · 2007Article
- Chromosome instability, chromosome transcriptome, and clonal evolution of tumor cell populations.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Microarray-based analysis for hepatocellular carcinoma: from gene expression profiling to new challenges.World journal of gastroenterology · 2007Review
Corrections and comments
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4 authors.
Funding
Abstract
backgroundRegional expression biases (REBs) are genetic intervals where gene expression is coordinately changed. For example, if a region of the genome is amplified, often the majority of genes that map within the amplified region show increased expression when compared to genes located in cytogenetically normal regions. As such, REBs have the potential to act as surrogates for cytogenetic data traditionally obtained using molecular technologies such as comparative genomic hybridization. However as REBs are identified using transcriptional information, detection of REBs may also identify local transcriptional abnormalities produced by both genetic and epigenetic mechanisms.
resultsREBs were identified from a set of hepatocellular carcinoma (HCC) gene expression profiles using a multiple span moving binomial test and compared to genetic abnormalities identified using array-based comparative genomic hybridization (aCGH). In the majority of cases, REBs overlapped genetic abnormalities as determined by aCGH. For example, both methods identified narrow regions of frequent amplification on chromosome 1p and narrow regions of frequent deletion on 17q. In a minority of cases, REBs were identified in regions not determined to be abnormal via other cytogenetic technologies. Specifically, expression biases reflective of cell proliferation were frequently identified on chromosome 6p21-23.
conclusionIdentification of REBs using a multiple span moving binomial test produced reasonable approximations of underlying cytogenetic abnormalities. However, caution should be used when attributing REBs identified on chromosome 6p to cytogenetic events in rapidly proliferating cells.
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