ArticleCancer research2008
Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors.
Article in Cancer research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 49 citations in OpenAlex.
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- Transcriptional down-regulation of metabolic genes by Gdown1 ablation induces quiescent cell re-entry into the cell cycle.Genes & development · 2020Article
- Transcriptomic profiling identifies novel mechanisms of transcriptional regulation of the cytochrome P450 (Cyp)3a11 gene.Scientific reports · 2019Article
- Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma.BMC genomics · 2018Article
- DNMT1 is a required genomic regulator for murine liver histogenesis and regeneration.Hepatology (Baltimore, Md.) · 2016Article
- Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia.Cancer cell · 2014Article
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- Pluripotent stem cells escape from senescence-associated DNA methylation changes.Genome research · 2013Article
- Identifying master regulators of cancer and their downstream targets by integrating genomic and epigenomic features.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2013Article
- Development of biomarkers for screening hepatocellular carcinoma using global data mining and multiple reaction monitoring.PloS one · 2013Article
- Integrative genomics: liver regeneration and hepatocellular carcinoma.Journal of cellular biochemistry · 2012Article
- Workflows for microarray data processing in the Kepler environment.BMC bioinformatics · 2012Article
- The histone demethylase Jhdm1a regulates hepatic gluconeogenesis.PLoS genetics · 2012Article
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- BeadDataPackR: A Tool to Facilitate the Sharing of Raw Data from Illumina BeadArray Studies.Cancer informatics · 2010Article
- Integrative epigenomic and genomic analysis of malignant pheochromocytoma.Experimental & molecular medicine · 2010Article
- Impairment of pre-mRNA splicing in liver disease: mechanisms and consequences.World journal of gastroenterology · 2010Review
- Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
There is widespread interest in efficient characterization of differences between tumor and normal samples. Here, we show an effective methodology for genome-scale characterization of tumors. Using matched normal and tumor samples from liver cancer patients, as well as non-cancer-related normal liver tissue, we first determined changes in gene expression as monitored on RNA expression arrays. We identified several hundred mRNAs that were consistently changed in the tumor samples. To characterize the mechanisms responsible for creation of the tumor-specific transcriptome, we performed chromatin immunoprecipitation on microarray experiments to assay binding of RNA polymerase II, H3me3K27, and H3me3K9 and DNA methylation in 25,000 promoter regions. These experiments identified changes in active and silenced regions of the genome in the tumor cells. Finally, we used a "virtual comparative genomic hybridization" method to identify copy number alterations in the tumor samples. Through comparison of RNA polymerase II binding, chromatin structure, DNA methylation, and copy number changes, we suggest that the major contributor to creation of the liver tumor transcriptome was changes in gene copy number.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.