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hepatocellular_carcinoma [2019/09/11 13:19] – [Current clinical risk assessment] Removed. admin | hepatocellular_carcinoma [2019/09/12 17:14] – [Related work] admin |
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==== Publication: ==== | ==== Publication: ==== |
Jessica Zavadil, Maryanne Herzig, Kim Hildreth, Amir Foroushani, William Boswell, Ronald Walter, Robert Reddick, Hugh White, Habil Zare. C3HeB/FeJ Mice Mimic Gene Expression and Pathobiological Features of Human Hepatocellular Carcinoma, //Molecular Carcinogenesis//, In press. | |
{{:wiki:public:jessica_compare.png?direct&400|}} | Jessica Zavadil, Maryanne Herzig, Kim Hildreth, Amir Foroushani, William Boswell, Ronald Walter, Robert Reddick, Hugh White, Habil Zare. "C3HeB/FeJ Mice mimic many aspects of gene expression and pathobiological features of human hepatocellular carcinoma." [[https://onlinelibrary.wiley.com/doi/abs/10.1002/mc.22929|Molecular carcinogenesis ]]58.3 (2019): 309-320. |
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==== Project 2: ==== | ==== Project 2: ==== |
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- Hart, Steven N., et al. "Calculating sample size estimates for RNA sequencing data." //Journal of Computational [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842884/|Biology]]//20.12 (2013): 970-978.Wu, Hao, Chi Wang, and Zhijin Wu. "PROPER: comprehensive power evaluation for differential expression using RNA-seq." //[[http://bioinformatics.oxfordjournals.org/content/31/2/233.short|Bioinformatics]]//31.2 (2015): 233-241.From [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842884/figure/f2/|Fig2]] and [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842884/figure/f2/|Fig3]] of Huang et al. paper, and [[http://bioinformatics.oxfordjournals.org.libproxy.txstate.edu/content/31/2/233/F5.expansion.html|Fig5]] of Hart et al., it seems that at least 5-7 samples are needed for each condition. | - Hart, Steven N., et al. "Calculating sample size estimates for RNA sequencing data." //Journal of Computational [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842884/|Biology]]//20.12 (2013): 970-978.Wu, Hao, Chi Wang, and Zhijin Wu. "PROPER: comprehensive power evaluation for differential expression using RNA-seq." //[[http://bioinformatics.oxfordjournals.org/content/31/2/233.short|Bioinformatics]]//31.2 (2015): 233-241.From [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842884/figure/f2/|Fig2]] and [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842884/figure/f2/|Fig3]] of Huang et al. paper, and [[http://bioinformatics.oxfordjournals.org.libproxy.txstate.edu/content/31/2/233/F5.expansion.html|Fig5]] of Hart et al., it seems that at least 5-7 samples are needed for each condition. |
- Ching, Travers, Sijia Huang, and Lana X. Garmire. "Power analysis and sample size estimation for RNA-Seq differential expression." //[[http://rnajournal.cshlp.org/content/early/2014/09/22/rna.046011.114|rna]]//20.11 (2014): 1684-1696. | - Ching, Travers, Sijia Huang, and Lana X. Garmire. "Power analysis and sample size estimation for RNA-Seq differential expression." //[[http://rnajournal.cshlp.org/content/early/2014/09/22/rna.046011.114|rna]]//20.11 (2014): 1684-1696. |
- Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma, [[http://www.cell.com/cell/abstract/S0092-8674(17)30639-6?innerTabgraphical_S0092867417306396|Cell]], 2017 [{{:ally-copmprehensive_and_integrative_genomic_char_of_hcc-cell-2017.pdf|pdf}} ]. TCGA's HCC data and subtyping using DNA copy number, DNA methylation, mRNA expression, miRNA expression and RPPA (protein expression). Links to the MDACC dataset with 100 HCC samples. | - Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma, [[http://www.cell.com/cell/abstract/S0092-8674(17)30639-6?innerTabgraphical_S0092867417306396|Cell]], 2017 [{{:ally-copmprehensive_and_integrative_genomic_char_of_hcc-cell-2017.pdf|pdf}} ]. TCGA's HCC data and subtyping using DNA copy number, DNA methylation, mRNA expression, miRNA expression and RPPA (protein expression). Links to the MDACC dataset with 100 HCC samples. |
| - Subramaniam, Somasundaram, Robin K. Kelley, and Alan P. Venook. "A review of hepatocellular carcinoma (HCC) staging systems." [[http://cco.amegroups.com/article/view/2528/3943|Chinese clinical oncology]] 2.4 (2013). |
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