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hepatocellular_carcinoma [2019/09/10 15:55] – [Related work] adminhepatocellular_carcinoma [2019/10/07 15:45] – [Objectives] admin
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 ====== Hepatocellular carcinoma ====== ====== Hepatocellular carcinoma ======
 ===== Objectives ===== ===== Objectives =====
-\\ Hepatocellular carcinoma (HCC) is a the most common type of liver cancer and the third leading cause of cancer deaths in the world. The goal of project one is to identify the genes that are associated with regressing tumors (regardless of type of treatment) vs. those that are growing from the C3HeB/FeJ mouse model. Normal liver is used as a control. The results will be useful in identifying new therapeutic targets and potential drug combinations which could lead to more efficient treatments. Project two is related to knockdown of a specific protein that results in HCC in a different mouse model. The goal in the second project is to identify the genes and pathways that correlate with this protein.\\ \\ + 
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 +Hepatocellular carcinoma (HCC) is a the most common type of liver cancer and the third leading cause of cancer deaths in the world. [[https://www.merckmanuals.com/home/liver-and-gallbladder-disorders/fibrosis-and-cirrhosis-of-the-liver/cirrhosis-of-the-liver#v28485447|Cirrhosis]] of the liver is a major risk and contributing factor for HCC. The goal of project one is to identify the genes that are associated with regressing tumors (regardless of type of treatment) vs. those that are growing from the C3HeB/FeJ mouse model. Normal liver is used as a control. The results will be useful in identifying new therapeutic targets and potential drug combinations which could lead to more efficient treatments. Project two is related to knockdown of a specific protein that results in HCC in a different mouse model. The goal in the second project is to identify the genes and pathways that correlate with this protein. 
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 ===== Data ===== ===== Data =====
  
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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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 +{{:wiki:public:jessica_compare.png?direct&400}} 
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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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-===== Current clinical risk assessment ===== 
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 =====   Related software   ===== =====   Related software   =====