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gene_networks_inference [2019/06/03 19:16]
admin [Software]
gene_networks_inference [2019/08/16 03:09] (current)
admin [Data]
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   - The [[https://​www.nature.com/​articles/​s41586-018-0623-z#​Sec38|BEAT]] ALM dataset of ~300 cases including gene expression, survival, ELN17, etc.   - The [[https://​www.nature.com/​articles/​s41586-018-0623-z#​Sec38|BEAT]] ALM dataset of ~300 cases including gene expression, survival, ELN17, etc.
   - [[https://​www.leukemiaatlas.org/​adultaml|Leukemia Protein Atlas]]: Expression of hundreds of proteins were measured in bone marrow and PB samples of ~200 AML cases. A good publicly available resource to validate findings based on gene expression assays.   - [[https://​www.leukemiaatlas.org/​adultaml|Leukemia Protein Atlas]]: Expression of hundreds of proteins were measured in bone marrow and PB samples of ~200 AML cases. A good publicly available resource to validate findings based on gene expression assays.
 +  - ~40K [[https://​www.cell.com/​cell/​fulltext/​S0092-8674(19)30094-7?​_returnURL=https://​linkinghub.elsevier.com/​retrieve/​pii/​S0092867419300947?​showall=true|single cell]] RNA-Seq data from 40 bone marrow aspirates, including 16 AML patients and \\  5 healthy donors.
  
  
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   - 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.
   - Guillamot, Maria, Luisa Cimmino, and Iannis Aifantis. "The impact of DNA methylation in hematopoietic malignancies."​ [[http://​www.cell.com/​trends/​cancer/​pdf/​S2405-8033(15)00089-8.pdf|Trends in cancer]] 2.2 (2016): 70-83. \\  Reviews and references DNA methylation studies and datasets on AML. E.g., [[http://​www.sciencedirect.com/​science/​article/​pii/​S1535610809004206|Figueroa]] et al. used DNA methylation for classification of 344 AML cases. [[http://​journals.plos.org/​plosgenetics/​article?​id=10.1371/​journal.pgen.1002781|Akalin]] et al. related DNA methylation patterns with mutations in 5 AML cases. "The methylation status of specific genes can predict the future survival of AML patients, suggesting that DNA methylation is a biomarker for clinical outcome"​ see e.g., Figueroa et al, [[http://​www.bloodjournal.org/​content/​bloodjournal/​113/​6/​1315.full.pdf?​sso-checked=true|Jiang]] 2009 (studied MDS to AML progression in 184 cases), and [[http://​www.bloodjournal.org/​content/​115/​3/​636.long?​sso-checked=true|Bullinger]] 2010 (analyzed 92 genomic regions in 182 patients).   - Guillamot, Maria, Luisa Cimmino, and Iannis Aifantis. "The impact of DNA methylation in hematopoietic malignancies."​ [[http://​www.cell.com/​trends/​cancer/​pdf/​S2405-8033(15)00089-8.pdf|Trends in cancer]] 2.2 (2016): 70-83. \\  Reviews and references DNA methylation studies and datasets on AML. E.g., [[http://​www.sciencedirect.com/​science/​article/​pii/​S1535610809004206|Figueroa]] et al. used DNA methylation for classification of 344 AML cases. [[http://​journals.plos.org/​plosgenetics/​article?​id=10.1371/​journal.pgen.1002781|Akalin]] et al. related DNA methylation patterns with mutations in 5 AML cases. "The methylation status of specific genes can predict the future survival of AML patients, suggesting that DNA methylation is a biomarker for clinical outcome"​ see e.g., Figueroa et al, [[http://​www.bloodjournal.org/​content/​bloodjournal/​113/​6/​1315.full.pdf?​sso-checked=true|Jiang]] 2009 (studied MDS to AML progression in 184 cases), and [[http://​www.bloodjournal.org/​content/​115/​3/​636.long?​sso-checked=true|Bullinger]] 2010 (analyzed 92 genomic regions in 182 patients).
-  - John [[https://​www.youtube.com/​watch?​v=Vyhq7GZFnes|Quackenbush'​s]] talk entitled: "Using Networks to Understand the Genotype-Phenotype Connection"​ \\+  - John [[https://​www.youtube.com/​watch?​v=Vyhq7GZFnes|Quackenbush'​s]] talk entitled: "Using Networks to Understand the Genotype-Phenotype Connection"​
 +  - Saelens, Wouter, Robrecht Cannoodt, and Yvan Saeys. "A comprehensive evaluation of module detection methods for gene expression data." [[https://​www.nature.com/​articles/​s41467-018-03424-4|Nature communications]] 9.1 (2018): 1090.  ​\\  "​Graph-based,​ representative-based,​ and hierarchical clustering all performed equally well, with the clustering method FLAME (Fuzzy clustering by Local Approximation of Memberships),​ one of the only clustering methods able to detect overlap, slightly outperforming other clustering methods"​ including WGCNA. Regularity networks that had been inferred using other data, e.g., "​binding motifs in active enhancers",​ were used as gold standard.
  
- \\ **Related software**+ 
 +===== Related software ​=====
  
   - Weighted Gene Co-expression Network Analysis ([[http://​labs.genetics.ucla.edu/​horvath/​CoexpressionNetwork/​|WGCNA]]) developed at UCLA. The page has links to some good introductory workshops.   - Weighted Gene Co-expression Network Analysis ([[http://​labs.genetics.ucla.edu/​horvath/​CoexpressionNetwork/​|WGCNA]]) developed at UCLA. The page has links to some good introductory workshops.