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gene_networks_inference [2019/01/15 14:54] – [Related work] admingene_networks_inference [2019/03/07 02:07] – [Data] admin
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   - 200 AML cases from TCGA (LAML dataset). Available data types include gene expression , DNA-methylation, CNV, mutation, etc. TCGA data moved to [[https://gdc-portal.nci.nih.gov/|GDC]] but DNA-methylation is not there. Instead, it can be retrieved from GDC Legacy Archive or the original [[https://tcga-data.nci.nih.gov/docs/publications/laml_2012/|paper]].   - 200 AML cases from TCGA (LAML dataset). Available data types include gene expression , DNA-methylation, CNV, mutation, etc. TCGA data moved to [[https://gdc-portal.nci.nih.gov/|GDC]] but DNA-methylation is not there. Instead, it can be retrieved from GDC Legacy Archive or the original [[https://tcga-data.nci.nih.gov/docs/publications/laml_2012/|paper]].
   - German [[https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37642|AMLCG]] 1999 provides microarray data of 562 AML samples.   - German [[https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37642|AMLCG]] 1999 provides microarray data of 562 AML samples.
-  - Papaemmanuil, Elli, et al. "Genomic classification and prognosis in acute myeloid leukemia." [[http://www.nejm.org/doi/full/10.1056/NEJMoa1516192#t=article|NEJM]] 374.23 (2016): 2209-2221. \\  The mutations of 111 genes in over **1,500 AML**  cases are reported. The authors used this information to classify cases into groups and showed these groups have different prognosis. I.,e., [[https://www.mskcc.org/sites/default/files/node/2246/documents/discrete-cpe.pdf|concordance]] (probability estimates) improves from 64% using only the European LeukemiaNet criteria to 71%. Using the alternative allele frequency, they estimated the time of occurrence for the driver mutations. The data are available through the links in the corresponding [[http://www.nature.com/ng/journal/v49/n3/full/ng.3756.html|Nature]] paper [[[:ng.3756.pdf?media=ng.3756.pdf|pdf]]]. Information on downloading these data is contained in the readme file found in genetwork:~/proj/genetwork/data/AML/gerstung/readme.txt. In particular, we have access to [[https://www.ebi.ac.uk/ega/studies/EGAS00001000275|EGAS00001000275]] through [[https://ega-archive.org/|EGA]] Archives. See [[:habils_lab_notebook|Habil's]] note on 2017/09/05 for more detail. Any member of Oncinfo Lab who touches (analyzes or views) these data from Sanger Institute must read and abide to the [[:sanger_data_agreement_2017-08-09.pdf?media=sanger_data_agreement_2017-08-09.pdf|agreement]].+  - Papaemmanuil, Elli, et al. "Genomic classification and prognosis in acute myeloid leukemia." [[http://www.nejm.org/doi/full/10.1056/NEJMoa1516192#t=article|NEJM]] 374.23 (2016): 2209-2221. \\  The mutations of 111 genes in over **1,500 AML**  cases are reported. The authors used this information to classify cases into groups and showed these groups have different prognosis. I.,e., [[https://www.mskcc.org/sites/default/files/node/2246/documents/discrete-cpe.pdf|concordance]] (probability estimates) improves from 64% using only the European LeukemiaNet criteria to 71%. Using the alternative allele frequency, they estimated the time of occurrence for the driver mutations. The data are available through the links in the corresponding [[http://www.nature.com/ng/journal/v49/n3/full/ng.3756.html|Nature]] paper [[:ng.3756.pdf?media=ng.3756.pdf|pdf]]]. Information on downloading these data is contained in the readme file found in genetwork:~/proj/genetwork/data/AML/gerstung/readme.txt. In particular, we have access to [[https://www.ebi.ac.uk/ega/studies/EGAS00001000275|EGAS00001000275]] through [[https://ega-archive.org/|EGA]] Archives. See [[:habils_lab_notebook|Habil's]] note on 2017/09/05 for more detail. Any member of Oncinfo Lab who touches (analyzes or views) these data from Sanger Institute must read and abide to the [[:sanger_data_agreement_2017-08-09.pdf?media=sanger_data_agreement_2017-08-09.pdf|agreement]].
   - RNA, DNA methylation, whole genome, etc. data of 960 (pediatric?) AML cases are available from [[https://ocg.cancer.gov/programs/target/acute-myeloid-leukemia|TARGET]] AML study.   - RNA, DNA methylation, whole genome, etc. data of 960 (pediatric?) AML cases are available from [[https://ocg.cancer.gov/programs/target/acute-myeloid-leukemia|TARGET]] AML study.
   - AML-NK gene expression data (RNA-Seq) from three datasets (TCGA, Leucegene, and PMP/BCCA). [[https://docs.google.com/a/princeton.edu/document/d/1tB75BDAoG6-ggkoKzxF_f8anTnaP0lOAZ4MG-wEWCyk/edit?usp=sharing|Full description]].   - AML-NK gene expression data (RNA-Seq) from three datasets (TCGA, Leucegene, and PMP/BCCA). [[https://docs.google.com/a/princeton.edu/document/d/1tB75BDAoG6-ggkoKzxF_f8anTnaP0lOAZ4MG-wEWCyk/edit?usp=sharing|Full description]].
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   - Genomic Data Commons ([[https://portal.gdc.cancer.gov/repository|GDC]]), which contains TCGA data and more.   - Genomic Data Commons ([[https://portal.gdc.cancer.gov/repository|GDC]]), which contains TCGA data and more.
   - [[https://amp.pharm.mssm.edu/archs4/|ARCHS4]], which was developed at the Icahn School of Medicine at Mount Sinai, and provides tools to download and analyze RNA-Seq data including single-cell gene expression.   - [[https://amp.pharm.mssm.edu/archs4/|ARCHS4]], which was developed at the Icahn School of Medicine at Mount Sinai, and provides tools to download and analyze RNA-Seq data including single-cell gene expression.
 +  - The [[https://www.nature.com/articles/s41586-018-0623-z#Sec38|BEAT]] ALM dataset of ~300 cases including gene expression, survival, ELN17, etc.
  
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