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gene_networks_inference [2019/01/15 16:54]
admin [Related work]
gene_networks_inference [2019/03/07 04:07] (current)
admin [Data]
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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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 ===== Related work ===== ===== Related work =====