3.点击左上角File 4.选择WXS，Masked Somatic Mutation，maf，simple nucleotide variation，Aliquot Ensemb...
1.打开TCGA网站，输入需要下载的肿瘤类型 2.点击WXS后面的数字51 3.点击左上角File 4.选择WXS，Masked...
|TCGA-LUSC |Lung Squamous Cell Carcinoma |TCGA-GBM |Glioblastoma Multiforme |TCGA-UVM |Uveal Melanoma |TCGA-LGG |Brain Lower Grade Glioma |HCMI-CMDC |NCI Cancer Model Development for the Human Cancer Model Initiative |TCGA-BRCA |Breast Invasive Carcinoma |TARGET-RT |Rhabdoid Tumor |TARGET-CCSK ...
query.met <- GDCquery(project = c("TCGA-GBM","TCGA-LGG"), legacy = TRUE, data.category = "DNA methylation", platform = "Illumina Human Methylation 450")query <- GDCquery(project = "TCGA-ACC", data.category = "Copy number variation", legacy = TRUE, file.type = "hg19.seg", ...
TCGA(The Cancer Genome Atlas, 癌症基因组图谱,https://portal.gdc.cancer.gov/)是美国国家癌症研究所(National Cancer Institute)和美国人类基因组研究所(National Human Genome Research Institute)共同监督的一个项目,旨在应用高通量的基因组分析技术,以帮助人们对癌症有个更好的认知,从而提高对于癌症的预防、诊断和...
#' - TCGA-GBM #' - TCGA-HNSC #' - TCGA-KICH #' - TCGA-KIRC #' - TCGA-KIRP #' - TCGA-LAML #' - TCGA-LGG #' - TCGA-LIHC #' - TCGA-LUAD #' - TCGA-LUSC #' - TCGA-MESO #' - TCGA-OV #' - TCGA-PAAD #' - TCGA-PCPG #' - TCGA-PRAD #' - TCGA-READ #' - ...
首先进入TCGA下载数据GBM的RNA-seq和甲基化数据,从下表可见GBM共有172套RNA-seq数据以及437套DNA甲基化数据,由于TCGA提供Infinium HumanMethylation27 BeadChip和Infinium HumanMethylation450 BeadChip两种芯片平台的数据,...
("TCGA-ACC","TCGA-LGG","TCGA-OV","TCGA-SKCM","TCGA-TGCT","TCGA-UCS" ) # ###在TCGA中正常样本大于0小于10,但可以匹配GTEx数据库中的正常样本的癌症类型 # proj5 <- c("TCGA-CESC","TCGA-GBM","TCGA-PAAD") # # ###在TCGA中正常样本大于0小于10,在GTEx数据库中也没有正常样本的癌症...
临床上,HGAP与其他高级别胶质瘤的区别很重要,因为HGAP的预后比PA和PXA更具侵袭性,但总体存活率明显高于IDH-野生型GBM。HGAP被误诊为GBM的情况并不少见,精准诊断在临床上具有十分重要的意义,因此将组织学相似的肿瘤分解为生物学和临床相关的类型是DNA甲基化分类的显著优势之一(图3)。
TCGA projects 里面包含的癌症种类非常多,但是我们分析数据时候常常用pan-cancer 12,pan-cancer 17,pan-cancer 21来表示数据集有多少种癌症,一般文献会给出癌症的简称或者全名: BLCA, BRCA, COADREAD, GBM, HNSC, KIRC, LAML, LGG, LUAD, LUSC, OV, PRAD, SKCM, STAD, THCA, UCEC. ...