TCGA Gene Expression Datasets

<strong>Abstract:</strong> The Cancer Genome Atlas (TCGA) was a large-scale collaborative project initiated by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI). It aimed to comprehensively characterize the genomic and molecular landscape of various cancer types. These datasets contain gene expression profiles of bladder urothelial carcinoma (BLCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), glioblastoma multiforme (GBM), head &amp; neck squamous cell carcinoma (HNSC), kidney renal clear cell carcinoma (KIRC), and lower grade glioma (LGG). The gene expression profiles for BLCA, CESC, HNSC, KIRC, and LGG were measured experimentally using the Illumina HiSeq 2000 RNA Sequencing platform by the University of North Carolina TCGA genome characterization center. The gene expression profile of the GBM dataset was measured experimentally using the Affymetrix HT Human Genome U133a microarray platform by the Broad Institute of MIT and Harvard University cancer genomic characterization center. <strong>Inspiration:</strong> This dataset was uploaded to UBRITE for GTKB project. <strong>Instruction:</strong> The log₂(x+1) normalization was removed, and z-normalization was performed on the BLCA, CESC, HNSC, KIRC, and LGG datasets. The log₂(x) normalization was removed, and z-normalization was performed on the GBM dataset. <strong>Acknowledgments:</strong> Goldman, M.J., Craft, B., Hastie, M. et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0546-8. The Cancer Genome Atlas Research Network., Weinstein, J., Collisson, E. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45, 1113–1120 (2013). https://doi.org/10.1038/ng.2764. <strong>U-BRITE last update: </strong>07/13/2023<strong>摘要：</strong> 癌症基因组图谱（The Cancer Genome Atlas, TCGA）是由美国国家癌症研究所（National Cancer Institute, NCI）与美国国家人类基因组研究所（National Human Genome Research Institute, NHGRI）发起的大型协作研究项目，旨在全面解析多种癌症类型的基因组与分子特征谱。本数据集包含膀胱尿路上皮癌（bladder urothelial carcinoma, BLCA）、宫颈鳞状细胞癌及宫颈内腺癌（cervical squamous cell carcinoma and endocervical adenocarcinoma, CESC）、多形性胶质母细胞瘤（glioblastoma multiforme, GBM）、头颈部鳞状细胞癌（head & neck squamous cell carcinoma, HNSC）、肾透明细胞癌（kidney renal clear cell carcinoma, KIRC）以及低级别胶质瘤（lower grade glioma, LGG）的基因表达谱。其中，BLCA、CESC、HNSC、KIRC与LGG的基因表达谱由北卡罗来纳大学TCGA基因组表征中心通过Illumina HiSeq 2000 RNA测序平台实验测定；而GBM数据集的基因表达谱则由麻省理工与哈佛大学博德研究所癌症基因组表征中心通过Affymetrix HT人类基因组U133a微阵列平台实验测定。 <strong>上传背景：</strong> 本数据集已上传至UBRITE平台，用于GTKB项目。 <strong>数据预处理说明：</strong> 针对BLCA、CESC、HNSC、KIRC及LGG数据集，已移除log₂(x+1)标准化流程，并完成z标准化处理；针对GBM数据集，已移除log₂(x)标准化流程，并完成z标准化处理。 <strong>致谢：</strong> Goldman, M.J., Craft, B., Hastie, M. 等. 通过Xena平台可视化并解析癌症基因组数据. 自然生物技术 (2020). https://doi.org/10.1038/s41587-020-0546-8. 癌症基因组图谱研究网络. Weinstein, J., Collisson, E. 等. 癌症基因组图谱泛癌分析项目. 自然遗传学 45, 1113–1120 (2013). https://doi.org/10.1038/ng.2764. <strong>U-BRITE最后更新时间：</strong> 2023年7月13日