CIBERSORT根据LM22来分类

发表在 Nat Methods. 2015 May;的文章,至今(2019-10-14)引用已经近1000啦,提出了一个非负矩阵分解的算法CIBERSORT根据LM22来计算不同类型细胞的比例。

CIBERSORT should enable large-scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets (http://cibersort.stanford.edu/).

数据在Supplementary Table 1

Leukocyte signature matrix (LM22). Details of LM22, including gene expression matrix and source data.

关于LM22

文章是这样描述的:It contains 547 genes that distinguish 22 human hematopoietic cell phenotypes, including seven T cell types, naïve and memory B cells, plasma cells, NK cells, and myeloid subsets (Supplementary Table 1, Supplementary Fig. 2, and Online Methods).

细胞类型特征基因集来源:

全部基因列表:

CIBERSORT同时提供R包和在线网页工具,可以对用户的表达矩阵进行非负矩阵分解后计算不同细胞类型的比例。(后面我们会出一系列教程)

这是一个很火爆的数据挖掘方向

我安排我们生信菜鸟团数据挖掘团队成员帮忙收集整理了全部使用CIBERSORTbulk癌症转录组数据看LM22免疫细胞比例的文章,详细列表如下:

癌症类型    题目  URL
ACC    NA  
BLCA    Tumor-infiltrating M2 macrophages driven by specific genomic alterations are associated with prognosis in bladder cancer    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6610042/
BRCA    Relevance of Tumor-Infiltrating Immune Cell Composition and Functionality for Disease Outcome in Breast Cancer  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284248/
CESC    NA  
CHOL    NA  
COAD    Immune cell infiltration as a biomarker for the diagnosis and prognosis of stage I–III colon cancer https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6426802/
ESCA    Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma   https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6524245/#CR23
GBM    Metabolic remodeling contributes towards an immune-suppressive phenotype in glioblastoma    https://link.springer.com/article/10.1007%2Fs00262-019-02347-3
HNSC    Sex Differences in Using Systemic Inflammatory Markers to Prognosticate Patients with Head and Neck Squamous Cell Carcinoma https://cebp.aacrjournals.org/content/27/10/1176.long
KIRC    Immune infiltration in renal cell carcinoma https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6501001/
KIRP    Immune infiltration in renal cell carcinoma https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6501001/
LGG    NA  
LIHC    Identification and Validation of Tumor Stromal Immunotype in Patients With Hepatocellular Carcinoma https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6691778/
LUAD    Prognostic Implications of Heterogeneity in Intra-tumoral Immune Composition for Recurrence in Early Stage Lung Cancer  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6196259/
LUSC    The prognostic landscape of tumor-infiltrating immune cell and immunomodulators in lung cancer  https://www.sciencedirect.com/science/article/pii/S0753332217320255?via%3Dihub
MESO    NA  
PCPG    NA  
PRAD    The establishment of immune infiltration based novel recurrence predicting nomogram in prostate cancer  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6718526/
SKCM    Association of LRP1B Mutation With Tumor Mutation Burden and Outcomes in Melanoma and Non-small Cell Lung Cancer Patients Treated With Immune Check-Point Blockades https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6536574/
STAD    Gene expression profiles for a prognostic immunoscore in gastric cancer https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6099214/
TGCT    NA  
THCA    Papillary thyroid carcinoma behavior: clues in the tumor microenvironment   https://erc.bioscientifica.com/view/journals/erc/26/6/ERC-19-0074.xml
UCEC    NA  
肝细胞癌    Tumor-Infiltrating Leukocyte Composition and Prognostic Power in Hepatitis B- and Hepatitis C-Related Hepatocellular Carcinomas https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6722571/

你可以根据我们收集整理的列表,自己去一个个下载这些文献,或者可以在我们生信技能树公众号后台回复LM22拿到使用CIBERSORTbulk癌症转录组数据看LM22免疫细胞比例的TCGA数据挖掘文章,建议回复之前先象征性的打赏一下,谢谢理解。

还有两个免疫基因集文章的介绍,会在今天生信菜鸟团发布,欢迎前往生信菜鸟团公众号阅读学习哦。

  • 28个免疫基因集把CRC区分成为有生存差异的两类
  • TCIA的28免疫细胞比例

原文发布于微信公众号 - 生信技能树(biotrainee)

原文发表时间:2019-10-15

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