- 综合排序
- 最热优先
- 最新优先
- 来自专栏生信小驿站
Unsupervised clustering reveals new prostate cancer subtypes摘要介绍方法
摘要 背景：前列腺癌是男性中第二常见的癌症。发展基于基因的分类方法是迫切的要求。我们的目标是建立基因分型。 方法：我们使用了四个前列腺癌数据集。癌症基因组图谱（TCGA）RNA-Seq数据用于训练分类器。基于分类器的三个亚型被测试是否具有临床数据存在显着差异。其他三组按分类器分类并验证。 结果：分类器有183个基因。前列腺癌亚型1（PCS1）的特征是高 GSTP1的表达，Gleason评分较低（P <0.001）。 PCS2有更高的Gleason评分，更多的淋巴淋巴结侵袭（P = 0.005）和病理T期（
97110发布于 2018-09-29 - 来自专栏生物信息云
TCGAbiolinks包帮助文档（英文版）
samples with both DNA methylation (HM450K) and Gene expression data from GDC databse PanCancerAtlas_subtypes Retrieve table with TCGA molecular subtypes TabSubtypesCol_merged TCGA samples with their Pam50 subtypes TCGAquery_subtype Retrieve molecular subtypes for a given tumor TCGAtumor_purity Filters TCGA barcodes according to purity parameters TCGAvisualize_BarPlot Barplot of subtypes and clinical info in groups Creates a volcano plot for DNA methylation or expression TCGA_MolecularSubtype Retrieve molecular subtypes
1.9K21发布于 2019-08-07 课前准备--CODEX（IMC）基础分析梳理
CD4 Tfh', grid=True, n_grids=5, show=False)plt.tight_layout()plt.show()Niche analysisniche_subtypes ('malignant/other') else: niche_subtypes.append(ct)adata.obs['niche_subtypes'] = niche_subtypesadata.obs ['niche_subtypes'] = adata.obs['niche_subtypes'].astype('category')print("Cell subtypes considered in = mb.calc.cellular_niches( adata, cell_type_key='niche_subtypes', radius=75, normalize_counts Generate UMAP plotssc.tl.umap(adata_neighbors_sub)sc.pl.umap( adata_neighbors_sub, color='niche_subtypes
66720编辑于 2025-07-31- 来自专栏R语言交流中心
R语言中的突变signature分析工具
package = "musicatk"), sep = "\t", header=TRUE) samp_annot(result, "Tumor_Subtypes ") <- annot$Tumor_Subtypes plot_exposures(result, plot_type = "bar", group_by = "annotation", annotation = "Tumor_Subtypes") ##绘制箱线图 plot_exposures(result, plot_type = "box", group_by = "annotation ", annotation = "Tumor_Subtypes") ##基于signature分组的箱线图绘制 plot_exposures(result, plot_type = "box", group_by = "signature", color_by = "annotation", annotation = "Tumor_Subtypes") 当然此包还支持plotly
1.8K31编辑于 2022-03-14 - 来自专栏生信技能树
ProTICS 揭示了不同分子亚型中肿瘤浸润免疫细胞的预后影响
因此，作者在文献中提及 ‘’To obtain the optimal number of subtypes, we traverse the number of subtypes from 2 to can be saved from part1.R subtypes<-survival_data$Subtype ID<- which(subtypes==1 | subtypes==2) Surv /R/functions/subtypes_DEA.R") GS<-subtypes_DEA(Surv,seqd) # 差异基因热图展示 sig_expr<-sig_expr[is.element( sig_expr$symbol,GS),] IDD<-c(which(subtypes==1),which(subtypes==2)) survd_new<-survival_data[IDD,] /output/overallsurvival_subtypes.txt", sep = "\t",header = TRUE) cell<-fread(file = ".
76620编辑于 2022-07-26 单细胞空间多组学揭示肿瘤相关成纤维细胞的保守空间亚型和细胞邻域-空间细胞亚群细分代码实现
2025年3月27日，Cancer Cell上在线发表了题为Conserved spatial subtypes and cellular neighborhoods of cancer-associated sklearn.neighbors import NearestNeighbors import matplotlib.pyplot as plt # 函数封装 def identify_spatial_subtypes neighbor_matrix_with_subtype = neighbor_matrix.copy() neighbor_matrix_with_subtype['subtype'] = subtypes neighbor_matrix_with_subtype.groupby('subtype').mean() # print(avg_neighbor_composition) n_subtypes = avg_neighbor_composition.shape[0] fig, axes = plt.subplots(1, n_subtypes, figsize=(n_subtypes
41000编辑于 2025-07-20- 来自专栏生物信息云
TCGA数据挖掘（四）：表达差异分析（4）
############ ####Molecular subtypes: ####Filtering data so all samples have a pam50 subtype for BRCA: <-c(rep("Normal", 100), TCGA_MolecularSubtype(colnames(dataFilt.brca.cancer))$subtypes$subtype) # All barcodes have available molecular subtype info mol_subtypes<-make.names(mol_subtypes) # to convert ENSEMBL logFC.cut = 1, voom = TRUE, Condtypes = mol_subtypes Normal") #in this DEA we use Normal as a reference, thus genes with LogFC > 1 are up regulated in the subtypes
4.9K51发布于 2019-09-18 - 来自专栏生信菜鸟团
【生信文献200篇】71 基于两大数据库进行TNBC再分析
TNBC molecular subtypes are associated with different clinic-pathological variables and clinical outcome 研究人员使用 PAM50 classifier 确定了 intrinsic molecular (PAM50) subtypes 在TNBC和5个稳定的TNBC亚型中的分布。 TNBC molecular subtypes exhibit heterogeneous mutational profiles 为了更深入地了解驱动这种异质性的潜在基因组异常，研究人员评估了靶向和全外显子组测序得出的 TNBC molecular subtypes display distinct genomic instability 由于TNBC肿瘤已知与不稳定的基因组相关，研究人员研究了染色体不稳定(CIN)， Different biological processes characterize TNBC subtypes according to hallmarks of cancer 研究人员根据癌症的特征来评估驱动每个
1.4K30发布于 2021-10-12 - 来自专栏生信技能树
乳腺癌预后基因集
Botstein (2003) "Repeated Observation of Breast Tumor Subtypes in Independent Gene Expression Data Sets Charles M. and Bernard, Philip S. (2009) "Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes (2008) "Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes Quackenbush J, Sotiriou C. (2012) "A three-gene model to robustly identify breast cancer molecular subtypes
48330发布于 2018-07-27 - 来自专栏生信技能树
使用MultiAssayExperiment结构探索TCGA数据
accmae)) ACC_annotations ACC_subtype 1 Patient_ID patientID 2 histological_subtypes Histology 3 mrna_subtypes C1A/C1B 4 mrna_subtypes mRNA_K4 5 cimp MethyLevel 6 microrna_subtypes miRNA cluster > sampleTables(accmae) $`ACC_CNASNP-20160128 PAM50 mRNA 3 mrna_subtypes SigClust Unsupervised mRNA 4 mrna_subtypes SigClust Intrinsic mRNA 5 microrna_subtypes miRNA Clusters 6 methylation_subtypes
47620编辑于 2022-07-26 - 来自专栏生信技能树
使用curatedTCGAData下载TCGA数据库信息好用吗
BRCA_annotations BRCA_subtype 1 Patient_ID patientID 2 mrna_subtypes PAM50 mRNA 3 mrna_subtypes SigClust Unsupervised mRNA 4 mrna_subtypes SigClust Intrinsic mRNA 5 microrna_subtypes miRNA Clusters 6 methylation_subtypes
1.1K20发布于 2020-12-03 - 来自专栏生信技能树
12月份第2周（总第46周）探索TNBC新的亚型分类
发表于：Clin Cancer Res. 2015 Apr 文章题目是：Comprehensive Genomic Analysis Identifies Novel Subtypes and Targets claudin-low-enriched mesenchymal mesenchymal stem-like immune response two cell cycle-disrupted basal subtypes 还针对最明显的两个类别，即 basal-like versus the remaining intrinsic subtypes进行了差异表达分析，然后根据 log2(Fold Change) (“FC PAM50” TNBC molecular classification (luminal A, luminal B, HER-2-positive, basal-like and normal-like subtypes basal-like-2, immunomodulatory, luminal androgen receptor (LAR), mesenchymal, and mesenchymal stem-like subtypes
1.1K20发布于 2018-12-12 - 来自专栏医学和生信笔记
免疫浸润结果分子分型（一致性聚类ConsensusClusterPlus）
分型后的数据 根据分型结果提取数据，我们选2： #提取结果 sample_subtypes <- ccres[[2]][["consensusClass"]] table(sample_subtypes ) ## sample_subtypes ## 1 2 ## 331 319 331个样本是第1型，319个样本是第2型。 = factor(sample_subtypes)) %>% pivot_longer(-c(ID,sample_subtypes), names_to = "cell_type",values_to = "value") %>% ggplot(aes(cell_type,value,fill=sample_subtypes))+ geom_boxplot()+ labs(x=NULL = factor(sample_subtypes)) %>% pivot_longer(-c(ID,sample_subtypes), names_to = "cell_type",values_to
2.4K20编辑于 2023-08-30 - 来自专栏芒果先生聊生信
免疫浸润：生信论文40乳腺癌引文写作
epidermal growth factor receptor‐2 (HER2), progesterone receptors (PR) and estrogen receptors (ER), four subtypes While triple‐negative breast cancer (TNBC), as the dominant type of basal‐like subtype and unlike other subtypes had described the expression profile–based characteristics and successfully divided TNBC into four subtypes Except the LAR, the mechanisms of the other three subtypes were all involved in the immune‐related pathways
71520发布于 2020-08-21 - 来自专栏生信技能树
TCGA和METABRIC的TNBC病人数量到底是多少
androgen receptor (LAR) 然后同样的作者，PLoS One. 2016 Jun 16;发文重新修订了 之前的分类，变成4类：(TNBCtype-4) tumor-specific subtypes BL2, M and LAR) 发表在：Clin Cancer Res. 2015 Apr ，题目是 Comprehensive Genomic Analysis Identifies Novel Subtypes 中国团队发表在 Breast Cancer Res. 2016;题目是：Comprehensive transcriptome analysis identifies novel molecular subtypes 发表在 Breast Cancer Res. 2019 May 的文章，题目是：Identification of three subtypes of triple-negative breast cancer
1.8K01发布于 2020-02-20 - 来自专栏生物信息云
TCGAbiolinks包下载TCGA数据进行表达差异分析-乳腺癌案例
为被过滤的数据， pure_barcodes是我们要的数据 Purity.BRCA<-purityDATA$pure_barcodes ################DEA with Molecular subtypes ############ ####Molecular subtypes: ####Filtering data so all samples have a pam50 subtype for BRCA <-c(rep("Normal", 100), TCGA_MolecularSubtype(colnames(dataFilt.brca.cancer))$subtypes$subtype) write.csv (mol_subtypes,file = "mol_subtypes.csv",quote = FALSE) mol_subtypes<-make.names(mol_subtypes) #dataFilt.brca Normal") #in this DEA we use Normal as a reference, thus genes with LogFC > 1 are up regulated in the subtypes
17.9K106发布于 2019-08-07 - 来自专栏生信技能树
TNBC分型研究的来龙去脉（逆向收费读文献2019-09）
的分子分型研究 依据全局基因表达进行分型最出名的是Lehmann的2011那篇JCI的芯片整合分析文章，还开发了网页工具：http://cbc.mc.vanderbilt.edu/tnbc/ 可以得到 7 subtypes Based on 3,247 gene expression profiles from 21 breast cancer data sets, we discovered six TNBC subtypes Informatics, 2012:11 147-156, doi:10.4137/CIN.S9983 Identification of human triple-negative breast cancer subtypes 所以后来作者2016年在plos one 发文重新修订了 之前的6分类，变成4类： (TNBCtype-4) tumor-specific subtypes (BL1, BL2, M and LAR) 文章 Differential response to neoadjuvant chemotherapy among 7 triple-negative breast cancer molecular subtypes
1.5K51发布于 2019-06-19 - 来自专栏文献分享
Science Advances｜快来学习这篇泛癌成纤维细胞的思路和绘图技巧！
Defining fibroblast subtypes from a curated collection of scRNA-seq datasets.研究团队收集到了从73个研究中收集到了跨十个组织的 Transcriptome heterogeneity of fibroblast subtypes研究团队对十八种成纤维细胞的亚型进行了细致的命名，并且发现了一种之前未被报道过的亚型——TSPAN8+ Differentiation status of fibroblast subtypes.研究团队使用Monocle2进行对成纤维细胞进行拟时序分析，同时结合上皮间充质转换和CytoTRACE评分确定起始点 Aging and cell senescence characteristics of fibroblast subtypes.研究团队进一步研究了成纤维细胞亚型和不同年龄及性别的关系。 The cell-cell interactions of fibroblast subtypes.研究团队进一步使用CellphoneDB研究成纤维细胞亚型的通讯网络，发现了成纤维细胞和上皮细胞和内皮细胞的相互作用强度是和免疫细胞相互作用强度的两倍
34200编辑于 2025-04-15 - 来自专栏单细胞天地
乳腺癌领域之PAM50分类
GSE10886，它研究了189个prototype samples，得到了一个50个分类基因与5个对照基因的RT-qPCR定量结果，得到4个gene expression–based “intrinsic” subtypes 关于这几种分子亚型的介绍：https://www.breastcancer.org/symptoms/types/molecular-subtypes Luminal A：hormone-receptor =subtypes > table(df[,c(1,5)]) subtypes g Basal Her2 LumA LumB Normal 1 36 30 205 13 # 在原来group_list基础上，添加亚型信息，为了下面pheatmap中的anno_col设置 tmp=data.frame(group=group_list, subtypes =subtypes) rownames(tmp)=colnames(x) # 画热图 library(pheatmap) pheatmap(x,show_rownames = T,show_colnames
6.9K51发布于 2020-03-31 - 来自专栏芒果先生聊生信
免疫浸润论文：生信论文40引文写作
epidermal growth factor receptor‐2 (HER2), progesterone receptors (PR) and estrogen receptors (ER), four subtypes While triple‐negative breast cancer (TNBC), as the dominant type of basal‐like subtype and unlike other subtypes had described the expression profile–based characteristics and successfully divided TNBC into four subtypes Except the LAR, the mechanisms of the other three subtypes were all involved in the immune‐related pathways
36621发布于 2020-08-20
腾讯云开发者
Copyright © 2013 - 2026 Tencent Cloud. All Rights Reserved. 腾讯云 版权所有
深圳市腾讯计算机系统有限公司 ICP备案/许可证号：粤B2-20090059 
粤公网安备44030502008569号
腾讯云计算（北京）有限责任公司 京ICP证150476号 | 京ICP备11018762号