SCS【32】基于scRNA-seq数据中推断单细胞的eQTLs (eQTLsingle)

最新推荐文章于 2024-07-16 14:30:37 发布

桓峰基因

最新推荐文章于 2024-07-16 14:30:37 发布

阅读量167

点赞数

文章标签：信息可视化

本文链接：https://blog.csdn.net/weixin_41368414/article/details/132614007

版权

单细胞生信分析教程

桓峰基因公众号推出单细胞生信分析教程并配有视频在线教程，目前整理出来的相关教程目录如下：

Topic 6. 克隆进化之 Canopy

Topic 7. 克隆进化之 Cardelino

Topic 8. 克隆进化之 RobustClone

SCS【1】今天开启单细胞之旅，述说单细胞测序的前世今生

SCS【2】单细胞转录组之 cellranger

SCS【3】单细胞转录组数据 GEO 下载及读取

SCS【4】单细胞转录组数据可视化分析 (Seurat 4.0)

SCS【5】单细胞转录组数据可视化分析 (scater)

SCS【6】单细胞转录组之细胞类型自动注释 (SingleR)

SCS【7】单细胞转录组之轨迹分析 (Monocle 3) 聚类、分类和计数细胞

SCS【8】单细胞转录组之筛选标记基因 (Monocle 3)

SCS【9】单细胞转录组之构建细胞轨迹 (Monocle 3)

SCS【10】单细胞转录组之差异表达分析 (Monocle 3)

SCS【11】单细胞ATAC-seq 可视化分析 (Cicero)

SCS【12】单细胞转录组之评估不同单细胞亚群的分化潜能 (Cytotrace)

SCS【13】单细胞转录组之识别细胞对“基因集”的响应 (AUCell)

SCS【14】单细胞调节网络推理和聚类 (SCENIC)

SCS【15】细胞交互：受体-配体及其相互作用的细胞通讯数据库 (CellPhoneDB)

SCS【16】从肿瘤单细胞RNA-Seq数据中推断拷贝数变化 (inferCNV)

SCS【17】从单细胞转录组推断肿瘤的CNV和亚克隆 (copyKAT)

SCS【18】细胞交互：受体-配体及其相互作用的细胞通讯数据库 (iTALK)

SCS【19】单细胞自动注释细胞类型 (Symphony)

SCS【20】单细胞数据估计组织中细胞类型(Music)

SCS【21】单细胞空间转录组可视化 (Seurat V5)

SCS【22】单细胞转录组之 RNA 速度估计 (Velocyto.R)

SCS【23】单细胞转录组之数据整合 (Harmony)

SCS【24】单细胞数据量化代谢的计算方法 (scMetabolism)

SCS【25】单细胞细胞间通信第一部分细胞通讯可视化（CellChat）

SCS【26】单细胞细胞间通信第二部分通信网络的系统分析（CellChat）

SCS【27】单细胞转录组之识别标记基因（scran）

SCS【28】单细胞转录组加权基因共表达网络分析(hdWGCNA)

SCS【29】单细胞基因富集分析 (singleseqgset)

SCS【30】单细胞空间转录组学数据库(STOmics DB)

SCS【31】减少障碍，加速单细胞研究数据库(Single Cell PORTAL)

简介

eQTL 研究对于理解基因组调控至关重要。遗传变异对基因调控的影响是细胞类型特异性和细胞环境相关的，因此在单细胞水平上研究 eQTL 是至关重要的。理想的解决方案是同时使用来自同一细胞的突变和表达数据。然而，目前这种单细胞配对数据的技术还不成熟。我们提出了一种新的方法，eQTLsingle 仅用 scRNA-seq 数据发现 eQTL，而不需要基因组数据。从 scRNA-seq 数据中检测突变，利用零膨胀负二项 (zero-inflated negative binomial, ZINB) 模型对不同基因型的基因表达进行建模，在单细胞水平上寻找基因型和表型之间的关联。基于胶质母细胞瘤和胶质瘤 scRNA-seq 数据集，eQTLsingle 发现了数百个细胞类型特异性肿瘤相关的 eQTL，其中大多数在批量eQTL研究中无法发现。对发现的 eQTL 的详细分析揭示了重要的潜在调控机制。eQTLsingle 是一个独特而强大的工具，可以利用大量的 scRNA-seq 资源进行单细胞 eQTL 研究。

eQTLsingle has two modes. Cleaned-data mode: take input as SNV matrix and expression matrix from single cells. If you have had SNV and expression information of the same cell before, you can use this mode to discover eQTLs Raw-data mode: take input as raw scRNA-seq data (fastq data). eQTLsingle can generate both SNV matrix and gene matrix, and discovers eQTLs based them

软件包安装

if(!require(devtools)) 
  install.packages("devtools")

devtools::install_github("horsedayday/eQTLsingle", build_vignettes = TRUE)

Cleaned-data mode

eQTLsingle接受两个输入:snvMatrix和expressionMatrix。

snvMatrix:一个数据框，描述 SNV 的基因型(以细胞为单位的基因座)，该数据框的行名是SNV id，该数据框的别名是CellId。(1) -1表示数据缺失(没有覆盖足够的读取);(2) 0表示该位点基因型为REF(非突变);(3) 1表示该基因座的基因型为ALT(突变);

expressionMatrix:一个数据框，描述基因表达(细胞的基因表达)，该数据框的行名为Geneid，该数据框的别名为CellId。

Step1: Build SNV-gene pairs

只对有效的突变和基因进行eQTL分析。因此，需要首先选择高可靠性的SNV基因对(SNV和基因都覆盖足够的细胞)。

# Load eQTLsingle and test data (SNV matrix and expression matrix)
library(eQTLsingle)
library(knitr)

## Warning: 程辑包'knitr'是用R版本4.2.3 来建造的

data("toy_snvMatrix")
kable(toy_snvMatrix[1:5,])

	cell_1	cell_2	cell_3	cell_4	cell_5	cell_6	cell_7	cell_8	cell_9	cell_10	cell_11	cell_12	cell_13	cell_14	cell_15	cell_16	cell_17	cell_18	cell_19	cell_20	cell_21	cell_22	cell_23	cell_24	cell_25	cell_26	cell_27	cell_28	cell_29	cell_30	cell_31	cell_32	cell_33	cell_34	cell_35	cell_36	cell_37	cell_38	cell_39	cell_40	cell_41	cell_42	cell_43	cell_44	cell_45	cell_46	cell_47	cell_48	cell_49	cell_50	cell_51	cell_52	cell_53	cell_54	cell_55	cell_56	cell_57	cell_58	cell_59	cell_60	cell_61	cell_62	cell_63	cell_64	cell_65	cell_66	cell_67	cell_68	cell_69	cell_70	cell_71	cell_72	cell_73	cell_74	cell_75	cell_76	cell_77	cell_78	cell_79	cell_80	cell_81	cell_82	cell_83	cell_84	cell_85	cell_86	cell_87	cell_88	cell_89	cell_90	cell_91	cell_92	cell_93	cell_94	cell_95	cell_96	cell_97	cell_98	cell_99	cell_100	cell_101	cell_102	cell_103	cell_104	cell_105	cell_106	cell_107	cell_108	cell_109	cell_110	cell_111	cell_112	cell_113	cell_114	cell_115	cell_116	cell_118	cell_119	cell_120	cell_121	cell_122	cell_123	cell_124	cell_125	cell_126	cell_127	cell_128	cell_129	cell_130	cell_131	cell_132	cell_133	cell_134	cell_135	cell_136	cell_137	cell_138	cell_139	cell_140	cell_141	cell_142	cell_143	cell_144	cell_145	cell_146	cell_147	cell_148	cell_149	cell_150	cell_151	cell_152	cell_153	cell_154	cell_155	cell_156	cell_157	cell_158	cell_159	cell_160	cell_161	cell_162	cell_163	cell_164	cell_165	cell_166	cell_167	cell_168	cell_169	cell_170	cell_171	cell_172	cell_173	cell_174	cell_175	cell_176	cell_177	cell_178	cell_179	cell_180	cell_181	cell_182	cell_183	cell_184	cell_185	cell_186	cell_187	cell_188	cell_189	cell_190	cell_191	cell_192	cell_193	cell_194	cell_195	cell_196	cell_197	cell_198	cell_199	cell_200
SNV_1	0	1	0	1	1	-1	1	0	0	1	0	1	1	1	0	1	-1	0	0	1	1	1	-1	0	1	1	1	1	0	1	1	0	1	1	1	0	1	1	1	1	1	0	1	1	1	0	0	1	0	1	-1	0	1	0	1	1	0	1	0	1	1	1	-1	0	1	1	1	1	1	1	0	-1	0	-1	1	0	1	1	1	1	1	1	0	1	0	0	-1	0	0	-1	1	1	1	0	0	0	1	1	0	0	1	1	0	0	1	-1	1	1	0	1	0	0	0	0	1	0	-1	0	0	0	0	1	1	-1	0	1	0	1	0	1	0	1	1	0	0	1	0	1	0	0	1	1	0	1	1	-1	1	1	0	0	0	0	0	0	0	0	0	0	1	-1	0	1	0	0	1	1	1	1	0	1	1	0	-1	0	0	1	0	0	0	0	0	0	1	0	1	1	1	1	1	1	1	1	1	1	1	0	0	1	1
SNV_2	1	-1	-1	-1	0	-1	1	-1	1	-1	1	-1	-1	-1	1	0	-1	-1	-1	-1	-1	-1	0	-1	-1	1	1	-1	0	-1	0	-1	0	-1	-1	-1	1	0	-1	-1	-1	0	0	-1	1	-1	-1	1	-1	-1	-1	-1	0	1	0	-1	-1	1	0	1	-1	-1	-1	1	-1	-1	-1	-1	-1	1	1	-1	0	-1	-1	0	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	1	-1	-1	-1	-1	-1	-1	-1	-1	1	-1	-1	-1	-1	-1	-1	0	-1	0	-1	-1	-1	-1	-1	0	-1	1	0	-1	-1	-1	-1	0	-1	-1	-1	-1	-1	-1	-1	0	-1	-1	0	-1	0	-1	-1	-1	0	-1	-1	-1	-1	-1	-1	-1	1	0	-1	1	-1	-1	-1	-1	-1	-1	1	-1	-1	1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	0	-1	1	0	-1	0	-1	-1	1	1	-1	-1	0	-1	0	0	0	1	-1
SNV_3	1	1	0	0	0	0	1	0	1	1	1	1	-1	1	1	-1	0	1	0	0	1	1	0	0	1	1	1	0	0	0	1	0	0	-1	0	0	1	-1	0	0	1	0	0	0	0	1	0	0	0	1	1	1	1	-1	1	-1	-1	0	1	1	0	0	0	0	1	1	0	1	0	0	-1	1	0	0	-1	0	-1	0	1	-1	1	1	1	0	1	1	0	0	0	1	0	-1	0	0	0	0	1	1	0	0	1	1	1	1	0	0	0	-1	0	0	1	1	1	1	0	1	0	1	0	1	1	0	1	1	1	0	1	1	1	1	1	0	1	-1	0	0	-1	0	1	0	-1	0	1	0	1	0	0	-1	0	-1	1	0	0	1	1	1	0	0	1	1	0	0	0	1	0	1	0	1	-1	-1	0	1	0	1	1	0	1	1	1	1	0	1	0	0	1	1	1	0	0	1	1	0	0	1	1	1	0	0	1
SNV_4	0	1	-1	1	-1	1	-1	0	0	1	0	0	-1	-1	-1	-1	0	-1	0	-1	-1	-1	-1	1	-1	-1	-1	-1	-1	-1	-1	-1	1	-1	-1	0	-1	-1	1	-1	-1	-1	1	-1	-1	-1	-1	0	1	-1	-1	-1	-1	0	-1	-1	-1	-1	-1	0	0	-1	-1	-1	0	-1	-1	1	1	-1	-1	-1	-1	-1	0	-1	-1	-1	1	-1	1	-1	-1	0	0	-1	1	-1	-1	-1	1	0	0	-1	-1	-1	0	-1	-1	-1	-1	-1	1	0	-1	-1	-1	-1	-1	-1	-1	1	-1	-1	1	-1	-1	1	-1	-1	1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	1	1	-1	-1	1	-1	-1	-1	-1	1	-1	1	0	-1	-1	-1	-1	-1	1	-1	-1	-1	1	-1	1	1	1	-1	-1	0	-1	1	-1	-1	-1	-1	-1	-1	-1	-1	-1	0	1	-1	0	1	-1	1	-1	-1	-1	0	-1	-1	-1	-1	0	0	-1	1	-1	-1	-1	-1	0	-1	1	-1
SNV_5	0	1	1	1	0	0	0	1	1	1	-1	1	1	0	0	0	1	-1	1	0	1	1	1	1	1	1	0	0	0	1	-1	0	1	0	0	0	1	1	1	1	1	0	1	0	1	0	1	0	1	1	0	1	1	0	0	-1	1	1	0	1	1	0	0	-1	1	1	1	1	1	0	1	1	1	0	-1	1	0	1	0	0	1	0	1	1	1	1	1	1	-1	0	0	0	1	1	-1	0	1	1	1	0	0	0	1	0	1	0	1	1	0	0	1	0	0	1	1	1	1	1	1	1	0	1	1	0	-1	0	0	-1	1	1	1	0	1	1	0	-1	-1	0	1	1	-1	1	1	-1	0	1	1	1	1	1	1	1	0	0	-1	0	0	1	0	1	1	0	0	0	1	1	0	1	1	1	0	1	1	1	-1	0	0	1	0	1	0	0	0	1	0	-1	0	1	1	0	0	0	1	-1	0	1	0	-1	0

data("toy_expressionMatrix")
kable(toy_expressionMatrix[1:5,])

	cell_1	cell_2	cell_3	cell_4	cell_5	cell_6	cell_7	cell_9	cell_10	cell_11	cell_12	cell_14	cell_15	cell_17	cell_18	cell_19	cell_20	cell_21	cell_23	cell_24	cell_25	cell_27	cell_28	cell_29	cell_31	cell_32	cell_33	cell_35	cell_36	cell_37	cell_38	cell_42	cell_43	cell_44	cell_45	cell_46	cell_47	cell_48	cell_50	cell_51	cell_52	cell_53	cell_54	cell_55	cell_56	cell_57	cell_58	cell_59	cell_60	cell_61	cell_62	cell_65	cell_67	cell_68	cell_69	cell_70	cell_71	cell_72	cell_73	cell_74	cell_75	cell_78	cell_79	cell_80	cell_81	cell_82	cell_83	cell_84	cell_85	cell_86	cell_87	cell_88	cell_89	cell_91	cell_92	cell_93	cell_94	cell_95	cell_96	cell_97	cell_99	cell_100	cell_102	cell_103	cell_104	cell_105	cell_106	cell_107	cell_110	cell_111	cell_112	cell_113	cell_114	cell_115	cell_116	cell_117	cell_118	cell_120	cell_122	cell_123	cell_124	cell_125	cell_126	cell_127	cell_128	cell_130	cell_131	cell_132	cell_133	cell_135	cell_136	cell_137	cell_138	cell_139	cell_140	cell_141	cell_142	cell_143	cell_144	cell_145	cell_146	cell_147	cell_149	cell_150	cell_152	cell_153	cell_154	cell_155	cell_156	cell_157	cell_158	cell_159	cell_160	cell_161	cell_162	cell_163	cell_164	cell_165	cell_166	cell_167	cell_168	cell_169	cell_170	cell_171	cell_172	cell_173	cell_174	cell_175	cell_176	cell_177	cell_178	cell_179	cell_180	cell_181	cell_182	cell_183	cell_184	cell_185	cell_186	cell_187	cell_188	cell_189	cell_191	cell_192	cell_193	cell_194	cell_195	cell_197	cell_198	cell_199
gene_1	0	0	66	0	0	70	0	0	55	59	0	0	0	0	0	58	0	0	0	0	0	0	32	0	0	31	35	0	0	57	0	52	0	41	0	0	0	0	0	65	0	0	0	0	37	0	0	64	60	0	85	55	0	50	51	0	0	0	0	0	0	0	47	0	42	53	43	74	49	69	0	0	44	41	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	0	52	0	0	58	53	0	49	0	41	0	80	0	0	0	48	48	27	0	50	63	41	0	0	0	0	60	46	0	55	63	0	0	0	0	0	0	0	0	0	0	0	0	0	53	0	0	0	71	43	0	39	0	0	0	0	0	0	0	54	0	0	45	52	0	0	0	0	0	65	0	0	0	0	0	49	0	0	0
gene_2	0	82	0	0	0	0	127	89	83	103	0	86	84	92	77	0	66	110	0	0	0	65	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	97	0	0	0	0	0	0	114	87	0	0	44	0	0	0	0	0	83	0	76	0	0	70	83	0	97	76	0	0	0	0	0	0	0	123	0	0	0	74	0	55	0	80	0	0	0	0	111	0	0	77	0	0	0	0	0	81	73	0	82	0	0	92	0	0	0	71	0	0	0	79	0	78	0	0	76	0	0	0	75	89	0	0	0	0	0	0	0	85	0	64	66	86	0	90	0	72	0	0	0	0	0	90	0	100	0	89	0	67	0	77	0	0	0	0	118	77	82	0	0	94	75	0	0	82	0	0	0	0	69	0	0
gene_3	0	82	96	0	0	95	0	77	77	73	0	0	76	0	61	0	0	0	92	59	0	85	0	0	50	64	0	0	82	0	0	0	0	84	0	68	80	70	66	0	81	0	94	85	0	0	0	68	0	61	94	0	85	0	0	0	62	0	79	71	0	0	89	0	0	66	0	0	0	0	78	73	0	0	75	0	0	0	83	107	90	118	74	87	79	0	73	0	0	0	0	0	0	86	82	0	0	92	0	0	0	0	88	0	0	0	0	0	75	68	0	70	0	0	67	90	76	0	0	89	0	0	78	94	99	0	0	0	70	0	0	0	84	0	0	0	91	0	109	0	0	0	0	0	0	0	82	75	97	86	0	89	0	0	0	0	82	87	0	0	0	79	0	85	0	62	0	0	0	0
gene_4	0	85	0	88	0	0	0	0	0	89	0	0	80	129	0	0	0	129	0	85	0	0	47	137	155	0	0	90	63	0	94	94	46	0	45	0	0	63	61	0	0	126	95	90	0	56	68	0	65	0	121	0	0	0	0	0	0	0	0	87	0	0	0	0	0	0	25	59	62	0	0	0	0	48	42	89	59	66	0	0	0	0	64	0	83	148	40	97	0	0	0	91	60	48	0	0	0	0	0	0	0	77	0	0	0	34	0	0	0	43	0	0	0	155	0	0	120	22	0	0	0	0	0	111	0	0	0	68	61	87	71	75	75	104	0	0	0	144	0	0	0	67	71	104	0	45	0	0	0	0	114	0	57	0	120	91	0	101	69	0	0	0	0	0	67	0	0	0	70	84
gene_5	42	0	0	0	69	0	0	0	0	0	49	0	0	63	0	95	0	0	0	71	67	0	0	50	0	0	0	56	0	0	69	46	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	73	54	0	43	69	0	0	0	0	0	61	0	0	59	0	0	0	0	45	0	0	64	0	0	69	68	54	0	0	66	58	0	55	0	0	0	0	66	0	0	0	0	52	0	0	0	0	0	46	0	0	0	61	56	54	0	43	0	0	0	57	63	84	74	0	0	46	52	44	0	54	0	0	0	0	0	0	0	70	0	42	0	0	67	0	0	0	54	65	0	0	0	0	0	0	0	75	0	0	0	0	58	0	0	0	53	67	0	0	0	0	0	0	71	0	0	0	0	0	0	64	0	43

# select valid SNV-gene pairs
# each genotype at least covers 30 cells
# each gene (expression level > 1) at least covers 30 cells
snv.gene.pair.metadata <- eQTLsingle_build_metadata(snvMatrix = toy_snvMatrix,
                                                    expressionMatrix = toy_expressionMatrix, 
                                                    snv.number.of.cells = 30, 
                                                    expression.min = 1, 
                                                    expression.number.of.cells = 30)

Format of snv.gene.pair.metadata,

SNVid: Id of SNV, represented as CHR__POS;

Num_cells_ref: Num_cells_ref: number of cells in REF group;

Num_cells_alt: Num_cells_alt: number of cells in ALT group;

Ref_cells: cell list of REF group;

Alt_cells: cell list of ALT group;

GeneList: gene list, these genes will be tested with the SNV in this row;

Num_gene: number of genes in gene list;

CellList: whole cell list of REF and ALT group.

实例操作

Step 2: Conduct eQTL analysis on valid SNV-gene pairs.

# conduct eQTL analysis on valid SNV-gene pairs
eQTL.result <- eQTLsingle(toy_expressionMatrix,
                          snv.gene.pair.metadata)

# Suppose we are interested at the pair between 
# SNV with snvid "SNV_3" 
# gene with geneid "gene_16"

Format of eQTL.result,

SNVid: Id of SNV, represented as CHR__POS;

Geneid: gene id of target gene;

sample_size_Ref, sample_size_Alt: number of cells in REF and ALT group;

theta_Ref, theta_Alt, mu_Ref, mu_Alt, size_Ref, size_Alt, prob_Ref, prob_Alt: estimated parameters of ZINB for REF group and ALT group;

total_mean_Ref, total_mean_Alt: mean of the REF group and ALT group;

foldChange: fold change of mean of REF group (total_mean_Ref) with respect to mean of ALT group (total_mean_Alt) chi2LR1: chi square statistic for the test;

pvalue, adjusted_pvalue: pvalue and adjusted pvalue of the test. If adjusted p-value is smaller than some threshold, this SNV shows significant eQTL effect on the target gene;

Remark: to record abnormity

Step 3: Visualize eQTL effect

# Suppose we are interested at the pair between 
# SNV with snvid "SNV_3" 
# gene with geneid "gene_16"


# select out a SNV-gene pair
eQTL.result.target <- eQTL.result[(eQTL.result$SNVid == "SNV_3") &
                                    (eQTL.result$Geneid == "gene_16"),]

kable(eQTL.result.target[1:5,])

	SNVid	Geneid	sample_size_Ref	sample_size_Alt	theta_Ref	theta_Alt	mu_Ref	mu_Alt	size_Ref	size_Alt	prob_Ref	prob_Alt	total_mean_Ref	total_mean_Alt	foldChange	chi2LR1	pvalue	adjusted_pvalue	Remark
18	SNV_3	gene_16	91	89	0.032967	0.0449438	59.94318	291.1177	9.247933	12.17195	0.1336578	0.0401331	57.96703	278.0337	0.2084892	337.0705	0	0	NA
NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.2	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.3	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA

# to draw violin plots of gene expression in both REF group and ALT group
eQTLsingle_visualization(eQTL.result.target,toy_expressionMatrix, snv.gene.pair.metadata)

Raw-data mode

这个可以参考网站，这时就需要有一定 shell 基础的同学，并且对一些生物学软件很熟练，但是还算好做，思路很清晰。

涉及到的软件：

samtools
featureCounts
GATK
picard
java
bam-readcount
Python3
Pandas

如果您只有FASTQ数据，并且希望使用我们的脚本生成表达式矩阵和SNV矩阵，则可以运行存储在。/inst/中的shell脚本。可以直接从R环境中执行这些脚本，但我们建议您在shell中使用，主要为两部，后面的就可以直接读入软件包 eQTLsingle 中操作了。

预处理:从FASTQ数据中生成突变谱和表达谱；
SNV质量控制:对选中的SNV进行读取计数，确认有效的突变，以便进行进一步的eQTL分析。

后续分析我们可以结合一些临床预测的方法，比如文章中的后续分析 Discoveries on the rs3169950-PSMB6 cis-eQTL pair in gliomaspheres。

(a)胶质球中REF/ALT型细胞rs3169950位点PSMB6的表达水平 (bonferroni校正p值= 2.93 × 10−12)。

(b) PSMB6基因表达与基于TCGA和GTEx数据的脑肿瘤(GBM和LGG)和正常脑样本。红色星号表示单因素方差分析检验p值≤0.05。

(c)按PSMB6基因表达水平分层的TCGA GBM和LGG患者Kaplan-Meier生存图患者分为低表达组和高表达组以PSMB6表达水平中位数作为截止值。

(d) GTEx脑数据中YY1与PSMB6基因表达的相关性。Pearson相关系数为0.57 (p值< 0.001)。

(e) PSMB6上转录因子YY1的ChIP-seq信号和rs3169950调控PSMB6的假设模型表达式。

Reference

Ma T, Li H, Zhang X. Discovering single-cell eQTLs from scRNA-seq data only. Gene. 2022;829:146520. doi:10.1016/j.gene.2022.146520

利用 Cleaned-data mode 还是很快分析出来，但是从 Raw-data mode 开始做还是要求有一定生信分析基础的，有需求的老师可以联系桓峰基因，关注桓峰基因公众号，轻松学生信，高效发文章！

桓峰基因，铸造成功的您！

未来桓峰基因公众号将不间断的推出单细胞系列生信分析教程，

敬请期待！！

桓峰基因官网正式上线，请大家多多关注，还有很多不足之处，大家多多指正！

http://www.kyohogene.com/

桓峰基因和投必得合作，文章润色优惠85折，需要文章润色的老师可以直接到网站输入领取桓峰基因专属优惠券码：KYOHOGENE，然后上传，付款时选择桓峰基因优惠券即可享受85折优惠哦！https://www.topeditsci.com/

桓峰基因

关注

0
点赞
踩
0

收藏

觉得还不错? 一键收藏
0
评论
SCS【32】基于scRNA-seq数据中推断单细胞的eQTLs (eQTLsingle)

f单细胞生信分析教程桓峰基因公众号推出单细胞生信分析教程并配有视频在线教程，目前整理出来的相关教程目录如下：Topic 6. 克隆进化之 CanopyTopic 7. 克隆进化之 CardelinoTopic 8. 克隆进化之 RobustCloneSCS【1】今天开启单细胞之旅，述说单细胞测序的前世今生SCS【2】单细胞转录组之 cellrangerSCS【3】单细胞转录组数据 GEO 下载及...
复制链接

扫一扫