分子特征数据库R包msigdb

最新推荐文章于 2025-05-28 18:02:14 发布

qq_27390023

最新推荐文章于 2025-05-28 18:02:14 发布

阅读量3.6k

点赞数 1

CC 4.0 BY-SA版权

文章标签： r语言生物信息学

本文链接：https://blog.csdn.net/qq_27390023/article/details/122250563

本文介绍了如何在R中使用msigdb包下载和处理MSigDB数据库，包括hallmark、curated、regulatory等不同类型的基因集。通过GSEABase和ExperimentHub，展示了如何获取、筛选和管理这些生物标志物集合，为基因表达分析提供资源。

摘要生成于 C知道，由 DeepSeek-R1 满血版支持，前往体验 >

msigdb软件包在R可访问对象中提供分子特征数据库（MSigDB）。分子特征集存储在GSEABase包的GeneSet类对象中，整个数据库存储在GeneSetCollection对象中。然后，这些数据将托管在ExperimentHub上。本文件包中使用的数据来自Broad Institute的MSigDB。每个基因集的元数据与基因集一起存储在基因集类对象中。

GSEA | MSigDB

H	hallmark gene sets are coherently expressed signatures derived by aggregating many MSigDB gene sets to represent well-defined biological states or processes.

C1	positional gene sets for each human chromosome and cytogenetic band.

C2	curated gene sets from online pathway databases, publications in PubMed, and knowledge of domain experts.

C3	regulatory target gene sets based on gene target predictions for microRNA seed sequences and predicted transcription factor binding sites.

C4	computational gene sets defined by mining large collections of cancer-oriented microarray data.

C5	ontology gene sets consist of genes annotated by the same ontology term.

C6	oncogenic signature gene sets defined directly from microarray gene expression data from cancer gene perturbations.

C7	immunologic signature gene sets represent cell states and perturbations within the immune system.

C8	cell type signature gene sets curated from cluster markers identified in single-cell sequencing studies of human tissue.

library(msigdb)
library(GSEABase)

ls("package:msigdb")

# Download molecular signatures database."hs" for human and "mm" for mouse
msigdb.hs = getMsigdb(org = 'hs',id = c("SYM", "EZID"))
# Downloading and integrating KEGG gene sets
msigdb.hs = appendKEGG(msigdb.hs)
length(msigdb.hs)

# 可以根据需求选择子基因集
listCollections(msigdb.hs)
#hallmarks = subsetCollection(msigdb.hs, 'h')
#c3<- subsetCollection(msigdb.hs, 'c3')

#listSubCollections(msigdb.hs)

# 基因集列表
msigdb_ids <- geneIds(msigdb.hs) # GSEABase::geneIds
class(msigdb_ids)  # list