GeneSets: Cell Cycle Gene Sets

In tallulandrews/CycleMix: Cell-Cycle using Mixture Models

Cell Cycle Gene Sets

Description

HGeneSets includes:

Whitfield original cell-cycle genes from Whitfield et al. 2002

Tirosh modification of Whitfield lists used in Tirosh et al. 2016

Macosko modification of Whitfield lists used in Macosko et al. 2015

Quiesc combination of G0 genes from Reactome, and quiescence markers from Cheung et al. 2013

Seurat originates from v4.4.0 of the Seurat package.

MGeneSets includes:

Cyclone all genes used by the pre-computed mouse classifier in cyclone (Scialdone et al. 2015). Each gene was assigned to the stage and direction for which it exhibited the largest fold-change relative to the overall mean in our example data.

Usage

HGeneSets
MGeneSets

Format

A list of dataframes each with three columns: Gene, Stage, Dir Genes are provided as HGNC gene symbols Stage is which cell-cycle stage the gene is differentially expressed in Dir is the direction of differential expression : 1=upregulated, -1=downregulated Note: Genes may be differentially expressed in more than one stage and may appear in multiple dataframes

Value

A list of dataframes

References

Cheung et al. (2013). Molecular regulation of stem cell quiescence (Table 1). Nat Rev Mol Cell Biol. 14:329-340. Macosko et al. (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using nanoliter Droplets (Table S2). Cell. 161(5):1202-1214. Scialdone et al. (2015) Computational assignment of cell-cycle stage from single-cell transcriptome data. Methods. 85:54-61 Tirosh et al. (2016) Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq (Table S5). Science. 352(6282):189-96. Whitfield et al. (2002) Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell. 13(6):1977-2000.

tallulandrews/CycleMix documentation built on Dec. 7, 2024, 1:06 p.m.