10 Regressing cell cycle signal (Optional)
From Barron and Li
During the cell cycle a cell increases in size, replicates its DNA and splits into daughter cells. Different cells are at different time points of this cycle, and thus they may have quite different expression profiles, even if they are cells of the same type. This within-type heterogeneity can seriously deteriorate the performance of clustering algorithms for cell type identification: it may blur clusters of cell types or cause cells of similar cell-cycle statuses to stand out as new clusters.
In Natian (through Seurat), you have the option to regress out variations generated through cell-cycle phase or activity. You can perform the analysis by selecting one of the two following options:
All cell cycle signal Subtracts (regress out) the effect of cell cycle based on S2 and G2/M scores. Refer to Seurat Vignette for details.
Cell cycle status (G2/S/M) Removes the effect of cell cycle based on the difference of S2 and G2/M scores. This in effect removes the differences between cells in S2 and G2/M phases. Refer to Seurat Vignette for details.
To perform this analysis select one of the category above and then click on the Filter cells and perform PCA.
Human genes used
| Category | Genes |
|---|---|
| S genes | UHRF1, MCM5, UNG, MCM6, BRIP1, TIPIN, UBR7, POLA1, RRM1, CLSPN, BLM, CHAF1B, MSH2, DTL, EXO1, NASP, CDC45, E2F8, HELLS, WDR76, RRM2, MCM2, USP1, TYMS, CASP8AP2, PCNA, GINS2, RPA2, RFC2, CDC6, GMNN, RAD51, CDCA7, ATAD2, PRIM1, SLBP, POLD3, DSCC1, FEN1, CCNE2, MCM4, RAD51AP1 |
| G2/M genes | CKAP5, CDK1, CDC25C, SMC4, NDC80, TACC3, MKI67, GAS2L3, HMGB2, HMMR, NUSAP1, CKAP2L, UBE2C, ANLN, CKS1B, BIRC5, NEK2, GTSE1, CKS2, CDC20, PSRC1, KIF2C, RANGAP1, AURKA, KIF11, G2E3, BUB1, CTCF, DLGAP5, LBR, CENPE, CKAP2, CENPA, TMPO, TOP2A, HJURP, KIF20B, CBX5, NCAPD2, TUBB4B, TTK, KIF23, CDCA3, CDCA2, ECT2, TPX2, AURKB, CENPF, CDCA8, CCNB2, ANP32E |
Mouse genes used
| Category | Genes |
|---|---|
| S genes | Chaf1b, Pold3, Prim1, Exo1, Mcm2, Gins2, Ccne2, Mcm4, Pola1, Msh2, Cdc6, Blm, Rad51ap1, Usp1, Rfc2, Dtl, Atad2, Brip1, Ung, Mcm6, E2f8, Rrm1, Tipin, Gmnn, Pcna, Ubr7, Casp8ap2, Ubr7, Cdc45, Tyms, Rpa2, Clspn, Fen1, Mcm5, Slbp, Wdr76, Hells, Uhrf1, Nasp, Cdca7, Dscc1, Rrm2, Rad51, Casp8ap2 |
| G2/M genes | Ckap5, Gas2l3, Cks1b, Kif2c, Ctcf, Tmpo, Tubb4b, Tpx2, Cdk1, Hmgb2, Birc5, Rangap1, Dlgap5, Top2a, Ttk, Aurkb, Cdc25c, Hmmr, Nek2, Aurka, Lbr, Hjurp, Kif23, Cenpf, Smc4, Nusap1, Gtse1, Kif11, Cenpe, Kif20b, Cdca3, Cdca8, Ndc80, Ckap2l, Cks2, G2e3, Ckap2, Cbx5, Cdca2, Ccnb2, Tacc3, Ube2c, Cdc20, Bub1, Cenpa, Ncapd2, Ect2, Anp32e, Mki67, Anln, Psrc1, Nuf2 |