Based on the human cell cycle genes, the cell cycle genes of the corresponding species were captured by homologous gene conversion.
Usage
CC_GenePrefetch(
species = "Homo_sapiens",
Ensembl_version = 103,
mirror = NULL,
max_tries = 5,
use_cached_gene = TRUE
)Arguments
- species
Latin names for animals,i.e., "Homo_sapiens", "Mus_musculus"
- Ensembl_version
Ensembl database version. If NULL, use the current release version.
- mirror
Specify an Ensembl mirror to connect to. The valid options here are 'www', 'uswest', 'useast', 'asia'.
- max_tries
The maximum number of attempts to connect with the BioMart service.
- use_cached_gene
Whether to use previously cached cell cycle gene conversion results for the species.
Examples
ccgenes <- CC_GenePrefetch("Homo_sapiens")
str(ccgenes)
#> List of 3
#> $ res: NULL
#> $ S : chr [1:43] "MCM5" "PCNA" "TYMS" "FEN1" ...
#> $ G2M: chr [1:54] "HMGB2" "CDK1" "NUSAP1" "UBE2C" ...
ccgenes <- CC_GenePrefetch("Mus_musculus")
#> ℹ [2025-07-03 08:13:47] Connect to the Ensembl archives...
#> ℹ [2025-07-03 08:13:48] Using the 103 version of biomart...
#> ℹ [2025-07-03 08:13:48] Connecting to the biomart...
#> ℹ [2025-07-03 08:13:49] Searching the dataset hsapiens ...
#> ℹ [2025-07-03 08:13:50] Connecting to the dataset hsapiens_gene_ensembl ...
#> ℹ [2025-07-03 08:13:50] Converting the geneIDs...
#> ℹ [2025-07-03 08:13:52] 97 genes mapped with ensembl_symbol
#> ℹ [2025-07-03 08:13:52] ==============================
#> 97 genes mapped
#> 0 genes unmapped
#> ==============================
str(ccgenes)
#> List of 3
#> $ res:List of 7
#> ..$ geneID_res :'data.frame': 99 obs. of 4 variables:
#> .. ..$ from_IDtype: chr [1:99] "ensembl_symbol" "ensembl_symbol" "ensembl_symbol" "ensembl_symbol" ...
#> .. ..$ from_geneID: chr [1:99] "NCAPD2" "ANLN" "UBR7" "TACC3" ...
#> .. ..$ to_IDtype : chr [1:99] "symbol" "symbol" "symbol" "symbol" ...
#> .. ..$ to_geneID : chr [1:99] "Ncapd2" "Anln" "Ubr7" "Tacc3" ...
#> ..$ geneID_collapse:'data.frame': 94 obs. of 2 variables:
#> .. ..$ from_geneID: chr [1:94] "ANLN" "ANP32E" "AURKA" "AURKB" ...
#> .. ..$ symbol :List of 94
#> .. .. ..$ : chr "Anln"
#> .. .. ..$ : chr "Anp32e"
#> .. .. ..$ : chr "Aurka"
#> .. .. ..$ : chr "Aurkb"
#> .. .. ..$ : chr "Birc5"
#> .. .. ..$ : chr "Blm"
#> .. .. ..$ : chr "Bub1"
#> .. .. ..$ : chr "Casp8ap2"
#> .. .. ..$ : chr "Cbx5"
#> .. .. ..$ : chr "Ccnb2"
#> .. .. ..$ : chr "Ccne2"
#> .. .. ..$ : chr "Cdc20"
#> .. .. ..$ : chr "Cdc25c"
#> .. .. ..$ : chr "Cdc45"
#> .. .. ..$ : chr "Cdc6"
#> .. .. ..$ : chr "Cdca2"
#> .. .. ..$ : chr "Cdca3"
#> .. .. ..$ : chr "Cdca7"
#> .. .. ..$ : chr "Cdca8"
#> .. .. ..$ : chr "Cdk1"
#> .. .. ..$ : chr "Cenpa"
#> .. .. ..$ : chr "Cenpe"
#> .. .. ..$ : chr "Cenpf"
#> .. .. ..$ : chr "Cenpu"
#> .. .. ..$ : chr "Chaf1b"
#> .. .. ..$ : chr "Ckap2"
#> .. .. ..$ : chr "Ckap2l"
#> .. .. ..$ : chr "Ckap5"
#> .. .. ..$ : chr "Cks1b"
#> .. .. ..$ : chr "Cks2"
#> .. .. ..$ : chr "Clspn"
#> .. .. ..$ : chr "Ctcf"
#> .. .. ..$ : chr "Dlgap5"
#> .. .. ..$ : chr "Dscc1"
#> .. .. ..$ : chr "Dtl"
#> .. .. ..$ : chr "E2f8"
#> .. .. ..$ : chr "Ect2"
#> .. .. ..$ : chr "Exo1"
#> .. .. ..$ : chr "Fen1"
#> .. .. ..$ : chr "G2e3"
#> .. .. ..$ : chr "Gas2l3"
#> .. .. ..$ : chr "Gins2"
#> .. .. ..$ : chr "Gmnn"
#> .. .. ..$ : chr "Gtse1"
#> .. .. ..$ : chr "Hells"
#> .. .. ..$ : chr "Hjurp"
#> .. .. ..$ : chr "Hmgb2"
#> .. .. ..$ : chr "Hmmr"
#> .. .. ..$ : chr "Kif11"
#> .. .. ..$ : chr "Kif20b"
#> .. .. ..$ : chr "Kif23"
#> .. .. ..$ : chr "Kif2c"
#> .. .. ..$ : chr "Lbr"
#> .. .. ..$ : chr "Mcm4"
#> .. .. ..$ : chr "Mcm5"
#> .. .. ..$ : chr "Mcm6"
#> .. .. ..$ : chr "Mcm7"
#> .. .. ..$ : chr "Mki67"
#> .. .. ..$ : chr "Mrpl36"
#> .. .. ..$ : chr "Msh2"
#> .. .. ..$ : chr "Nasp"
#> .. .. ..$ : chr "Ncapd2"
#> .. .. ..$ : chr "Ndc80"
#> .. .. ..$ : chr "Nek2"
#> .. .. ..$ : chr "Nuf2"
#> .. .. ..$ : chr "Nusap1"
#> .. .. ..$ : chr "Pcna"
#> .. .. ..$ : chr "Pimreg"
#> .. .. ..$ : chr "Pola1"
#> .. .. ..$ : chr "Polr1b"
#> .. .. ..$ : chr "Prim1"
#> .. .. ..$ : chr "Psrc1"
#> .. .. ..$ : chr "Rad51"
#> .. .. ..$ : chr "Rad51ap1"
#> .. .. ..$ : chr "Rangap1"
#> .. .. ..$ : chr "Rfc2"
#> .. .. ..$ : chr "Rrm1"
#> .. .. ..$ : chr "Rrm2"
#> .. .. ..$ : chr "Slbp"
#> .. .. ..$ : chr "Smc4"
#> .. .. ..$ : chr "Tacc3"
#> .. .. ..$ : chr "Tipin"
#> .. .. ..$ : chr "Tmpo"
#> .. .. ..$ : chr "Top2a"
#> .. .. ..$ : chr "Tpx2"
#> .. .. ..$ : chr "Ttk"
#> .. .. ..$ : chr "Tubb4b"
#> .. .. ..$ : chr "Tyms"
#> .. .. ..$ : chr "Ube2c"
#> .. .. ..$ : chr "Ubr7"
#> .. .. ..$ : chr "Uhrf1"
#> .. .. ..$ : chr "Ung"
#> .. .. ..$ : chr "Usp1"
#> .. .. ..$ : chr "Wdr76"
#> .. .. ..- attr(*, "class")= chr "AsIs"
#> ..$ geneID_expand :'data.frame': 94 obs. of 2 variables:
#> .. ..$ from_geneID: chr [1:94] "ANLN" "ANP32E" "AURKA" "AURKB" ...
#> .. ..$ symbol : chr [1:94] "Anln" "Anp32e" "Aurka" "Aurkb" ...
#> ..$ Ensembl_version: chr "103"
#> ..$ Datasets :'data.frame': 202 obs. of 3 variables:
#> .. ..$ dataset : 'AsIs' chr [1:202] "abrachyrhynchus_gene_ensembl" "acalliptera_gene_ensembl" "acarolinensis_gene_ensembl" "acchrysaetos_gene_ensembl" ...
#> .. ..$ description: 'AsIs' chr [1:202] "Pink-footed goose genes (ASM259213v1)" "Eastern happy genes (fAstCal1.2)" "Anole lizard genes (AnoCar2.0)" "Golden eagle genes (bAquChr1.2)" ...
#> .. ..$ version : 'AsIs' chr [1:202] "ASM259213v1" "fAstCal1.2" "AnoCar2.0" "bAquChr1.2" ...
#> ..$ Attributes :'data.frame': 3183 obs. of 3 variables:
#> .. ..$ name : chr [1:3183] "ensembl_gene_id" "ensembl_gene_id_version" "ensembl_transcript_id" "ensembl_transcript_id_version" ...
#> .. ..$ description: chr [1:3183] "Gene stable ID" "Gene stable ID version" "Transcript stable ID" "Transcript stable ID version" ...
#> .. ..$ page : chr [1:3183] "feature_page" "feature_page" "feature_page" "feature_page" ...
#> ..$ geneID_unmapped: chr(0)
#> $ S : chr [1:41] "Mcm5" "Pcna" "Tyms" "Fen1" ...
#> $ G2M: chr [1:53] "Hmgb2" "Cdk1" "Nusap1" "Ube2c" ...