A named list that organizes gene signatures into functional or biological
categories. Each element of the list is a character vector containing the
names of gene signatures defined in signature_collection. A total of
43 signature groups are included, covering tumour intrinsic pathways,
immune-related processes, stromal activity, TME characteristics and
immuno-oncology biomarkers. These groups are used in IOBR to conveniently
select sets of signatures for scoring and visualization.
Usage
data(sig_group)Format
A named list of length 43. Each element is a character vector of signature names. Representative groups include:
- tumor_signature
Signatures related to intrinsic tumour biology such as cell cycle, DNA damage repair and histone regulation.
- EMT
Epithelial–mesenchymal transition (EMT)–associated signatures.
- io_biomarkers
Immuno-oncology biomarker–related signatures.
- immu_microenvironment
Immune microenvironment–related signatures.
- immu_suppression
Immune suppression–related signatures.
- immu_exclusion
Signatures associated with immune exclusion and stromal barriers.
- TCR_BCR
T-cell and B-cell receptor pathway signatures.
- tme_signatures1
Tumour microenvironment signature panel (set 1).
- tme_signatures2
Tumour microenvironment signature panel (set 2).
- ...
Additional groups are included (43 total), but not listed individually here; all groups follow the same structure.
Examples
data(sig_group)
head(sig_group)
#> $tumor_signature
#> [1] "CellCycle_Reg"
#> [2] "Cell_cycle"
#> [3] "DDR"
#> [4] "Mismatch_Repair"
#> [5] "Histones"
#> [6] "Homologous_recombination"
#> [7] "Nature_metabolism_Hypoxia"
#> [8] "Molecular_Cancer_m6A"
#> [9] "MT_exosome"
#> [10] "Positive_regulation_of_exosomal_secretion"
#> [11] "Ferroptosis"
#> [12] "EV_Cell_2020"
#>
#> $EMT
#> [1] "Pan_F_TBRs" "EMT1" "EMT2" "EMT3" "WNT_target"
#>
#> $io_biomarkers
#> [1] "TMEscore_CIR" "TMEscoreA_CIR"
#> [3] "TMEscoreB_CIR" "T_cell_inflamed_GEP_Ayers_et_al"
#> [5] "CD_8_T_effector" "IPS_IPS"
#> [7] "Immune_Checkpoint" "Exhausted_CD8_Danaher_et_al"
#> [9] "Pan_F_TBRs" "Mismatch_Repair"
#> [11] "APM"
#>
#> $immu_microenvironment
#> [1] "GPAGs" "PPAGs"
#> [3] "Pan_F_TBRs" "MDSC_Peng_et_al"
#> [5] "TAM_Peng_et_al" "MicroenvironmentScore_xCell"
#> [7] "TMEscore" "ImmuneScore_xCell"
#> [9] "ImmuneScore_estimate" "StromalScore_estimate"
#>
#> $immu_suppression
#> [1] "Pan_F_TBRs"
#> [2] "Fibroblasts_MCPcounter"
#> [3] "Immune_Checkpoint"
#> [4] "Exhausted_CD8_Danaher_et_al"
#> [5] "MDSC_Wang_et_al"
#> [6] "Macrophages_M2_cibersort"
#> [7] "Tregs_quantiseq"
#> [8] "T_cells_regulatory_(Tregs)_CIBERSORT"
#>
#> $immu_exclusion
#> [1] "Pan_F_TBRs"
#> [2] "CAF_Peng_et_al"
#> [3] "Fibroblasts_MCPcounter"
#> [4] "CAFs_EPIC"
#> [5] "EMT1"
#> [6] "EMT2"
#> [7] "WNT_target"
#> [8] "TGFb_Family_Member_Receptor_Li_et_al"
#> [9] "TGFb_Family_Member_Li_et_al"
#> [10] "Macrophages_M2_CIBERSORT"
#> [11] "Macrophages_M2_quantiseq"
#> [12] "TAM_Peng_et_al"
#>