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Gene and Geneset File Structure

Source: R/data.R
Gene_Geneset.Rd

A nested list structure containing file paths for gene and geneset definitions for human and mouse species. This dataset provides organized access to various gene sets and gene collections used in immune response and metabolic pathway analyses.

Usage

Gene_Geneset

Format

A nested list with 2 top-level elements:

Human

List containing gene and geneset collections for human

Mouse

List containing gene and geneset collections for mouse

Source

Internal package data compiled from various public databases:

  • GO: Gene Ontology Consortium

  • KEGG: Kyoto Encyclopedia of Genes and Genomes

  • Reactome: Reactome Pathway Database

  • MSigDB: Molecular Signatures Database

Details

The structure follows this hierarchy:

  • Species (Human/Mouse)

  • Type (Gene/Geneset)

  • Category (GO, KEGG, Reactome, MSigDB, etc.)

  • Specific gene set files

Human Gene Collections

Human_Infection_Immunity_gene

Genes involved in infection and immunity

Human_Macrophage_gene

Macrophage-associated genes

Human_PRR_gene

Pattern recognition receptor genes

Human Geneset Collections

GO_BP_Detect_bacterial

GO biological process terms for bacterial detection

GO_BP_Detect_viral

GO biological process terms for viral detection

MSigDB_Hallmark

MSigDB hallmark gene sets

PCD_geneset

Programmed cell death gene sets

KEGG_Detect_bacterial

KEGG pathways for bacterial detection

KEGG_Detect_parasitic

KEGG pathways for parasitic detection

KEGG_Detect_viral

KEGG pathways for viral detection

KEGG_Metabolism

KEGG metabolism pathways

Reactome_Metabolism

Reactome metabolism pathways

Mouse Gene Collections

Mouse_Infection_Immunity_gene

Mouse genes involved in infection and immunity

Mouse_Macrophage_gene

Mouse macrophage-associated genes

Mouse_PRR_gene

Mouse pattern recognition receptor genes

Mouse Geneset Collections

GO_BP_Detect_bacterial

Mouse GO biological process terms for bacterial detection

GO_BP_Detect_viral

Mouse GO biological process terms for viral detection

KEGG_Detect_bacterial

Mouse KEGG pathways for bacterial detection

KEGG_Detect_parasitic

Mouse KEGG pathways for parasitic detection

KEGG_Detect_viral

Mouse KEGG pathways for viral detection

KEGG_Metabolism

Mouse KEGG metabolism pathways

HotSpot_geneset

Mouse HotSpot gene sets

MSigDB_Hallmark

Mouse MSigDB hallmark gene sets

PCD_geneset

Mouse programmed cell death gene sets

Reactome_Metabolism

Mouse Reactome metabolism pathways

Examples

# Access human gene sets
Gene_Geneset$Human$Gene$Human_Macrophage_gene
#> # A tibble: 15 × 3
#>    M1      M2     Fusion 
#>    <chr>   <chr>  <chr>  
#>  1 FCGR3A  CD163  ADAM9  
#>  2 CD86    MRC1   CD44   
#>  3 CD14    ARG1   CD81   
#>  4 NOS2    CHI3L1 DCSTAMP
#>  5 IL6     RETN   OCSTAMP
#>  6 TNF     IL10   STAT1  
#>  7 IL1B    TGFB1  TREM2  
#>  8 IL12B   PPARG  TYROBP 
#>  9 CXCL9   KLF4   NA     
#> 10 CXCL10  IL4R   NA     
#> 11 CD80    CCL17  NA     
#> 12 HLA-DRA CCL22  NA     
#> 13 IRF5    NA     NA     
#> 14 SOCS3   NA     NA     
#> 15 FPR2    NA     NA     

# List all mouse KEGG pathways
names(Gene_Geneset$Mouse$Geneset$KEGG)
#> [1] "Mouse_KEGG_Detect_bacterial_geneset" "Mouse_KEGG_Detect_parasitic_geneset"
#> [3] "Mouse_KEGG_Detect_viral_geneset"     "Mouse_KEGG_Metabolism_geneset"      

# Get all human geneset categories
names(Gene_Geneset$Human$Geneset)
#> [1] "GO"                            "Human_MSigDB_Hallmark_geneset"
#> [3] "Human_PCD_geneset"             "KEGG"                         
#> [5] "Reactome"