proteinatlas_genesets_fdb11: Protein Atlas useful genesets for visualization

In jmw86069/pajam: Protein Atlas data and visualization

Description

Protein Atlas useful genesets for visualization

Usage

proteinatlas_genesets_fdb11

Format

list of character vector, whose values match rownames(proteinatlas_expr_fdb11).

Details

This object includes a list of genesets in the form of character vectors of rownames aligned with proteinatlas_expr_fdb11. The genesets are some useful annotations for visualization that include:

• "Plasma" - found in circulating blood plasma

• "secreted_proteins" - secreted proteins

• "membrane_proteins" - membrane-bound proteins

• "FDA" - gene targets of FDA-approved drugs

• "NOT_membrane_secreted" - non-membrane and non-secreted proteins (intracellular)

• "TFs" - transcription factors

• "HKs" - housekeeper genes

• "rna_lymphoid" - RNA-lymphoid associated genes

The annotations are not intended to be fully exhaustive, but are intended to represent some useful annotations not necessarily associated directly with the biological function of each gene/protein. For example, it may be useful to see whether most up-regulated proteins are secreted or intracellular, or perhaps most up-regulated gene transcripts are transcription factors and are not secreted.

See Also

Other pajam data: proteinatlas_expr_fdb11

Examples

use_im <- c("secreted_proteins",
   "membrane_proteins",
   "NOT_membrane_secreted",
   "TFs");
proteinatlas_im <- list2im_opt(proteinatlas_genesets_fdb11[use_im]);
test_genes <- c("DKK1","DKK4","CXCL12","IL6R","MET",
   "HK2","FTL","FTH1","STAT1","STAT3","CDKN1B");

proteinatlas_heatmap(genes=test_genes,
   type="Blood",
   centered=TRUE,
   gene_im=proteinatlas_im);

proteinatlas_heatmap(genes=test_genes,
   type="Blood",
   centered=TRUE,
   column_filter=4,
   row_cex=0.8,
   column_names_max_height=grid::unit(12, "cm"),
   gene_im=proteinatlas_im);

jmw86069/pajam documentation built on Feb. 6, 2022, 1:30 p.m.