HMDB pathway enrichment

Xiaotao Shen PhD (https://www.shenxt.info/)

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Created on 2020-03-28 and updated on 2021-03-13

Source: vignettes/hmdb_pathway_enrichment.Rmd

Load HMDB pathway database 

data("hmdb_pathway", package = "metPath")
hmdb_pathway
#> ---------Pathway source&version---------
#> SMPDB & 2021-03-02 
#> -----------Pathway information------------
#> 48703 pathways 
#> 0 pathways have genes 
#> 48642 pathways have proteins 
#> 48674 pathways have compounds 
#> Pathway class: Metabolic;primary_pathway;Disease;primary_pathway;Drug Action;primary_pathway;Physiological;Physiological;primary_pathway;Drug Action;Signaling;primary_pathway;Protein;primary_pathway;Drug Metabolism;primary_pathway;Metabolic;Disease;Signaling
get_pathway_class(hmdb_pathway)
#> # A tibble: 12 x 2
#>    class                               n
#>  * <chr>                           <int>
#>  1 Disease                         20016
#>  2 Disease;primary_pathway           232
#>  3 Drug Action                         1
#>  4 Drug Action;primary_pathway       403
#>  5 Drug Metabolism;primary_pathway    64
#>  6 Metabolic                       27777
#>  7 Metabolic;primary_pathway         105
#>  8 Physiological                       2
#>  9 Physiological;primary_pathway      14
#> 10 Protein;primary_pathway            76
#> 11 Signaling                           1
#> 12 Signaling;primary_pathway          12

Pathway enrichment

We use the demo compound list from metPath.

data("query_id_hmdb", package = "metPath")
query_id_hmdb
#>  [1] "HMDB0000060" "HMDB0000056" "HMDB0000064" "HMDB0000092" "HMDB0000134"
#>  [6] "HMDB0000123" "HMDB0000742" "HMDB0000574" "HMDB0000159" "HMDB0000187"
#> [11] "HMDB0000167" "HMDB0000158" "HMDB0000883" "HMDB0000205" "HMDB0000237"
#> [16] "HMDB0000243" "HMDB0000271"
result = 
enrich_hmdb(query_id = query_id_hmdb, 
            query_type = "compound", 
            id_type = "HMDB",
            pathway_database = hmdb_pathway,
            only_primary_pathway = TRUE,
            p_cutoff = 0.05, 
            p_adjust_method = "BH", 
            threads = 3)

Check the result:

result
#> ---------Pathway database&version---------
#> SMPDB & 2021-03-02 
#> -----------Enrichment result------------
#> 874 pathways are enriched 
#> 121 pathways p-values < 0.05 
#> 3-Phosphoglycerate Dehydrogenase Deficiency;Dihydropyrimidine Dehydrogenase Deficiency (DHPD);Dimethylglycine Dehydrogenase Deficiency;Glycine and Serine Metabolism;Hyperglycinemia, Non-Ketotic ... (only top 5 shows)

Plot to show Pathway enrichment 

enrich_bar_plot(
  object = result,
  x_axis = "p_value_adjust",
  cutoff = 0.05,
  top = 10
)

enrich_scatter_plot(object = result)

enrich_network(object = result)