Human genome-scale metabolic model (Human-GEM) containing reaction, gene, and pathway information for metabolic flux analysis.
Format
A data frame with 13,082 rows (reactions) and 16 variables:
- #
Row number
- ID
Reaction ID
- NAME
Reaction name
- EQUATION
Stoichiometric equation
- EC-NUMBER
Enzyme Commission number
- GENE ASSOCIATION
Gene-protein-reaction rule
- LOWER BOUND
Lower flux bound
- UPPER BOUND
Upper flux bound
- OBJECTIVE
Objective function coefficient (1 for biomass)
- COMPARTMENT
Cellular compartment
- MIRIAM
MIRIAM annotations
- SUBSYSTEM
Metabolic pathway/subsystem
- REPLACEMENT ID
Alternative reaction ID
- NOTE
Additional notes
- REFERENCE
Literature references
- CONFIDENCE SCORE
Reaction confidence score
Examples
data(human_gem)
head(human_gem)
#> # A tibble: 6 x 16
#> `#` ID NAME EQUATION `EC-NUMBER` `GENE ASSOCIATION` `LOWER BOUND`
#> <lgl> <chr> <chr> <chr> <chr> <chr> <lgl>
#> 1 NA HMR_3905 NA ethanol[c] ~ 1.1.1.1;1.~ ENSG00000147576 o~ NA
#> 2 NA HMR_3907 NA ethanol[c] ~ 1.1.1.2 ENSG00000117448 NA
#> 3 NA HMR_4097 NA acetate[c] ~ 6.2.1.1 ENSG00000131069 NA
#> 4 NA HMR_4099 NA acetate[m] ~ 6.2.1.1 ENSG00000111058 o~ NA
#> 5 NA HMR_4108 NA acetyl aden~ 6.2.1.1 ENSG00000131069 NA
#> 6 NA HMR_4133 NA acetate[c] ~ 6.2.1.1 ENSG00000131069 NA
#> # i 9 more variables: `UPPER BOUND` <lgl>, OBJECTIVE <lgl>, COMPARTMENT <lgl>,
#> # MIRIAM <chr>, SUBSYSTEM <chr>, `REPLACEMENT ID` <lgl>, NOTE <lgl>,
#> # REFERENCE <chr>, `CONFIDENCE SCORE` <dbl>