vignettes/kegg_pathway.Rmd
kegg_pathway.RmdGet the information of all pathways in KEGG (https://www.genome.jp/kegg/pathway.html).
library(massdatabase)
pathway_info <-
request_kegg_pathway_info(organism = "hsa")
head(pathway_info)
#> KEGG.ID Pathway.name
#> 1 hsa00010 Glycolysis / Gluconeogenesis - Homo sapiens (human)
#> 2 hsa00020 Citrate cycle (TCA cycle) - Homo sapiens (human)
#> 3 hsa00030 Pentose phosphate pathway - Homo sapiens (human)
#> 4 hsa00040 Pentose and glucuronate interconversions - Homo sapiens (human)
#> 5 hsa00051 Fructose and mannose metabolism - Homo sapiens (human)
#> 6 hsa00052 Galactose metabolism - Homo sapiens (human)Get the information of one pathway.
pathway <-
request_kegg_pathway(pathway_id = "hsa00010")
pathway
#> $ENTRY
#> Pathway
#> "hsa00010"
#>
#> $NAME
#> [1] "Glycolysis / Gluconeogenesis - Homo sapiens (human)"
#>
#> $DESCRIPTION
#> [1] "Glycolysis is the process of converting glucose into pyruvate and generating small amounts of ATP (energy) and NADH (reducing power). It is a central pathway that produces important precursor metabolites: six-carbon compounds of glucose-6P and fructose-6P and three-carbon compounds of glycerone-P, glyceraldehyde-3P, glycerate-3P, phosphoenolpyruvate, and pyruvate [MD:M00001]. Acetyl-CoA, another important precursor metabolite, is produced by oxidative decarboxylation of pyruvate [MD:M00307]. When the enzyme genes of this pathway are examined in completely sequenced genomes, the reaction steps of three-carbon compounds from glycerone-P to pyruvate form a conserved core module [MD:M00002], which is found in almost all organisms and which sometimes contains operon structures in bacterial genomes. Gluconeogenesis is a synthesis pathway of glucose from noncarbohydrate precursors. It is essentially a reversal of glycolysis with minor variations of alternative paths [MD:M00003]."
#>
#> $CLASS
#> [1] "Metabolism; Carbohydrate metabolism"
#>
#> $PATHWAY_MAP
#> hsa00010
#> "Glycolysis / Gluconeogenesis"
#>
#> $MODULE
#> hsa_M00001
#> "Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate [PATH:hsa00010]"
#> hsa_M00002
#> "Glycolysis, core module involving three-carbon compounds [PATH:hsa00010]"
#> hsa_M00003
#> "Gluconeogenesis, oxaloacetate => fructose-6P [PATH:hsa00010]"
#> hsa_M00307
#> "Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:hsa00010]"
#>
#> $NETWORK
#> $NETWORK$NETWORK
#> [1] "nt06017 Glycogen metabolism"
#>
#> $NETWORK$ELEMENT
#> [1] "N00731 Glycolysis"
#>
#>
#> $DRUG
#> [1] "D00123" "Cyanamide (JP18)"
#> [3] "D00131" "Disulfiram (JP18/USP/INN)"
#> [5] "D07257" "Lonidamine (INN)"
#> [7] "D08970" "Piragliatin (USAN)"
#> [9] "D11342" "Dorzagliatin (USAN)"
#> [11] "D11408" "Mitapivat sulfate (USAN)"
#> [13] "D12320" "Cadisegliatin (USAN)"
#> [15] "D12362" "Etavopivat (USAN/INN)"
#>
#> $DBLINKS
#> [1] "GO: 0006096 0006094"
#>
#> $ORGANISM
#> Homo sapiens (human) [GN:hsa]
#> "NA Homo sapiens (human) [GN:hsa]"
#>
#> $GENE
#> [1] "3101"
#> [2] "HK3; hexokinase 3 [KO:K00844] [EC:2.7.1.1]"
#> [3] "3098"
#> [4] "HK1; hexokinase 1 [KO:K00844] [EC:2.7.1.1]"
#> [5] "3099"
#> [6] "HK2; hexokinase 2 [KO:K00844] [EC:2.7.1.1]"
#> [7] "80201"
#> [8] "HKDC1; hexokinase domain containing 1 [KO:K00844] [EC:2.7.1.1]"
#> [9] "2645"
#> [10] "GCK; glucokinase [KO:K12407] [EC:2.7.1.2]"
#> [11] "2821"
#> [12] "GPI; glucose-6-phosphate isomerase [KO:K01810] [EC:5.3.1.9]"
#> [13] "5213"
#> [14] "PFKM; phosphofructokinase, muscle [KO:K00850] [EC:2.7.1.11]"
#> [15] "5214"
#> [16] "PFKP; phosphofructokinase, platelet [KO:K00850] [EC:2.7.1.11]"
#> [17] "5211"
#> [18] "PFKL; phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]"
#> [19] "2203"
#> [20] "FBP1; fructose-bisphosphatase 1 [KO:K03841] [EC:3.1.3.11]"
#> [21] "8789"
#> [22] "FBP2; fructose-bisphosphatase 2 [KO:K03841] [EC:3.1.3.11]"
#> [23] "230"
#> [24] "ALDOC; aldolase, fructose-bisphosphate C [KO:K01623] [EC:4.1.2.13]"
#> [25] "226"
#> [26] "ALDOA; aldolase, fructose-bisphosphate A [KO:K01623] [EC:4.1.2.13]"
#> [27] "229"
#> [28] "ALDOB; aldolase, fructose-bisphosphate B [KO:K01623] [EC:4.1.2.13]"
#> [29] "7167"
#> [30] "TPI1; triosephosphate isomerase 1 [KO:K01803] [EC:5.3.1.1]"
#> [31] "2597"
#> [32] "GAPDH; glyceraldehyde-3-phosphate dehydrogenase [KO:K00134] [EC:1.2.1.12]"
#> [33] "26330"
#> [34] "GAPDHS; glyceraldehyde-3-phosphate dehydrogenase, spermatogenic [KO:K10705] [EC:1.2.1.12]"
#> [35] "5232"
#> [36] "PGK2; phosphoglycerate kinase 2 [KO:K00927] [EC:2.7.2.3]"
#> [37] "5230"
#> [38] "PGK1; phosphoglycerate kinase 1 [KO:K00927] [EC:2.7.2.3]"
#> [39] "5223"
#> [40] "PGAM1; phosphoglycerate mutase 1 [KO:K01834] [EC:5.4.2.11]"
#> [41] "5224"
#> [42] "PGAM2; phosphoglycerate mutase 2 [KO:K01834] [EC:5.4.2.11]"
#> [43] "441531"
#> [44] "PGAM4; phosphoglycerate mutase family member 4 [KO:K01834] [EC:5.4.2.11]"
#> [45] "2027"
#> [46] "ENO3; enolase 3 [KO:K01689] [EC:4.2.1.11]"
#> [47] "2026"
#> [48] "ENO2; enolase 2 [KO:K01689] [EC:4.2.1.11]"
#> [49] "2023"
#> [50] "ENO1; enolase 1 [KO:K01689] [EC:4.2.1.11]"
#> [51] "387712"
#> [52] "ENO4; enolase 4 [KO:K01689] [EC:4.2.1.11]"
#> [53] "5315"
#> [54] "PKM; pyruvate kinase M1/2 [KO:K00873] [EC:2.7.1.40]"
#> [55] "5313"
#> [56] "PKLR; pyruvate kinase L/R [KO:K12406] [EC:2.7.1.40]"
#> [57] "5161"
#> [58] "PDHA2; pyruvate dehydrogenase E1 subunit alpha 2 [KO:K00161] [EC:1.2.4.1]"
#> [59] "5160"
#> [60] "PDHA1; pyruvate dehydrogenase E1 subunit alpha 1 [KO:K00161] [EC:1.2.4.1]"
#> [61] "5162"
#> [62] "PDHB; pyruvate dehydrogenase E1 subunit beta [KO:K00162] [EC:1.2.4.1]"
#> [63] "1737"
#> [64] "DLAT; dihydrolipoamide S-acetyltransferase [KO:K00627] [EC:2.3.1.12]"
#> [65] "1738"
#> [66] "DLD; dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]"
#> [67] "160287"
#> [68] "LDHAL6A; lactate dehydrogenase A like 6A [KO:K00016] [EC:1.1.1.27]"
#> [69] "92483"
#> [70] "LDHAL6B; lactate dehydrogenase A like 6B [KO:K00016] [EC:1.1.1.27]"
#> [71] "3939"
#> [72] "LDHA; lactate dehydrogenase A [KO:K00016] [EC:1.1.1.27]"
#> [73] "3945"
#> [74] "LDHB; lactate dehydrogenase B [KO:K00016] [EC:1.1.1.27]"
#> [75] "3948"
#> [76] "LDHC; lactate dehydrogenase C [KO:K00016] [EC:1.1.1.27]"
#> [77] "124"
#> [78] "ADH1A; alcohol dehydrogenase 1A (class I), alpha polypeptide [KO:K13951] [EC:1.1.1.1]"
#> [79] "125"
#> [80] "ADH1B; alcohol dehydrogenase 1B (class I), beta polypeptide [KO:K13951] [EC:1.1.1.1]"
#> [81] "126"
#> [82] "ADH1C; alcohol dehydrogenase 1C (class I), gamma polypeptide [KO:K13951] [EC:1.1.1.1]"
#> [83] "131"
#> [84] "ADH7; alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide [KO:K13951] [EC:1.1.1.1]"
#> [85] "127"
#> [86] "ADH4; alcohol dehydrogenase 4 (class II), pi polypeptide [KO:K13980] [EC:1.1.1.1]"
#> [87] "128"
#> [88] "ADH5; alcohol dehydrogenase 5 (class III), chi polypeptide [KO:K00121] [EC:1.1.1.284 1.1.1.1]"
#> [89] "130"
#> [90] "ADH6; alcohol dehydrogenase 6 (class V) [KO:K13952] [EC:1.1.1.1]"
#> [91] "10327"
#> [92] "AKR1A1; aldo-keto reductase family 1 member A1 [KO:K00002] [EC:1.1.1.2]"
#> [93] "217"
#> [94] "ALDH2; aldehyde dehydrogenase 2 family member [KO:K00128] [EC:1.2.1.3]"
#> [95] "224"
#> [96] "ALDH3A2; aldehyde dehydrogenase 3 family member A2 [KO:K00128] [EC:1.2.1.3]"
#> [97] "219"
#> [98] "ALDH1B1; aldehyde dehydrogenase 1 family member B1 [KO:K00128] [EC:1.2.1.3]"
#> [99] "501"
#> [100] "ALDH7A1; aldehyde dehydrogenase 7 family member A1 [KO:K14085] [EC:1.2.1.31 1.2.1.8 1.2.1.3]"
#> [101] "223"
#> [102] "ALDH9A1; aldehyde dehydrogenase 9 family member A1 [KO:K00149] [EC:1.2.1.47 1.2.1.3]"
#> [103] "221"
#> [104] "ALDH3B1; aldehyde dehydrogenase 3 family member B1 [KO:K00129] [EC:1.2.1.5]"
#> [105] "222"
#> [106] "ALDH3B2; aldehyde dehydrogenase 3 family member B2 [KO:K00129] [EC:1.2.1.5]"
#> [107] "218"
#> [108] "ALDH3A1; aldehyde dehydrogenase 3 family member A1 [KO:K00129] [EC:1.2.1.5]"
#> [109] "84532"
#> [110] "ACSS1; acyl-CoA synthetase short chain family member 1 [KO:K01895] [EC:6.2.1.1]"
#> [111] "55902"
#> [112] "ACSS2; acyl-CoA synthetase short chain family member 2 [KO:K01895] [EC:6.2.1.1]"
#> [113] "130589"
#> [114] "GALM; galactose mutarotase [KO:K01785] [EC:5.1.3.3]"
#> [115] "5236"
#> [116] "PGM1; phosphoglucomutase 1 [KO:K01835] [EC:5.4.2.2]"
#> [117] "55276"
#> [118] "PGM2; phosphoglucomutase 2 [KO:K15779] [EC:5.4.2.2 5.4.2.7]"
#> [119] "2538"
#> [120] "G6PC1; glucose-6-phosphatase catalytic subunit 1 [KO:K01084] [EC:3.1.3.9]"
#> [121] "57818"
#> [122] "G6PC2; glucose-6-phosphatase catalytic subunit 2 [KO:K01084] [EC:3.1.3.9]"
#> [123] "92579"
#> [124] "G6PC3; glucose-6-phosphatase catalytic subunit 3 [KO:K01084] [EC:3.1.3.9]"
#> [125] "83440"
#> [126] "ADPGK; ADP dependent glucokinase [KO:K08074] [EC:2.7.1.147]"
#> [127] "669"
#> [128] "BPGM; bisphosphoglycerate mutase [KO:K01837] [EC:5.4.2.4 5.4.2.11]"
#> [129] "9562"
#> [130] "MINPP1; multiple inositol-polyphosphate phosphatase 1 [KO:K03103] [EC:3.1.3.62 3.1.3.80]"
#> [131] "5105"
#> [132] "PCK1; phosphoenolpyruvate carboxykinase 1 [KO:K01596] [EC:4.1.1.32]"
#> [133] "5106"
#> [134] "PCK2; phosphoenolpyruvate carboxykinase 2, mitochondrial [KO:K01596] [EC:4.1.1.32]"
#>
#> $COMPOUND
#> C00022
#> "Pyruvate"
#> C00024
#> "Acetyl-CoA"
#> C00031
#> "D-Glucose"
#> C00033
#> "Acetate"
#> C00036
#> "Oxaloacetate"
#> C00068
#> "Thiamin diphosphate"
#> C00074
#> "Phosphoenolpyruvate"
#> C00084
#> "Acetaldehyde"
#> C00103
#> "D-Glucose 1-phosphate"
#> C00111
#> "Glycerone phosphate"
#> C00118
#> "D-Glyceraldehyde 3-phosphate"
#> C00186
#> "(S)-Lactate"
#> C00197
#> "3-Phospho-D-glycerate"
#> C00221
#> "beta-D-Glucose"
#> C00236
#> "3-Phospho-D-glyceroyl phosphate"
#> C00267
#> "alpha-D-Glucose"
#> C00469
#> "Ethanol"
#> C00631
#> "2-Phospho-D-glycerate"
#> C00668
#> "alpha-D-Glucose 6-phosphate"
#> C01159
#> "2,3-Bisphospho-D-glycerate"
#> C01172
#> "beta-D-Glucose 6-phosphate"
#> C01451
#> "Salicin"
#> C05125
#> "2-(alpha-Hydroxyethyl)thiamine diphosphate"
#> C05345
#> "beta-D-Fructose 6-phosphate"
#> C05378
#> "beta-D-Fructose 1,6-bisphosphate"
#> C06186
#> "Arbutin"
#> C06187
#> "Arbutin 6-phosphate"
#> C06188
#> "Salicin 6-phosphate"
#> C15972
#> "Enzyme N6-(lipoyl)lysine"
#> C15973
#> "Enzyme N6-(dihydrolipoyl)lysine"
#> C16255
#> "[Dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine"
#>
#> $REL_PATHWAY
#> hsa00020 hsa00030
#> "Citrate cycle (TCA cycle)" "Pentose phosphate pathway"
#> hsa00500 hsa00620
#> "Starch and sucrose metabolism" "Pyruvate metabolism"
#> hsa00640
#> "Propanoate metabolism"
#>
#> $KO_PATHWAY
#> [1] "ko00010"
#>
#> $REFERENCE
#> $REFERENCE[[1]]
#> $REFERENCE[[1]]$REFERENCE
#> [1] ""
#>
#> $REFERENCE[[1]]$AUTHORS
#> [1] "Nishizuka Y (ed)."
#>
#> $REFERENCE[[1]]$TITLE
#> [1] "[Metabolic Maps] (In Japanese)"
#>
#> $REFERENCE[[1]]$JOURNAL
#> [1] "Tokyo Kagaku Dojin (1980)"
#>
#>
#> $REFERENCE[[2]]
#> $REFERENCE[[2]]$REFERENCE
#> [1] ""
#>
#> $REFERENCE[[2]]$AUTHORS
#> [1] "Nishizuka Y, Seyama Y, Ikai A, Ishimura Y, Kawaguchi A (eds)."
#>
#> $REFERENCE[[2]]$TITLE
#> [1] "[Cellular Functions and Metabolic Maps] (In Japanese)"
#>
#> $REFERENCE[[2]]$JOURNAL
#> [1] "Tokyo Kagaku Dojin (1997)"
#>
#>
#> $REFERENCE[[3]]
#> $REFERENCE[[3]]$REFERENCE
#> [1] ""
#>
#> $REFERENCE[[3]]$AUTHORS
#> [1] "Michal G."
#>
#> $REFERENCE[[3]]$TITLE
#> [1] "Biochemical Pathways"
#>
#> $REFERENCE[[3]]$JOURNAL
#> [1] "Wiley (1999)"Download the human pathway data.
download_kegg_pathway(path = "kegg_human_pathway",
sleep = 1,
organism = "hsa")Read the download pathway data.
data <-
read_kegg_pathway(path = "kegg_human_pathway")
class(data)
#> [1] "list"
length(data)
#> [1] 347
data[[1]]$pathway_id
#> Pathway
#> "hsa00010"
data[[1]]$pathway_name
#> [1] "Glycolysis / Gluconeogenesis"
data[[1]]$pathway_class
#> [1] "Metabolism; Carbohydrate metabolism"
data[[1]]$compound_list
#> KEGG.ID
#> C00022 C00022
#> C00024 C00024
#> C00031 C00031
#> C00033 C00033
#> C00036 C00036
#> C00068 C00068
#> C00074 C00074
#> C00084 C00084
#> C00103 C00103
#> C00111 C00111
#> C00118 C00118
#> C00186 C00186
#> C00197 C00197
#> C00221 C00221
#> C00236 C00236
#> C00267 C00267
#> C00469 C00469
#> C00631 C00631
#> C00668 C00668
#> C01159 C01159
#> C01172 C01172
#> C01451 C01451
#> C05125 C05125
#> C05345 C05345
#> C05378 C05378
#> C06186 C06186
#> C06187 C06187
#> C06188 C06188
#> C15972 C15972
#> C15973 C15973
#> C16255 C16255
#> Compound.name
#> C00022 Pyruvate
#> C00024 Acetyl-CoA
#> C00031 D-Glucose
#> C00033 Acetate
#> C00036 Oxaloacetate
#> C00068 Thiamin diphosphate
#> C00074 Phosphoenolpyruvate
#> C00084 Acetaldehyde
#> C00103 D-Glucose 1-phosphate
#> C00111 Glycerone phosphate
#> C00118 D-Glyceraldehyde 3-phosphate
#> C00186 (S)-Lactate
#> C00197 3-Phospho-D-glycerate
#> C00221 beta-D-Glucose
#> C00236 3-Phospho-D-glyceroyl phosphate
#> C00267 alpha-D-Glucose
#> C00469 Ethanol
#> C00631 2-Phospho-D-glycerate
#> C00668 alpha-D-Glucose 6-phosphate
#> C01159 2,3-Bisphospho-D-glycerate
#> C01172 beta-D-Glucose 6-phosphate
#> C01451 Salicin
#> C05125 2-(alpha-Hydroxyethyl)thiamine diphosphate
#> C05345 beta-D-Fructose 6-phosphate
#> C05378 beta-D-Fructose 1,6-bisphosphate
#> C06186 Arbutin
#> C06187 Arbutin 6-phosphate
#> C06188 Salicin 6-phosphate
#> C15972 Enzyme N6-(lipoyl)lysine
#> C15973 Enzyme N6-(dihydrolipoyl)lysine
#> C16255 [Dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine
data[[1]]$related_module
#> Module.ID
#> hsa_M00001 hsa_M00001
#> hsa_M00002 hsa_M00002
#> hsa_M00003 hsa_M00003
#> hsa_M00307 hsa_M00307
#> Module.name
#> hsa_M00001 Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate [PATH:hsa00010]
#> hsa_M00002 Glycolysis, core module involving three-carbon compounds [PATH:hsa00010]
#> hsa_M00003 Gluconeogenesis, oxaloacetate => fructose-6P [PATH:hsa00010]
#> hsa_M00307 Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:hsa00010]
# kegg_human_pathway <-
# convert_kegg2metpath(data = data,
# path = "kegg_human_pathway",
# threads = 3)
# kegg_human_pathway
sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur ... 10.16
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] massdatabase_0.99.14
#>
#> loaded via a namespace (and not attached):
#> [1] readxl_1.4.0 circlize_0.4.15
#> [3] systemfonts_1.0.4 igraph_1.3.2
#> [5] plyr_1.8.7 lazyeval_0.2.2
#> [7] BiocParallel_1.30.3 listenv_0.8.0
#> [9] ChemmineR_3.48.0 GenomeInfoDb_1.32.2
#> [11] ggplot2_3.3.6 Rdisop_1.56.0
#> [13] digest_0.6.29 foreach_1.5.2
#> [15] yulab.utils_0.0.5 htmltools_0.5.2
#> [17] viridis_0.6.2 massdataset_1.0.5
#> [19] fansi_1.0.3 magrittr_2.0.3
#> [21] memoise_2.0.1 metpath_0.99.4
#> [23] cluster_2.1.3 doParallel_1.0.17
#> [25] tzdb_0.3.0 openxlsx_4.2.5
#> [27] limma_3.52.2 graphlayouts_0.8.0
#> [29] readr_2.1.2 ComplexHeatmap_2.12.0
#> [31] globals_0.15.1 Biostrings_2.64.0
#> [33] matrixStats_0.62.0 pkgdown_2.0.5
#> [35] prettyunits_1.1.1 colorspace_2.0-3
#> [37] ggrepel_0.9.1 rvest_1.0.2
#> [39] metid_1.2.15 textshaping_0.3.6
#> [41] xfun_0.31 dplyr_1.0.9
#> [43] crayon_1.5.1 RCurl_1.98-1.7
#> [45] jsonlite_1.8.0 impute_1.70.0
#> [47] iterators_1.0.14 glue_1.6.2
#> [49] polyclip_1.10-0 gtable_0.3.0
#> [51] zlibbioc_1.42.0 XVector_0.36.0
#> [53] GetoptLong_1.0.5 DelayedArray_0.22.0
#> [55] shape_1.4.6 BiocGenerics_0.42.0
#> [57] scales_1.2.0 vsn_3.64.0
#> [59] DBI_1.1.3 Rcpp_1.0.8.3
#> [61] mzR_2.30.0 progress_1.2.2
#> [63] viridisLite_0.4.0 clue_0.3-61
#> [65] gridGraphics_0.5-1 preprocessCore_1.58.0
#> [67] stats4_4.2.1 MsCoreUtils_1.8.0
#> [69] rsvg_2.3.1 DT_0.23
#> [71] htmlwidgets_1.5.4 httr_1.4.3
#> [73] RColorBrewer_1.1-3 ellipsis_0.3.2
#> [75] farver_2.1.1 pkgconfig_2.0.3
#> [77] XML_3.99-0.10 sass_0.4.1
#> [79] utf8_1.2.2 ggplotify_0.1.0
#> [81] tidyselect_1.1.2 rlang_1.0.3
#> [83] munsell_0.5.0 cellranger_1.1.0
#> [85] tools_4.2.1 cachem_1.0.6
#> [87] cli_3.3.0 generics_0.1.3
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