Lets try some kegg analyses with some specific gene sets.
all_ids <- read.csv2("downloaded/tcruzi_ids.txt", header=FALSE)
de_ids <- read.csv2("downloaded/de_ids.txt", header=FALSE)
all <- as.character(all_ids$V1)
de <- as.character(de_ids$V1)
pct_kegg_diff(all, de, organism="tcr", pathway="tcr00670")## The file already exists, loading from it.## 0% nodes differentially expressed in pathway 00670: 'One carbon pool by folate - Trypanosoma cruzi'.## 0% edges differentially expressed in pathway 00670: 'One carbon pool by folate - Trypanosoma cruzi'.## $pathway
## [1] "00670"
##
## $filename
## [1] "kegg_pathways/tcr00670.xml"
##
## $percent_nodes
## [1] 0
##
## $percent_edges
## [1] 0
##
## $all_nodes
## [1] "tcr:509153.90, tcr:511741.50, tcr:504017.40, tcr:511231.50, tcr:509937.150, tcr:510407.90"
##
## $diff_nodes
## [1] ""
##
## $all_edges
## [1] "c(\"tcr:509153.90\", \"tcr:511741.50\", \"tcr:509937.150\", \"tcr:510407.90\", \"tcr:504017.40\", \"tcr:511231.50\"), c(\"tcr:509937.150\", \"tcr:510407.90\", \"tcr:504017.40\", \"tcr:511231.50\", \"tcr:511741.50\"), tcr:511741.50, tcr:511741.50, tcr:511741.50, tcr:511741.50"
##
## $diff_edges
## [1] ""de_df <- as.data.frame(cbind(ID=de, logFC=4))
de_df$logFC <- as.numeric(de_df$logFC)
rownames(de_df) <- paste0("TcCLB.", de_df$ID)
tt_pathview <- hpgl_pathview(de_df, species="tcr", verbose=TRUE)## Here are some path gene examples: bsid:84786, genome:T01012, 503687.20, 503723.90, 504105.140, 504163.40## Here are your genes: 508111.30, 507853.10, 506621.30, 510311.90, 507897.20, 506367.30## 1/99: Finished glycolysis_/_gluconeogenesis id: tcr00010.## Here are some path gene examples: bsid:84787, genome:T01012, 503935.20, 506025.60, 506195.110, 506337.70## Here are your genes: 508111.30, 507853.10, 506621.30, 510311.90, 507897.20, 506367.30## 2/99: Finished citrate_cycle_(tca_cycle) id: tcr00020.## Here are some path gene examples: bsid:84788, genome:T01012, 503477.20, 504163.40, 504163.50, 506321.310## Here are your genes: 508111.30, 507853.10, 506621.30, 510311.90, 507897.20, 506367.30## 3/99: Finished pentose_phosphate_pathway id: tcr00030.## 4/99: Finished pentose_and_glucuronate_interconversions id: tcr00040.## 5/99: Finished fructose_and_mannose_metabolism id: tcr00051.## 6/99: Finished galactose_metabolism id: tcr00052.## 7/99: Finished ascorbate_and_aldarate_metabolism id: tcr00053.## 8/99: Finished fatty_acid_biosynthesis id: tcr00061.## 9/99: Finished fatty_acid_elongation id: tcr00062.## 10/99: Finished fatty_acid_degradation id: tcr00071.## 11/99: Finished synthesis_and_degradation_of_ketone_bodies id: tcr00072.## 12/99: Finished steroid_biosynthesis id: tcr00100.## 13/99: Finished ubiquinone_and_other_terpenoid-quinone_biosynthesis id: tcr00130.## 14/99: Finished oxidative_phosphorylation id: tcr00190.## 15/99: Finished arginine_biosynthesis id: tcr00220.## 16/99: Finished purine_metabolism id: tcr00230.## 17/99: Finished pyrimidine_metabolism id: tcr00240.## 18/99: Finished alanine,_aspartate_and_glutamate_metabolism id: tcr00250.## 19/99: Finished glycine,_serine_and_threonine_metabolism id: tcr00260.## 20/99: Finished cysteine_and_methionine_metabolism id: tcr00270.## 21/99: Finished valine,_leucine_and_isoleucine_degradation id: tcr00280.## 22/99: Finished lysine_degradation id: tcr00310.## 23/99: Finished arginine_and_proline_metabolism id: tcr00330.## 24/99: Finished histidine_metabolism id: tcr00340.## 25/99: Finished tyrosine_metabolism id: tcr00350.## 26/99: Finished phenylalanine_metabolism id: tcr00360.## 27/99: Finished tryptophan_metabolism id: tcr00380.## 28/99: Finished phenylalanine,_tyrosine_and_tryptophan_biosynthesis id: tcr00400.## 29/99: Finished beta-alanine_metabolism id: tcr00410.## 30/99: Finished phosphonate_and_phosphinate_metabolism id: tcr00440.## 31/99: Finished selenocompound_metabolism id: tcr00450.## 32/99: Finished cyanoamino_acid_metabolism id: tcr00460.## 33/99: Finished glutathione_metabolism id: tcr00480.## 34/99: Finished starch_and_sucrose_metabolism id: tcr00500.## 35/99: Finished n-glycan_biosynthesis id: tcr00510.## 36/99: Finished other_glycan_degradation id: tcr00511.## 37/99: Finished amino_sugar_and_nucleotide_sugar_metabolism id: tcr00520.## 38/99: Finished neomycin,_kanamycin_and_gentamicin_biosynthesis id: tcr00524.## 39/99: Finished glycerolipid_metabolism id: tcr00561.## 40/99: Finished inositol_phosphate_metabolism id: tcr00562.## 41/99: Finished glycosylphosphatidylinositol_(gpi)-anchor_biosynthesis id: tcr00563.## 42/99: Finished glycerophospholipid_metabolism id: tcr00564.## 43/99: Finished ether_lipid_metabolism id: tcr00565.## 44/99: Finished arachidonic_acid_metabolism id: tcr00590.## 45/99: Finished alpha-linolenic_acid_metabolism id: tcr00592.## 46/99: Finished sphingolipid_metabolism id: tcr00600.## 47/99: Finished pyruvate_metabolism id: tcr00620.## 48/99: Finished glyoxylate_and_dicarboxylate_metabolism id: tcr00630.## 49/99: Finished propanoate_metabolism id: tcr00640.## 50/99: Finished butanoate_metabolism id: tcr00650.## 51/99: Finished one_carbon_pool_by_folate id: tcr00670.## 52/99: Finished thiamine_metabolism id: tcr00730.## 53/99: Finished riboflavin_metabolism id: tcr00740.## 54/99: Finished vitamin_b6_metabolism id: tcr00750.## 55/99: Finished nicotinate_and_nicotinamide_metabolism id: tcr00760.## 56/99: Finished pantothenate_and_coa_biosynthesis id: tcr00770.## 57/99: Finished biotin_metabolism id: tcr00780.## 58/99: Finished lipoic_acid_metabolism id: tcr00785.## 59/99: Finished folate_biosynthesis id: tcr00790.## 60/99: Finished porphyrin_and_chlorophyll_metabolism id: tcr00860.## 61/99: Finished terpenoid_backbone_biosynthesis id: tcr00900.## 62/99: Finished nitrogen_metabolism id: tcr00910.## 63/99: Finished sulfur_metabolism id: tcr00920.## 64/99: Finished aminoacyl-trna_biosynthesis id: tcr00970.## 65/99: Finished biosynthesis_of_unsaturated_fatty_acids id: tcr01040.## 66/99: Finished metabolic_pathways id: tcr01100.## 67/99: Finished biosynthesis_of_secondary_metabolites id: tcr01110.## 68/99: Finished biosynthesis_of_antibiotics id: tcr01130.## 69/99: Finished carbon_metabolism id: tcr01200.## 70/99: Finished 2-oxocarboxylic_acid_metabolism id: tcr01210.## 71/99: Finished fatty_acid_metabolism id: tcr01212.## 72/99: Finished biosynthesis_of_amino_acids id: tcr01230.## 73/99: Finished abc_transporters id: tcr02010.## 74/99: Finished ribosome_biogenesis_in_eukaryotes id: tcr03008.## 75/99: Finished ribosome id: tcr03010.## 76/99: Finished rna_transport id: tcr03013.## 77/99: Finished mrna_surveillance_pathway id: tcr03015.## 78/99: Finished rna_degradation id: tcr03018.## 79/99: Finished rna_polymerase id: tcr03020.## 80/99: Finished basal_transcription_factors id: tcr03022.## 81/99: Finished dna_replication id: tcr03030.## 82/99: Finished spliceosome id: tcr03040.## 83/99: Finished proteasome id: tcr03050.## 84/99: Finished protein_export id: tcr03060.## 85/99: Finished base_excision_repair id: tcr03410.## 86/99: Finished nucleotide_excision_repair id: tcr03420.## 87/99: Finished mismatch_repair id: tcr03430.## 88/99: Finished homologous_recombination id: tcr03440.## 89/99: Finished non-homologous_end-joining id: tcr03450.## 90/99: Finished phosphatidylinositol_signaling_system id: tcr04070.## 91/99: Finished ubiquitin_mediated_proteolysis id: tcr04120.## 92/99: Finished sulfur_relay_system id: tcr04122.## 93/99: Finished snare_interactions_in_vesicular_transport id: tcr04130.## 94/99: Finished protein_processing_in_endoplasmic_reticulum id: tcr04141.## 95/99: Finished endocytosis id: tcr04144.## 96/99: Finished phagosome id: tcr04145.## 97/99: Finished peroxisome id: tcr04146.## 98/99: Finished age-rage_signaling_pathway_in_diabetic_complications id: tcr04933.## 99/99: Finished chagas_disease_(american_trypanosomiasis) id: tcr05142.## tcr00650 has ~37% total/unique in hpgl_pathview
tt <- pct_kegg_diff(all, de, organism="tcr", pathway="tcr00650")## The file already exists, loading from it.## 16.67% nodes differentially expressed in pathway 00650: 'Butanoate metabolism - Trypanosoma cruzi'.## 0% edges differentially expressed in pathway 00650: 'Butanoate metabolism - Trypanosoma cruzi'.ttt <- hpgl_pathview(de_df, species="tcr", pathway="tcr04933")## Here are some path gene examples: bsid:1320238, genome:T01012, 504149.110, 504149.160, 508859.90, 509553.60## Here are your genes: 508111.30, 507853.10, 506621.30, 510311.90, 507897.20, 506367.30## 1/1: Finished age-rage_signaling_pathway_in_diabetic_complications id: tcr04933.kegg_list = epi_cl14clbr_table$logFC
names(kegg_list) = rownames(epi_cl14clbr_table)
epi_cl14clbr_paths = hpgl_pathview(kegg_list, species="tcr", indir="pathview_in", outdir="pathview_epi_cl14clbr", string_from="TcCLB.", string_to="")
head(epi_cl14clbr_paths)
a60_cl14clbr_table = all_tables$a60_cl14clbr
kegg_list = a60_cl14clbr_table$logFC
names(kegg_list) = rownames(a60_cl14clbr_table)
a60_cl14clbr_paths = hpgl_pathview(kegg_list, species="tcr", indir="pathview_in", outdir="pathview_a60_cl14clbr", string_from="TcCLB.", string_to="")
head(a60_cl14clbr_paths)
a96_cl14clbr_table = all_tables$a96_cl14clbr
kegg_list = a96_cl14clbr_table$logFC
names(kegg_list) = rownames(a96_cl14clbr_table)
a96_cl14clbr_paths = hpgl_pathview(kegg_list, species="tcr", indir="pathview_in", outdir="pathview_a96_cl14clbr", string_from="TcCLB.", string_to="")
head(a96_cl14clbr_paths)
tryp_cl14clbr_table = all_tables$a96_cl14clbr
kegg_list = tryp_cl14clbr_table$logFC
names(kegg_list) = rownames(tryp_cl14clbr_table)
tryp_cl14clbr_paths = hpgl_pathview(kegg_list, species="tcr", indir="pathview_in", outdir="pathview_tryp_cl14clbr", string_from="TcCLB.", string_to="")
head(tryp_cl14clbr_paths)