diff --git a/README.md b/README.md index 5e9ef98..194b667 100755 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ Reference: Pan-organ model integration of metabolic and regulatory processes in Authors: Marouen Ben Guebila and Ines Thiele. -Corresponding author: Ines Thiele ines.thiele@gmail.com +Corresponding author: Ines Thiele ines.thiele AT gmail.com ## System requirements diff --git a/common/lib/metaSubsystems.csv b/common/lib/metaSubsystems.csv new file mode 100755 index 0000000..b794412 --- /dev/null +++ b/common/lib/metaSubsystems.csv @@ -0,0 +1,102 @@ +Recon 2.1 unique subSystems,Meta subSystems +"'Transport, lysosomal'",TRANSPORT +"'Transport, mitochondrial'",TRANSPORT +"'Transport, endoplasmic reticular'",TRANSPORT +'beta-Alanine metabolism',amino acid metabolism +'Vitamin D metabolism',vitamin metabolism +"'Transport, extracellular'",TRANSPORT +'Lysine metabolism',amino acid metabolism +"'Glycine, serine, alanine and threonine metabolism'",amino acid metabolism +'Methionine and cysteine metabolism',amino acid metabolism +'Pyrimidine catabolism',nucleotide metabolism +'Propanoate metabolism',miscellaneous +'Tryptophan metabolism',amino acid metabolism +'Tyrosine metabolism',amino acid metabolism +'Ubiquinone synthesis',miscellaneous +"'Transport, nuclear'",TRANSPORT +"'Valine, leucine, and isoleucine metabolism'",amino acid metabolism +'Sphingolipid metabolism',lipid metabolism +'Butanoate metabolism',miscellaneous +'Purine catabolism',nucleotide metabolism +'Taurine and hypotaurine metabolism',amino acid metabolism +'Arginine and Proline Metabolism',amino acid metabolism +'Cytochrome metabolism',ETC +'Steroid metabolism',lipid metabolism +'Heme synthesis',heme metabolism +'N-glycan degradation',carbohydrate metabolism +'O-glycan synthesis',carbohydrate metabolism +'Blood group synthesis',carbohydrate metabolism +'Glutamate metabolism',amino acid metabolism +'Pentose phosphate pathway',carbohydrate metabolism +'Cholesterol metabolism',lipid metabolism +'Fatty acid oxidation',lipid metabolism +"'Transport, peroxisomal'",TRANSPORT +"'Transport, golgi apparatus'",TRANSPORT +'Aminosugar metabolism',carbohydrate metabolism +'Phosphatidylinositol phosphate metabolism',lipid metabolism +'Urea cycle',amino acid metabolism +'Glycerophospholipid metabolism',lipid metabolism +'Citric acid cycle',carbohydrate metabolism +'Pyruvate metabolism',miscellaneous +'Bile acid synthesis',lipid metabolism +'Vitamin B2 metabolism',vitamin metabolism +'Glycolysis/gluconeogenesis',carbohydrate metabolism +'Nucleotide interconversion',nucleotide metabolism +'Nucleotide salvage pathway',nucleotide metabolism +'Selenoamino acid metabolism',amino acid metabolism +'Purine synthesis',nucleotide metabolism +'Keratan sulfate synthesis',carbohydrate metabolism +'Triacylglycerol synthesis',lipid metabolism +'Alanine and aspartate metabolism',amino acid metabolism +'Miscellaneous',miscellaneous +'Eicosanoid metabolism',lipid metabolism +'Glutathione metabolism',amino acid metabolism +'Starch and sucrose metabolism',carbohydrate metabolism +'Biotin metabolism',vitamin metabolism +'R group synthesis',lipid metabolism +'Unassigned',unassigned +'Vitamin C metabolism',vitamin metabolism +'Pyrimidine synthesis',nucleotide metabolism +'Oxidative phosphorylation',ETC +'Vitamin A metabolism',vitamin metabolism +"'Stilbene, coumarine and lignin synthesis'",miscellaneous +'N-glycan synthesis',carbohydrate metabolism +'Heme degradation',heme metabolism +Limonene and pinene degradation',lipid metabolism +'ROS detoxification',ROS +'Vitamin B12 metabolism',vitamin metabolism +'C5-branched dibasic acid metabolism',miscellaneous +'Alkaloid synthesis',miscellaneous +'Chondroitin sulfate degradation',carbohydrate metabolism +'D-alanine metabolism',amino acid metabolism +'Fatty acid synthesis',lipid metabolism +'Folate metabolism',vitamin metabolism +'Tetrahydrobiopterin metabolism',miscellaneous +'Exchange/demand reaction',exchange +'CoA synthesis',vitamin metabolism +'Keratan sulfate degradation',carbohydrate metabolism +'Fructose and mannose metabolism',carbohydrate metabolism +'Glyoxylate and dicarboxylate metabolism',miscellaneous +'Galactose metabolism',carbohydrate metabolism +'Nucleotide sugar metabolism',nucleotide metabolism +'Chondroitin synthesis',carbohydrate metabolism +'Heparan sulfate degradation',carbohydrate metabolism +'Hyaluronan metabolism',carbohydrate metabolism +'Histidine metabolism',amino acid metabolism +'Vitamin B6 metabolism',vitamin metabolism +'Inositol phosphate metabolism',lipid metabolism +'CoA catabolism',vitamin metabolism +'NAD metabolism',vitamin metabolism +'Phenylalanine metabolism',amino acid metabolism +'Thiamine metabolism',vitamin metabolism +'Androgen and estrogen synthesis and metabolism',lipid metabolism +'Lipoate metabolism',vitamin metabolism +'Arachidonic acid metabolism',lipid metabolism +'Vitamin E metabolism',vitamin metabolism +'Linoleate metabolism',lipid metabolism +'Glycosphingolipid metabolism',lipid metabolism +'Xenobiotics metabolism',xenobiotic metabolism +'Dietary fiber binding',carbohydrate metabolism +'Squalene and cholesterol synthesis',lipid metabolism +'Hippurate metabolism',amino acid metabolism +'Peptide metabolism',amino acid metabolism