FLUXestimater

M171:This is the central metabolic map of human. This metabolic network covers the metabolism, transport, and biosynthesis of carbohydrate, amino acids, fatty acids and lipids, glycan, and nucleic acids in human, including 663 genes of 395 enzymes, 1381 reactions, 1468 metabolites, and 116 transporter genes of 35 metabolites in human collected from KEGG and other literatures. After the network simplification, we have simplified and reconstructed this network into 171 modules belong to 22 super module classes and 70 metabolites, out of which 66 are intermediate substrates. We recommend this network for a general characterization of metabolic landscapes.

The 22 super module classes cover glycolysis and TCA cycle, serine and related amino acids metabolism, pentose phosphate, fatty acids biosynthesis/metabolism, aspartate and related amino acids metabolism, beta-alanie metabolism, propanoyl-CoA metabolism, glutamate, glutamine and related amino acids metabolism, leucine and valine and isoleucine (branched chain amin acids) metabolism, urea cycle, spermine metabolism, transporters, hyaluronic acid synthesis, glycogen synthesis, N-linked glycan synthesis, O-linked glycan synthesis, sialic acid synthesis, chondroitin sulfate, dermatan sulfate, heparan sulfate and other glycosaminoglycan biosynthesis, purine synthesis, pyrimidine synthesis, and steroid hormone synthesis.

The figure below illustrates the reconstructed network and super modules. Complete information of the reconstructed network is available in the downloads.

M171

KEGG:KEGG directly offers 245 metabolic modules. A module in KEGG is a functional unit of reactions in metabolic pathways that form a chain or chain-like shape. Each module has one or a few inputs or outputs and its intermediate steps do not contain significant in-/out-branches. Thus, the KEGG modules naturally form a genome scale metabolic network. Compared to the M171 network, the KEGG module network omits more branches and contains multiple disconnected subnetworks. When building species specific networks, we first took the modules that are present in the species, identified the subnetworks formed by the modules and removed single modules. Single modules are excluded from FLUXestimator analysis.

The KEGG-module formed genome-wide metabolic map of human is formed by 100 modules, including 10 sub-networks, 1333 metabolic genes and 570 intermediate metabolites. We recommend this network for a general characterization of global metabolic variations. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

KEGG

GGSL:We collected the central metabolism network and its branches of glucose and glutamine metabolism in subcellular localization resolution from KEGG database. We further manually curated the reaction information from literature data, based on our previously curated metabolic network. This subnetwork is named Glucose-Glutamine Subcellular Localization (GGSL) network. As subcellular compartments have different levels of enzymes, substrates, biochemical characteristics, and kinetic parameters, sub-cellular localization information of reactions is needed to accurately assess their stoichiometric relations. The reconstructed GGSL network includes six major pathways, namely glycolysis, upper and lower parts of TCA cycle, glutaminolysis, glutamine and glutamate metabolism, and glutathione metabolism, and six minor branches, namely Glyceraldehyde 3-phosphate (G3P) to nucleotide synthesis, 3-Phospho-D-glycerate (3PD) to serine synthesis, aspartate-malate shuttle, mitochondrial citrate fueling of fatty acid synthesis, transport of 2-Oxoglutarate (2OG) to cytosol, and transform of 2OG to 2-Hydroxyglutarate (2HG). The human GGSL network covers 41 reaction modules, 37 intermediate metabolites, 241 enzymes, and 254 genes in cytosol, mitochondria, and extracellular regions.

We recommend this network for characterization of the central metabolic variations in cancer and inflammatory diseases or conditions with varied redox balance. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

GGSL

Glucose-TCAcycle:This metabolic network is formed by glycolysis, pentose phosphate and TCA cycle pathways in human, which covers essential metabolites in fueling energy production and cell growth. This model focuses on a closed system of metabolism that assumes the major source of glucose are for feeding the energy production and biosynthesis. The network includes 65 genes of 45 enzymes. We reconstructed this network into 15 modules and 12 intermediate metabolites.

We recommend this network for characterization of glycolysis and TCA cycle only. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Glucose-TCAcycle

Glucose-Glutaminolysis:This metabolic network is formed by glycolysis, pentose phosphate, TCA cycle, and glutaminolysis pathways in human, which covers essential metabolites in fueling energy production and cell growth. This model focuses on a closed system of glucose and glutamine metabolism that assumes the major source of glucose and glutamine are for feeding the energy production. The network includes 132 genes of 61 enzymes, 175 reactions and 194 metabolites. We reconstructed this network into 23 modules, 17 intermediate metabolites and 4 pseudo-end metabolites.

We recommend this network for characterization of glycolysis, TCA cycle, glutaminolysis and their impacts when users assume the major flow of glutamine is utilized to fuel the TCA cycle, such as in certain cancer systems. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Glucose-Glutaminolysis

Glucose-Glutamine:This metabolic network is formed by glycolysis, pentose phosphate, TCA cycle, and glutaminolysis pathways in human, which covers essential metabolites in fueling energy production and cell growth. This model focuses on a closed system of glucose and glutamine metabolism that assumes the major source of glucose and glutamine are for feeding the energy production. The network includes 176 genes of 101 enzymes, 247 reactions and 288 metabolites. We reconstructed this network into 27 modules, 17 intermediate metabolites and 8 pseudo-end metabolites (which include the exchange between glutamine and glutamate, and synthesis/transform of glutamine and glutamate from other amino acids).

We recommend this network for a general characterization of the central metabolic pathway, evaluating flux distribution of different carbon sources, and studying glutamate and GABA biosynthesis in the neuron system. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Glucose-Glutamine

BCAA:This is the metabolic network of Branched Chain Amino Acids (BCAA) metabolism in human. We have collected related reactions including leucine, valine and isoleucine metabolism and biosynthesis of branched chain fatty acids. The network includes 60 genes of 52 enzymes, 207 reactions and 261 metabolites. We reconstructed this network into 15 modules, 6 intermediate metabolites and 1 pseudo-end metabolites.

We recommend this network for the specific analysis of BCAA metabolism. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

BCAA

Acetylcholine:This is the metabolic network of biosynthesis and metabolism of the neurotransmitter acetylcholine in human. We have collected related reactions from glycerol 3-phosphate to acetylcholine and its metabolism into choline. The network includes 80 genes of 29 enzymes, 76 reactions and 103 metabolites. We reconstructed this network into 15 modules, 6 intermediate metabolites and 2 pseudo-end metabolites.

We recommend this network for the specific analysis of acetylcholine metabolism. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Acetylcholine

Dopamine:This is the metabolic network of biosynthesis and metabolism of the neurotransmitter dopamine in human. We have collected related reactions from tyrosine to dopamine and its metabolism/biosynthesis into downstream products such as noradrenaline and adrenaline. The network includes 23 genes of 15 enzymes, 107 reactions and 152 metabolites. We reconstructed this network into 9 modules, 4 intermediate metabolites and 5 pseudo-end metabolites.

We recommend this network for the specific analysis of dopamine metabolism. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Dopamine

Histamine:This is the metabolic network of biosynthesis and metabolism of the neurotransmitter histamine in human, which also serves as an organic nitrogenous compound involved in local immune responses. We have collected related reactions from histidine to carnosine and histamine. The network includes 23 genes of 17 enzymes, 85 reactions and 129 metabolites. We reconstructed this network into 6 modules, 3 intermediate metabolites and 2 pseudo-end metabolites.

We recommend this network for the specific analysis of histamine metabolism. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Histamine

Serotonin:This is the metabolic network of biosynthesis and metabolism of the neurotransmitter serotonin in human. We have collected related reactions from tryptophan to oxitriptan and serotonin, and its downstream metabolism into melatonin and degradation. The network includes 24 genes of 17 enzymes, 155 reactions and 241 metabolites. We reconstructed this network into 8 modules, 4 intermediate metabolites and 5 pseudo-end metabolites.

We recommend this network for the specific analysis of serotonin metabolism. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Serotonin

IronIon:This is the sub-cellular specific metabolic network of iron ion in human. We have collected the reactions including iron ion transportation, ferric ion reduction, and utilization of iron ion in heme and ion sulfur biosynthesis and Fenton reaction. The network includes 141 genes of 24 enzymes, 47 reactions and 105 metabolites. We reconstructed this network into 15 modules, 8 intermediate metabolites and 4 pseudo-end metabolites.

We recommend this network for the specific analysis of iron ion metabolism. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

IronIon

MGF:The Methionine Glutathione Folic Acid (MGF) network specifically focuses on methionine, DNA methylation and related metabolism. It includes seven major modules that cover the metabolism of methionine, glutathione, and folic acids. The human MGF network includes 98 genes of 72 enzymes. We reconstructed this network into 8 modules and 5 intermediate metabolites.

We recommend this network for characterizing the metabolic flux distribution of methionine metabolism, DNA methylation, glutathione biosynthesis and metabolism, and folic acid metabolism. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

MGF

Lipid metabolism:The lipids metabolism network was manually curated by including the biosynthesis and metabolism of Fatty Acyls, Phospholipids, Lysophospholipids, Glycerolipids, Sphingolipids, Prenol lipids, Sterol lipids, Steroid Hormone Biosynthesis, Primary Bile Acids, and Steroid, etc. The human Lipids metabolism network includes 320 genes of 165 enzymes. We reconstructed this network into 112 modules and 93 intermediate metabolites.

We recommend this network for characterizing the metabolism and biosynthesis of lipids. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Lipid metabolism

MHC-I:MHC Class I Antigen Presentation (MHC-I) network can be viewed as a metabolic process. To the best of our knowledge, there is no established systems biology model of this process in the public domain. We first manually collected and curated the biological processes that are involved in the MHC class I antigen presentation pathway via an extensive literature review by multiple immunologists studying antigen presentation, exocytosis, endocytosis. The first step of MHC class I antigen presentation is ubiquitination and proteolysis, which involves E1/E2/E3 and proteosome complexes. We also consider the approach of de-ubiquitination, which serves as an out branch of ubiquitination that decreases the number of ubiquitinated proteins. We consider the generation of MHC class I complex include three major steps in ER, namely (1) transporting of peptide into ER, (2) trimming of peptides in ER, and (3) peptide loading complex that generate MHC class I complex with loaded antigens. The MHC class I complex is further transported from ER to Golgi and from Golgi to cell membrane, which involve the genes in exocytosis process. Regulatory genes of vesicular transport, antigen quality checking genes, and the flow from trans-Golgi network to late endosome serve as out branch in these approaches. Noted, we also consider the recycling of the MHC class I complex expressed on cell surface, which involves the endocytosis and retrograde transport processes. We further collected the genes involved in these biological processes via multiple pathway resources including KEGG, Reactome, and Gene Ontology.

The human MHC-I metabolism network includes 325 genes of 9 major reaction steps. We reconstructed this network into 9 modules and 8 intermediate metabolites.

We recommend this network for characterizing the activity level of MHC class I antigen presentation only for the MHC class I presenting cells or tissues. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

MHC-I

M171:This is the central metabolic map of human. This metabolic network covers the metabolism, transport, and biosynthesis of carbohydrate, amino acids, fatty acids and lipids, glycan, and nucleic acids in mouse, including 719 genes of 395 enzymes, 1381 reactions, 1468 metabolites, and 116 transporter genes of 35 metabolites in human collected from KEGG and other literatures. After the network simplification, we have simplified and reconstructed this network into 171 modules belong to 22 super module classes and 70 metabolites, out of which 66 are intermediate substrates. We recommend this network for a general characterization of metabolic landscapes.

The 22 super module classes cover glycolysis and TCA cycle, serine and related amino acids metabolism, pentose phosphate, fatty acids biosynthesis/metabolism, aspartate and related amino acids metabolism, beta-alanie metabolism, propanoyl-CoA metabolism, glutamate, glutamine and related amino acids metabolism, leucine and valine and isoleucine (branched chain amin acids) metabolism, urea cycle, spermine metabolism, transporters, hyaluronic acid synthesis, glycogen synthesis, N-linked glycan synthesis, O-linked glycan synthesis, sialic acid synthesis, chondroitin sulfate, dermatan sulfate, heparan sulfate and other glycosaminoglycan biosynthesis, purine synthesis, pyrimidine synthesis, and steroid hormone synthesis.

The figure below illustrates the reconstructed network and super modules. Complete information of the reconstructed network is available in the downloads.

M171

KEGG:met downloads.

KEGG

GGSL:met downloads.

GGSL

Glucose-TCAcycle:met downloads.

Glucose-TCAcycle

Glucose-Glutaminolysis:This metabolic network is formed by glycolysis, pentose phosphate, TCA cycle, and glutaminolysis pathways in mouse, which covers essential metabolites in fueling energy production and cell growth. This model focuses on a closed system of glucose and glutamine metabolism that assumes the major source of glucose and glutamine are for feeding the energy production. The network includes 134 genes of 61 enzymes, 175 reactions and 194 metabolites. We reconstructed this network into 23 modules, 17 intermediate metabolites and 4 pseudo-end metabolites.

We recommend this network for characterization of glycolysis, TCA cycle, glutaminolysis and their impacts when users assume the major flow of glutamine is utilized to fuel the TCA cycle, such as in certain cancer systems. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Glucose-Glutaminolysis

Glucose-Glutamine:This metabolic network is formed by glycolysis, pentose phosphate, TCA cycle, and glutaminolysis pathways in mouse, which covers essential metabolites in fueling energy production and cell growth. This model focuses on a closed system of glucose and glutamine metabolism that assumes the major source of glucose and glutamine are for feeding the energy production. The network includes 165 genes of 101 enzymes, 247 reactions and 288 metabolites. We reconstructed this network into 27 modules, 17 intermediate metabolites and 8 pseudo-end metabolites (which include the exchange between glutamine and glutamate, and synthesis/transform of glutamine and glutamate from other amino acids).

We recommend this network for a general characterization of the central metabolic pathway, evaluating flux distribution of different carbon sources, and studying glutamate and GABA biosynthesis in the neuron system. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Glucose-Glutamine

BCAA:This is the metabolic network of Branched Chain Amino Acids (BCAA) metabolism in mouse. We have collected related reactions including leucine, valine and isoleucine metabolism and biosynthesis of branched chain fatty acids. The network includes 64 genes of 52 enzymes, 207 reactions and 261 metabolites. We reconstructed this network into 15 modules, 6 intermediate metabolites and 1 pseudo-end metabolites.

We recommend this network for the specific analysis of BCAA metabolism. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

BCAA

Acetylcholine:This is the metabolic network of biosynthesis and metabolism of the neurotransmitter acetylcholine in mouse. We have collected related reactions from glycerol 3-phosphate to acetylcholine and its metabolism into choline. The network includes 86 genes of 29 enzymes, 76 reactions and 103 metabolites. We reconstructed this network into 15 modules, 6 intermediate metabolites and 2 pseudo-end metabolites.

We recommend this network for the specific analysis of acetylcholine metabolism. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Acetylcholine

Dopamine:This is the metabolic network of biosynthesis and metabolism of the neurotransmitter dopamine in mouse. We have collected related reactions from tyrosine to dopamine and its metabolism/biosynthesis into downstream products such as noradrenaline and adrenaline. The network includes 24 genes of 15 enzymes, 107 reactions and 152 metabolites. We reconstructed this network into 9 modules, 4 intermediate metabolites and 5 pseudo-end metabolites.

We recommend this network for the specific analysis of dopamine metabolism. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Dopamine

Histamine:This is the metabolic network of biosynthesis and metabolism of the neurotransmitter histamine in mouse, which also serves as an organic nitrogenous compound involved in local immune responses. We have collected related reactions from histidine to carnosine and histamine. The network includes 24 genes of 17 enzymes, 85 reactions and 129 metabolites. We reconstructed this network into 6 modules, 3 intermediate metabolites and 2 pseudo-end metabolites.

We recommend this network for the specific analysis of histamine metabolism. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Histamine

Serotonin:This is the metabolic network of biosynthesis and metabolism of the neurotransmitter serotonin in mouse. We have collected related reactions from tryptophan to oxitriptan and serotonin, and its downstream metabolism into melatonin and degradation. The network includes 26 genes of 17 enzymes, 155 reactions and 241 metabolites. We reconstructed this network into 8 modules, 4 intermediate metabolites and 5 pseudo-end metabolites.

We recommend this network for the specific analysis of serotonin metabolism. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

Serotonin

IronIon:This is the sub-cellular specific metabolic network of iron ion in mouse. We have collected the reactions including iron ion transportation, ferric ion reduction, and utilization of iron ion in heme and ion sulfur biosynthesis and Fenton reaction. The network includes 152 genes of 24 enzymes, 47 reactions and 105 metabolites. We reconstructed this network into 15 modules, 8 intermediate metabolites and 4 pseudo-end metabolites.

We recommend this network for the specific analysis of iron ion metabolism. The figure below illustrates the reconstructed network. Complete information of the reconstructed network is available in the downloads.

IronIon

MGF:met downloads.

MGF

Lipid metabolism:met downloads.

Lipid metabolism

MHC-I:met downloads.

MHC-I

Ciona robusta:met downloads.

Ciona robusta

Zea mays:met downloads.

Zea mays

Danio rerio:met downloads.

Danio rerio

Gallus gallus:met downloads.

Gallus gallus

Xenopus tropicalis:met downloads.

Xenopus tropicalis

Rattus norvegicus:met downloads.

Rattus norvegicus

Escherichia coli K-12:met downloads.

Escherichia coli K-12

Bacillus subtilis 168:met downloads.

Bacillus subtilis 168

Pseudomonas fluorescens SBW25:met downloads.

Pseudomonas fluorescens SBW25

Arabidopsis thaliana:met downloads.

Arabidopsis thaliana

Azotobacter vinelandii DJ:met downloads.

Azotobacter vinelandii DJ

Synechocystis PCC 6803:met downloads.

Synechocystis PCC 6803

Methanococcus voltae A3:met downloads.

Methanococcus voltae A3

Streptomyces coelicolor A3(2):met downloads.

Streptomyces coelicolor A3(2)

Methanosarcina acetivorans C2A:met downloads.

Methanosarcina acetivorans C2A