scFLUX

A webserver to estimate cell-/sample-wise metabolic fluxome by using scRNA-seq or general transcriptomics data

About

Step1

Select species and metabolic (sub)networks

Please select the species of your data and to-be-analyzed metabolic network in the left boxes.


Homo sapiens M171

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

Homo sapiens GlucoseGlutamineClose

GlucoseGlutamineClose: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.

GlucoseGlutamineClose

Homo sapiens GlucoseGlutamineOpen

GlucoseGlutamineOpen: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.

GlucoseGlutamineOpen

Homo sapiens BCAA

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

Homo sapiens Acetylcholine

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

Homo sapiens Dopamine

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

Homo sapiens Histamine

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

Homo sapiens Serotonin

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

Homo sapiens IronIon

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

Mus musculus M171

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

Mus musculus GlucoseGlutamineClose

GlucoseGlutamineClose: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.

GlucoseGlutamineClose

Mus musculus GlucoseGlutamineOpen

GlucoseGlutamineOpen: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.

GlucoseGlutamineOpen

Mus musculus BCAA

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

Mus musculus Acetylcholine

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

Mus musculus Dopamine

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

Mus musculus Histamine

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

Mus musculus Serotonin

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

Mus musculus IronIon

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

Step2

Upload input data

The input of scFEA is a scRNA-seq or general transcriptomics data, in which each row is one gene and each column is one sample. TPM (or CPM/FPKM) normalized data is recommended. scFEA webserver accepts comma-(.csv), space-(.txt), tab-(.txt) delimited input fills. Please make sure the input data is in a matrix form and contains row/column names. Both gene symbol and Ensembl gene ID are accepted. For a large data set, we recommend to only upload gene expression data of the scFEA metabolic genes that will be used for flux computation. The maximal input file size should be smaller than 500MB. For a large data set, we recommend to only upload gene expression data of the scFEA metabolic genes that will be utilized for flux computation (scFEA human genes, scFEA mouse genes). See more details in Tutorial. Note: it may take a few minutes to upload a data > 100MB.

You can choose or download example input data files below.

Step3

Imputation

scFEA utilizes MAGIC for a data imputation. We recommend this step for snRNA-seq or drop-seq data that have a high sparsity level.


Normalization

Step4

Submit Task

Make sure you have finnished step1 to step3 before you submit your tasks.



Step5

Check Your Result

Make sure you have submit your task, and it is finnished.