FLUXestimator

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

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The following resources are provided, including (1) seven example inputs of scFEA, (2) module information and gene sets of 28 reconstructed metabolic subnetworks in human and mouse, (3) KEGG metabolic module-based metabolic map for 15 experimental organisms, and (4) predicted metabolic flux and imputed metabolomic profiles on TCGA, GTEx, CCLE and three example scRNA-seq/snRNA-seq data.

Example input files GSE72056 scRNA-seq example input GSE72056_example.txt
GSE103322 scRNA-seq example input GSE103322_example
Pa03c cell scRNA-seq example input Pa03c.csv
ROSMAP snRNA-seq example input ROSMAP.csv
CCLE example input CCLE.csv
GTEx example input GTEX.csv
TCGA example input TCGA.csv
Human module files Module information of the M171 metabolic network in human scFEA.M171.human.moduleinfo.csv
Genes in the M171 metabolic network in human scFEA.M171.human.v1.symbols.gmt
This network is the M171 network plus a consideration of redox balance by including the balance of the production and consumption of NAD+. scFEA.M171_NAD.human.moduleinfo.csv
Genes in the M171_NAD metabolic network in human scFEA.M171_NAD.human.symbols.gmt
Module information of GGSL metabolic network in human scFEA.GGSL.human.moduleinfo.csv
Genes in GGSL metabolic network in human scFEA.GGSL.human.v1.symbols.gmt
Module information of Glucose-TCAcycle metabolic network in human scFEA.Glucose-TCAcycle.human.moduleinfo.csv
Genes in Glucose-TCAcycle metabolic network in human scFEA.Glucose-TCAcycle.human.v1.symbols.gmt
Module information of Glucose-Glutaminolysis metabolic network in human scFEA.Glucose-Glutaminolysis.human.moduleinfo.csv
Genes in Glucose-Glutaminolysis metabolic network in human scFEA.Glucose-Glutaminolysis.human.v1.symbols.gmt
Module information of Glucose-Glutamine metabolic network in human scFEA.Glucose-Glutamine.human.moduleinfo.csv
Genes in Glucose-Glutamine metabolic network in human scFEA.Glucose-Glutamine.human.v1.symbols.gmt
Module information of BCAA metabolic network in human scFEA.BCAA.human.moduleinfo.csv
Genes in BCAA metabolic network in human scFEA.BCAA.human.v1.symbols.gmt
Module information of Acetylcholine metabolic network in human scFEA.Acetylcholine.human.moduleinfo.csv
Genes in Acetylcholine metabolic network in human scFEA.Acetylcholine.human.v1.symbols.gmt
Module information of Dopamine metabolic network in human scFEA.Dopamine.human.moduleinfo.csv
Genes in Dopamine metabolic network in human scFEA.Dopamine.human.v1.symbols.gmt
Module information of Histamine metabolic network in human scFEA.Histamine.human.moduleinfo.csv
Genes in Histamine metabolic network in human scFEA.Histamine.human.v1.symbols.gmt
Module information of Serotonin metabolic network in human scFEA.Serotonin.human.moduleinfo.csv
Genes in Serotonin metabolic network in human scFEA.Serotonin.human.v1.symbols.gmt
Module information of IronIon metabolic network in human scFEA.IronIon.human.moduleinfo.csv
Genes in IronIon metabolic network in human scFEA.IronIon.human.v1.symbols.gmt
Module information of MGF metabolic network in human scFEA.MGF.human.moduleinfo.csv
Genes in MGF metabolic network in human scFEA.MGF.human.v1.symbols.gmt
Module information of MHC-I metabolic network in human scFEA.MHC-I.human.moduleinfo.csv
Genes in MHC-I metabolic network in human scFEA.MHC-I.human.v1.symbols.gmt
scFEA human genes scFEA.human.genes.txt
Mouse module files Module information of the M171 metabolic network in mouse scFEA.M171.mouse.moduleinfo.csv
Genes in the M171 metabolic network in mouse scFEA.M171.mouse.v1.symbols.gmt
This network is the M171 network plus a consideration of redox balance by including the balance of the production and consumption of NAD+. scFEA.M171_NAD.mouse.moduleinfo.csv
Genes in the M171_NAD metabolic network in mouse scFEA.M171_NAD.mouse.symbols.gmt
Module information of GGSL metabolic network in mouse scFEA.GGSL.mouse.moduleinfo.csv
Genes in GGSL metabolic network in mouse scFEA.GGSL.mouse.v1.symbols.gmt
Module information of Glucose-TCAcycle metabolic network in mouse scFEA.Glucose-TCAcycle.mouse.moduleinfo.csv
Genes in Glucose-TCAcycle metabolic network in mouse scFEA.Glucose-TCAcycle.mouse.v1.symbols.gmt
Module information of Glucose-Glutaminolysis metabolic network in mouse scFEA.Glucose-Glutaminolysis.mouse.moduleinfo.csv
Genes in Glucose-Glutaminolysis metabolic network in mouse scFEA.Glucose-Glutaminolysis.mouse.v1.symbols.gmt
Module information of Glucose-Glutamine metabolic network in mouse scFEA.Glucose-Glutamine.mouse.moduleinfo.csv
Genes in Glucose-Glutamine metabolic network in mouse scFEA.Glucose-Glutamine.mouse.v1.symbols.gmt
Module information of BCAA metabolic network in mouse scFEA.BCAA.mouse.moduleinfo.csv
Genes in BCAA metabolic network in mouse scFEA.BCAA.mouse.v1.symbols.gmt
Module information of Acetylcholine metabolic network in mouse scFEA.Acetylcholine.mouse.moduleinfo.csv
Genes in Acetylcholine metabolic network in mouse scFEA.Acetylcholine.mouse.v1.symbols.gmt
Module information of Dopamine metabolic network in mouse scFEA.Dopamine.mouse.moduleinfo.csv
Genes in Dopamine metabolic network in mouse scFEA.Dopamine.mouse.v1.symbols.gmt
Module information of Histamine metabolic network in mouse scFEA.Histamine.mouse.moduleinfo.csv
Genes in Histamine metabolic network in mouse scFEA.Histamine.mouse.v1.symbols.gmt
Module information of Serotonin metabolic network in mouse scFEA.Serotonin.mouse.moduleinfo.csv
Genes in Serotonin metabolic network in mouse scFEA.Serotonin.mouse.v1.symbols.gmt
Module information of IronIon metabolic network in mouse scFEA.IronIon.mouse.moduleinfo.csv
Genes in IronIon metabolic network in mouse scFEA.IronIon.mouse.v1.symbols.gmt
Module information of MGF metabolic network in mouse scFEA.MGF.mouse.moduleinfo.csv
Genes in MGF metabolic network in mouse scFEA.MGF.mouse.v1.symbols.gmt
Module information of MHC-I metabolic network in mouse scFEA.MHC-I.mouse.moduleinfo.csv
Genes in MHC-I metabolic network in mouse scFEA.MHC-I.mouse.v1.symbols.gmt
scFEA mouse genes scFEA.mouse.genes.txt
KEGG module files Module information of KEGG module map in human scFEA.KEGG.human.moduleinfo.csv
Genes in KEGG module map in human scFEA.KEGG.human.v1.symbols.gmt
Module information of KEGG module map in mouse scFEA.KEGG.mouse.moduleinfo.csv
Genes in KEGG module map in mouse scFEA.KEGG.mouse.v1.symbols.gmt
Module information of the KEGG module map in Ciona robusta scFEA.KEGG.Ciona-robusta.moduleinfo.csv
Genes in KEGG module map in Ciona robusta scFEA.KEGG.Ciona-robusta.v1.symbols.gmt
Module information of KEGG module map in Zea mays scFEA.KEGG.Zea-mays.moduleinfo.csv
Genes in KEGG module map in Zea mays scFEA.KEGG.Zea-mays.v1.symbols.gmt
Module information of KEGG module map in Danio rerio scFEA.KEGG.Danio-rerio.moduleinfo.csv
Genes in KEGG module map in Danio rerio scFEA.KEGG.Danio-rerio.v1.symbols.gmt
Module information of KEGG module map in Gallus gallus scFEA.KEGG.Gallus-gallus.moduleinfo.csv
Genes in KEGG module map in Gallus gallus scFEA.KEGG.Gallus-gallus.v1.symbols.gmt
Module information of KEGG module map in Xenopus tropicalis scFEA.KEGG.Xenopus-tropicalis.moduleinfo.csv
Genes in KEGG module map in Xenopus tropicalis scFEA.KEGG.Xenopus-tropicalis.v1.symbols.gmt
Module information of KEGG module map in Rattus norvegicus scFEA.KEGG.Rattus-norvegicus.moduleinfo.csv
Genes in KEGG module map in Rattus norvegicus scFEA.KEGG.Rattus-norvegicus.v1.symbols.gmt
Module information of KEGG module map in Escherichia coli K-12 scFEA.KEGG.Escherichia-coli-K-12.moduleinfo.csv
Genes in KEGG module map in Escherichia coli K-12 scFEA.KEGG.Escherichia-coli-K-12.v1.symbols.gmt
Module information of KEGG module map in Bacillus subtilis 168 scFEA.KEGG.Bacillus-subtilis-168.moduleinfo.csv
Genes in KEGG module map in Bacillus subtilis 168 scFEA.KEGG.Bacillus-subtilis-168.v1.symbols.gmt
Module information of KEGG module map in Pseudomonas fluorescens SBW25 scFEA.KEGG.Pseudomonas-fluorescens-SBW25.moduleinfo.csv
Genes in KEGG module map in Pseudomonas fluorescens SBW25 scFEA.KEGG.Pseudomonas-fluorescens-SBW25.v1.symbols.gmt
Module information of KEGG module map in Arabidopsis thaliana scFEA.KEGG.Arabidopsis-thaliana.moduleinfo.csv
Genes in KEGG module map in Arabidopsis thaliana scFEA.KEGG.Arabidopsis-thaliana.v1.symbols.gmt
Module information of KEGG module map in Azotobacter vinelandii DJ scFEA.KEGG.Azotobacter-vinelandii-DJ.moduleinfo.csv
Genes in KEGG module map in Azotobacter vinelandii DJ scFEA.KEGG.Azotobacter-vinelandii-DJ.v1.symbols.gmt
Module information of KEGG module map in Synechocystis PCC 6803 scFEA.KEGG.Synechocystis-PCC-6803.moduleinfo.csv
Genes in KEGG module map in Synechocystis PCC 6803 scFEA.KEGG.Synechocystis-PCC-6803.v1.symbols.gmt
Module information of KEGG module map in Methanococcus voltae A3 scFEA.KEGG.Methanococcus-voltae-A3.moduleinfo.csv
Genes in KEGG module map in Methanococcus voltae A3 scFEA.KEGG.Methanococcus-voltae-A3.v1.symbols.gmt
Module information of KEGG module map in Streptomyces coelicolor A3(2) scFEA.KEGG.Streptomyces-coelicolor-A3(2).moduleinfo.csv
Genes in KEGG module map in Streptomyces coelicolor A3(2) scFEA.KEGG.Streptomyces-coelicolor-A3(2).v1.symbols.gmt
Module information of KEGG module map in Methanosarcina acetivorans C2A scFEA.KEGG.Methanosarcina-acetivorans-C2A.moduleinfo.csv
Genes in KEGG module map in Methanosarcina acetivorans C2A scFEA.KEGG.Methanosarcina-acetivorans-C2A.v1.symbols.gmt
Results derived from commonly unilized data sets Predict flux of modules in human M171 network of CCLE data CCLE data flux.csv
Imputed metabolomics profile of metabolites in human M171 network of CCLE data CCLE data imputed metabolomics profile.csv
Predict flux of modules in human M171 network of GTEx data GTEX data flux.csv
Imputed metabolomics profile of metabolites in human M171 network of GTEx data GTEX data imputed metabolomics profile.csv
Predict flux of modules in human M171 network of TCGA data TCGA data flux.csv
Imputed metabolomics profile of metabolites in human M171 network of TCGA data TCGA data imputed metabolomics profile.csv
Results drvived from selected scRNA-seq data sets Predict flux of modules in human M171 network of GSE72056 data GSE72056 flux.csv
Imputed metabolomics profile of metabolites in human M171 network of GSE72056 data GSE72056 imputed metabolomics profile.csv
Predict flux of modules in human M171 network of GSE103322 data GSE103322 flux.csv
Imputed metabolomics profile of metabolites in human M171 network of GSE103322 data GSE103322 imputed metabolomics profile.csv
Predict flux of modules in human M171 network of ROSMAP snRNA-seq data ROSMAP brain scRNA-seq data flux.csv
Imputed metabolomics profile of metabolites in human M171 network of ROSMAP snRNA-seq data ROSMAP brain scRNA-seq data imputed metabolomics profile.csv