FLUXestimator

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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