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
	Human M171_NAD pathway stoichiometry matrix	cmMat_M171_NAD_human.csv
	Human GGSL pathway stoichiometry matrix	GGSL_human_cmMat.csv
	Human GlucoseTCAcycle pathway stoichiometry matrix	GlucoseTCAcycle_human_cmMat.csv
	Human kegg pathway stoichiometry matrix	kegg_human_cmMat.csv
	Human Lipid pathway stoichiometry matrix	Lipid_human_cmMat.csv
	Human Methionine pathway stoichiometry matrix	Methionine_human_cmMat.csv
	Human mhc pathway stoichiometry matrix	mhc_human_cmMat.csv
	Human Acetylcholine pathway stoichiometry matrix	cmMat_Acetylcholine_human_c6_m15.csv
	Human BCAA pathway stoichiometry matrix	cmMat_BCAA_human_c6_m14.csv
	Human Dopamine pathway stoichiometry matrix	cmMat_Dopamine_human_c5_m9.csv
	Human Glucose-Glutamine pathway stoichiometry matrix	cmMat_Glucose-Glutamine_human_c17_m23.csv
	Human Glucose-Glutaminolysis pathway stoichiometry matrix	cmMat_Glucose-Glutaminolysis_human_c17_m27.csv
	Human Histamine pathway stoichiometry matrix	cmMat_Histamine_human_c3_m6.csv
	Human IronIon pathway stoichiometry matrix	cmMat_IronIon_human_c8_m15.csv
	Human M171 pathway stoichiometry matrix	cmMat_M171_human_c70_m168.csv
	Human Serotonin pathway stoichiometry matrix	cmMat_Serotonin_human_c4_m8.csv
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
	Mouse M171_NAD pathway stoichiometry matrix	cmMat_M171_NAD_mouse.csv
	Mouse Lipid pathway stoichiometry matrix	Lipid_mouse_cmMat.csv
	Mouse Methionine pathway stoichiometry matrix	Methionine_mouse_cmMat.csv
	Mouse mhc pathway stoichiometry matrix	mhc_mouse_cmMat.csv
	Mouse GGSL pathway stoichiometry matrix	GGSL_mouse_cmMat.csv
	Mouse GlucoseTCAcycle pathway stoichiometry matrix	GlucoseTCAcycle_mouse_cmMat.csv
	Mouse kegg pathway stoichiometry matrix	kegg_mouse_cmMat.csv
	Mouse Acetylcholine pathway stoichiometry matrix	cmMat_Acetylcholine_mouse_c6_m15.csv
	Mouse BCAA pathway stoichiometry matrix	cmMat_BCAA_mouse_c6_m14.csv
	Mouse Dopamine pathway stoichiometry matrix	cmMat_Dopamine_mouse_c5_m9.csv
	Mouse Glucose-Glutamine pathway stoichiometry matrix	cmMat_Glucose-Glutamine_mouse_c17_m27.csv
	Mouse Glucose-Glutaminolysis pathway stoichiometry matrix	cmMat_Glucose-Glutaminolysis_mouse_c17_m23.csv
	Mouse Histamine pathway stoichiometry matrix	cmMat_Histamine_mouse_c3_m6.csv
	Mouse IronIon pathway stoichiometry matrix	cmMat_IronIon_mouse_c8_m15.csv
	Mouse M171 pathway stoichiometry matrix	cmMat_M171_mouse_c70_m168.csv
	Mouse Serotonin pathway stoichiometry matrix	cmMat_Serotonin_mouse_c4_m8.csv
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
	Ciona robusta pathway stoichiometry matrix	cin_cmMat.csv
	Zea mays pathway stoichiometry matrix	zma_cmMat.csv
	Danio rerio pathway stoichiometry matrix	dre_cmMat.csv
	Gallus gallus pathway stoichiometry matrix	gga_cmMat.csv
	Xenopus tropicalis pathway stoichiometry matrix	xtr_cmMat.csv
	Rattus norvegicus pathway stoichiometry matrix	rno_cmMat.csv
	Escherichia coli K-12 pathway stoichiometry matrix	eco_cmMat.csv
	Bacillus subtilis 168 pathway stoichiometry matrix	bsu_cmMat.csv
	Pseudomonas fluorescens SBW25 pathway stoichiometry matrix	pfs_cmMat.csv
	Arabidopsis thaliana pathway stoichiometry matrix	ath_cmMat.csv
	Azotobacter vinelandii DJ pathway stoichiometry matrix	avn_cmMat.csv
	Synechocystis PCC 6803 pathway stoichiometry matrix	syn_cmMat.csv
	Methanococcus voltae A3 pathway stoichiometry matrix	mvo_cmMat.csv
	Streptomyces coelicolor A3(2) pathway stoichiometry matrix	sco_cmMat.csv
	Methanosarcina acetivorans C2A pathway stoichiometry matrix	mac_cmMat.csv
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