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Authors: Pallavi Subhraveti Ron Caspi Peter Midford Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000262635Cyc: Salmonella enterica enterica serovar Typhi str. UJ308A Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari sn-glycerol an amino an amino a hexose 6- 3-phosphate a dipeptide thr O-acetyl-L-serine phosphate phosphate acid acid a dipeptide O-acetyl-L-serine 1-(β-D 1-(β-D cefoperazone cefoperazone cefoperazone cefoperazone 2-dehydro- phosphate sulfate galactitol 2-dehydro- D-sorbitol 2+ phosphate phosphate an amino an amino an amino an amino an amino an amino a tripeptide a tripeptide L-homoserine cys cys ribofuranosyl) ribofuranosyl) Fe glucosyl-oleandomycin glucosyl-oleandomycin glucosyl-oleandomycin 3-deoxy-D- phosphate glutathione thiosulfate 3-deoxy-D- sn-glycerol α-L- thiamine glucosyl-oleandomycin D-fructuronate sulfate sulfate sulfate sulfate sulfate galactitol D-mannitol D-mannitol ammonium 2-oxoglutarate acid acid acid acid acid acid nicotinamide nicotinamide enterobactin cys sulfate 3-phosphate predicted rhamnopyranose gluconate gluconate predicted predicted predicted predicted predicted predicted ATP-driven predicted ABC ABC ABC ABC ABC PEP-driven transporter PEP-driven RS0102480 RS0107390 RS0116890 RS0119850 transporter transporter RS0114335 RS0119560 RS0119570 RS0113385 RS0117195 RS0121950 RS0103580 RS0100680 ThiQ RS0104585 RS0112865 RS0122375 RS0101440 RS0115795 RS0117875 MdtK RS0116300 RS0120245 RS0105495 RS0119310 transporter transporter RS0113400 RS0110045 RS0108565 RS0102410 RS0102550 transporter RS0108760 RS0112090 RS0105145 transporter RS0105525 RS0123255 GlpT of sn- RS0119480 RS0114850 RS0118295 RS0103625 transporter of an of an of phosphate of phosphate of sulfate of galactitol glycerol 3- of D-sorbitol amino acid amino acid cefoperazone cefoperazone cefoperazone cefoperazone phosphate thr O-acetyl-L-serine O-acetyl-L-serine 1-(β-D 1-(β-D Fe 2+ 2-dehydro- phosphate glutathione thiosulfate galactitol 1- 2-dehydro- D-mannitol D-mannitol α-L- glucosyl-oleandomycin glucosyl-oleandomycin glucosyl-oleandomycin glucosyl-oleandomycin D-fructuronate sulfate sulfate sn-glycerol an amino an amino an amino an amino an amino an amino a tripeptide L-homoserine cys cys thiamine ribofuranosyl) ribofuranosyl) 3-deoxy-D- phosphate phosphate sulfate sulfate sulfate phosphate 3-deoxy-D- 1-phosphate 1-phosphate ammonium 2-oxoglutarate rhamnopyranose a tripeptide enterobactin a hexose 6- cys sulfate 3-phosphate acid acid acid acid acid nicotinamide nicotinamide gluconate galactitol 1- gluconate D-sorbitol acid a dipeptide a dipeptide phosphate phosphate phosphate sulfate phosphate sn-glycerol 6-phosphate an amino an amino acid acid 3-phosphate propane-1,2,3- propane-1,2,3- TcuC tricarboxylate tricarboxylate Inorganic Nutrient Metabolism A(H2) thiosulfate Cofactor, Prosthetic Group, Electron Carrier, and Vitamin Biosynthesis Hormone Biosynthesis tetrathionate Macromolecule Modification queuosine biosynthesis 2457 2605 a protein 3-(all-trans- a ribonucleoside adenosine reductase (aminomethyl)phosphonate degradation core an E. coli phosphoenol an [HPr]- an N-modified a 23S rRNA uridine uridine DNA combined (S)-1-pyrroline- cob(II)yrinate a,c- a purine 1911/1915/1917 (S)-mandelate A tetrathionate superpathway of thiamine diphosphate biosynthesis I superpathway of pyridoxal 5'-phosphate biosynthesis and salvage superpathway of indole-3-acetate superpathway of sulfate assimilation and cysteine biosynthesis 2-aminoethylphosphonate an L-1- oligosaccharide- osmoregulated an L-1- a tRNA precursor ATP pyruvate L-histidine uridine in 23S rRNA in 23S rRNA with incorrect nonaprenyl) with exogenous 2',3'-cyclic 2',3'-cyclic a protein 5-carboxylate a protein [2Fe-2S] iron-sulfur cluster biosynthesis superpathway of adenosylcobalamin salvage from cobinamide I ubiquinol-8 biosynthesis (prokaryotic) superpathway of tetrahydrofolate biosynthesis superpathay of heme b adeninyl adenosylcobamide 2-methyladeninyl NAD salvage preQ Aldehyde Degradation ribonucleoside adenosylcobinamide CTP aminoacyl-[tRNA] diamide biosynthesis I biosynthesis VI (bacteria) 0 lipid A (E. coli periplasmic phosphoenolpyruvate- bifunctional tRNA bifunctional tRNA bifunctional tRNA disulfide bonds benzene-1,2-diol DNA to form a phosphate monophosphate mandelate racemase/ trifunctional predicted biosynthesis from demethylmenaquinol-8 biosynthesis I adenosylcobamide biosynthesis pathway IV (from Aromatic Compound Biosynthesis (aminomethyl) degradation I phosphatidylethanolamine phosphatidylethanolamine aminoacyl-tRNA thiol:disulfide interchange bifunctional 3- bifunctional 2',3'- multifunctional CCA D-alanyl-D-alanine- HslU--HslV (early cobalt insertion) biosynthesis from glutamate NADPH-dependent 7- phosphoethanolamine 5'-triphosphate bifunctional multifunctional CCA muconate lactonizing transcriptional ABC all-trans- D-erythrose phosphonate sulfate phosphoethanolamineK-12 core type) glucan (OPG) protein hydrolase: pseudouridine(32) pseudouridine(32) pseudouridine(32) protein DsbG: demethylubiquinone 3- recombinational tRNA nucleotidyl carboxypeptidase/ peptidase cob(II)inamide adenosylcobinamide-GDP from adenosylcobinamide-GDP nicotinamide riboside) cyano-7-deazaguanine aminoalkylphosphonate (2-aminoethyl) methylglyoxal degradation I transferase CptA: crossover junction cyclic-nucleotide 2'- ornithine ornithine uroporphyrinogen-III L-cysteine desulfurase 4-hydroxybenzoate octaprenyl cys 4-phosphate chorismate 1-(β-D selenate reduction L-lactaldehyde transferase CptA: adenosylcobinamide tRNA nucleotidyl phosphotransferase PtsP: STUJ308A_RS0123065 synthase/ribosomal large synthase/ribosomal large synthase/ribosomal large STUJ308A_RS0100185 junction enzyme family protein: endopeptidase AmpH: regulator/proline transporter GTP trp chorismate biosynthesis I N-acetyltransferase: phosphonate STUJ308A_RS0100165 O-methyltransferase/2- endodeoxyribonuclease phosphodiesterase/ transferase/2'3'-cyclic ATPase arg arg trp RS0112240 trp diphosphate glu 2-methyladenine ribofuranosyl) 4-hydroxyphenylpyruvate reductase QueF: sulfate adenylyltransferase: 2-aminoethylphosphonate- degradation STUJ308A_RS0100165 kinase/ transferase/2'3'-cyclic STUJ308A_RS0122645 subunit pseudouridine subunit pseudouridine subunit pseudouridine STUJ308A_RS0106625 dehydrogenase/L- of L-arginine/ uroporphyrinogen-III ATP:cob(I)alamin 4-hydroxybenzoate adenine D-erythrose- aminoacyl-tRNA bifunctional protein- octaprenyl-6-hydroxy RuvC: 3'-nucleotidase: cpdB phosphodiesterase/ STUJ308A_RS0107735 subunit: cysteine cysteine isochorismate nicotinate-nucleotide-- biosynthesis STUJ308A_RS0114060 STUJ308A_RS0107775 -pyruvate methylglyoxal phosphoethanolamine adenosylcobinamide- phosphodiesterase/ synthase RluA: synthase RluA: glutamate gamma- ornithine C-methyltransferase: octaprenyltransferase: nicotinamidetrifunctional D-erythrose (acetamidomethyl) STUJ308A_RS0109330 selenate (anaerobic) phosphoethanolamine phosphoenolpyruvate- hydrolase: synthase RluA: disulfide isomerase/ phenol methylase: STUJ308A_RS0106215 2'nucleotidase/ mandelate racemase/ [+ 3 isozymes] hslU adenosyltransferase: GTP cyclohydrolase desulfurase CsdA: nicotinate-nucleotide-- 4-phosphate synthase EntC: dimethylbenzimidazole preQ multifunctional CCA desulfurase CsdA: 1 aminotransferase: phnW lactoylglutathione lyase: transferase: phosphate 2'nucleotidase/ STUJ308A_RS0108345 STUJ308A_RS0108345 STUJ308A_RS0108345 semialdehyde STUJ308A_RS0123085 ubiA dehydrogenase: nicotinamide-nucleotide (indol-3- 4-phosphate phosphonate sulfate adenylyltransferase sulfate transferase: -protein STUJ308A_RS0121190 oxidoreductase DsbC: 2-methoxy-STUJ308A_RS0121355 phosphatase: muconate lactonizing a peptide STUJ308A_RS0114140 STUJ308A_RS0100395 3-octaprenyl-4- I FolE: an L-glutamyl- STUJ308A_RS0114140 dimethylbenzimidazole STUJ308A_RS0122380 phosphoribosyltransferase: 3-deoxy-7- Metabolic Regulator Biosynthesis phosphonoacetaldehyde (S)-lactaldehyde an E.
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  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD

    Supplementary Table S4. FGA Co-Expressed Gene List in LUAD

    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase