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Table 1 Topics found for KEGG Metabolic pathways

From: GeneTopics - interpretation of gene sets via literature-driven topic models

KEGG Id Pathway Name LDA model # Best Topic pvalue Topic words (stemmed)
hsa00010 Glycolysis / Gluconeogenesis 25 Topic11 6.60E-23 strain,acet,mutant,acid,growth,glucos,cerevisia,plant,yeast,enzym,ferment,synthetas,coli,acetylcoa,gene,product,encod,activ,saccharomyc,ac
hsa00020 Citrate cycle (TCA cycle) 10 Topic7 1.87E-08 mitochondri,activ,enzym,oxid,aconitas,b5,dehydrogenas,reductas,cytochrom,malat,inhibit,mitochondria,reduct,nadhcytochrom,b5r,alphaketoglutar,cytosol,kgdhc,citrat,inactiv
hsa00030 Pentose phosphate pathway 25 Topic7 1.82E-12 enzym,activ,pfk,fructos,inhibit,ph,purifi,atp,subunit,concentr,pfk1,kinet,degre,aldolas,alloster,affin,kda,molecular,appar,purif
hsa00040 Pentose and glucuronate interconversions 25 Topic19 1.20E-20 glucuronid,human,ugt,liver,microsom,ugt2b7,activ,udpglucuronosyltransferas,ugt1a9,ugt1a6,ugt1a4,substrat,ugt1a1,isoform,ugt1a3,ugt1a10,valu,acid,express,format
hsa00051 Fructose and mannose metabolism 25 Topic19 1.58E-10 fructos,fructokinas,activ,enzym,pmm,sugar,plant,phosphoryl,khk,sucros,substrat,mannos,l,km,character,glucos,ketohexokinas,gene,clone,metabol
hsa00052 Galactose metabolism 25 Topic14 3.05E-09 mutat,diseas,patient,defici,gene,caus,allel,clinic,storag,case,acid,glycogen,type,muscl,identifi,disord,or,genet,polymorph,lysosom
hsa00053 Ascorbate and aldarate metabolism 50 Topic2 1.60E-13 glucuronid,human,ugt,liver,microsom,activ,ugt2b7,udpglucuronosyltransferas,ugt1a9,substrat,ugt1a1,valu,ugt1a6,ugt1a3,ugt1a4,metabol,enzym,kinet,microm,inhibit
hsa00062 Fatty acid elongation 10 Topic9 1.53E-08 peroxisom,enzym,dehydrogenas,hydratas,activ,acid,thiolas,betaoxid,enoylcoa,acylcoa,fatti,coli,3ketoacylcoa,prolin,p5cdh,substrat,liver,coa,oxid,catalyz
hsa00071 Fatty acid metabolism 50 Topic19 1.76E-16 enzym,activ,substrat,structur,dehydrogenas,residu,bind,site,catalyt,acid,mutant,dhdps,coli,specif,reaction,inhibit,form,studi,kinet,differ
hsa00100 Steroid biosynthesis 10 Topic4 6.45E-10 cholesterol,acat2,ester,acat,lipas,acat1,esteras,intestin,lipoprotein,lipid,cholesteryl,ldl,acyltransferas,liver,mice,cel,pancreat,plasma,bile,acid
  1. The table shows the GeneTopics results for KEGG metabolic pathway. Only the best topic with the smallest pvalue is shown. Many of the topic words are either part of the labelled pathway name or are closely related terms.