"Pathway" "Pathway.source" "V3" "V4" "V5" "V6" "IN TWO DATA SETS" "sum.of.scores" "sum.of.genes" "secondary metabolism" "FunCat" 42 7 "Biosynthesis of Amino Acids and Derivatives" "BioPath" 40 7 "jasmonic acid biosynthesis" "TAIR-GO" 40 8 "jasmonic acid biosynthesis" "TAIR-GO" 40 8 "Methionin/SAM/ethylene metabolism from cysteine and aspartate" "BioPath" 34 6 "Benzoate degradation via CoA ligation" "KEGG" 31 11 "Inositol phosphate metabolism" "KEGG" 31 11 "Nicotinate and nicotinamide metabolism" "KEGG" 31 11 "Chlorophyll biosynthesis and breakdown" "BioPath" 30 3 "biosynthesis of proto- and siroheme" "AraCyc" 30 3 "Porphyrin and chlorophyll metabolism" "KEGG" 30 3 "chlorophyll and phytochromobilin metabolism" "LitPath" 30 3 "response to wounding" "TAIR-GO" 28 6 "defense response" "TAIR-GO" 22.5 5 "phospholipid biosynthesis II" "AraCyc" 22 3 "Leaf Glycerolipid Biosynthesis in Plastid" "BioPath" 20 2 "gibberellic acid catabolism" "TAIR-GO" 20 2 "growth" "TAIR-GO" 20 4 "lipid metabolism" "TAIR-GO" 20 2 "phenylpropanoid metabolism" "TAIR-GO" 20 2 "phospholipid metabolism" "TAIR-GO" 20 2 "lipoxygenase pathway" "AraCyc" 20 4 "triacylglycerol biosynthesis" "AraCyc" 20 2 "aerobic respiration" "FunCat" 20 2 "biogenesis of chloroplast" "FunCat" 20 2 "respiration" "FunCat" 20 2 "Diterpenoid biosynthesis" "KEGG" 20 2 "Synthesis of membrane lipids in plastids" "AcylLipid" 20 2 "Gibberellin metabolism" "LitPath" 20 2 "giberelin catabolism" "LitPath" 20 2 "phytochromobilin biosynthesis" "LitPath" 20 2 "biogenesis of cell wall" "FunCat" 18 3 "cellulose biosynthesis" "BioPath" 16 2 "hemicellulose biosynthesis" "BioPath" 16 2 "ORGAN DATA SET" "quantDE" 4.536798 "maxDE" 6.6787515 "ORGAN DATA SET" "STRESS DATA SET" "quantDE" 4.895966 "maxDE" 9.555716 "STRESS DATA SET" "HORMONE DATA SET" "quantDE" 2.19419 "maxDE" 10.3953416 "HORMONE DATA SET" "secondary metabolism" "FunCat" 22 2.51086133321237E-018 4 0.000156452057818124 "Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone)" "BioPath" 20 0.00000216160469588628 2 0.055174372233925 "Chlorophyll biosynthesis and breakdown" "BioPath" 20 0.000000000000333116989762753 2 0.00465417779063057 "Biosynthesis of Amino Acids and Derivatives" "BioPath" 20 0.00132332367475647 4 0.027457554133013 "biosynthesis of proto- and siroheme" "AraCyc" 20 7.69359159067294E-017 2 0.00612942683451833 "Porphyrin and chlorophyll metabolism" "KEGG" 20 1.60063698114207E-019 2 0.00154316224521291 "chlorophyll and phytochromobilin metabolism" "LitPath" 20 0.0000000305704341098649 2 0.00995356604202019 "Lipid signaling" "AcylLipid" 18 0.00428303475917976 4 0.111763302344563 "Methionin/SAM/ethylene metabolism from cysteine and aspartate" "BioPath" 14 0.000000000854980076287039 3 0.000225828516488629 "response to wounding" "TAIR-GO" 14 0.00000000102070400828852 3 0.000268212910061075 "defense response" "TAIR-GO" 12.5 0.0000000267790539980058 3 0.000181478565614653 "Leaf Glycerolipid Biosynthesis in Plastid" "BioPath" 10 0.00192769287720829 1 0.12030115575136 "gibberellic acid catabolism" "TAIR-GO" 10 0.0000000000026850325289551 1 0.00219507189929603 "growth" "TAIR-GO" 10 0.00000414454181419315 2 0.0052524988046315 "jasmonic acid biosynthesis" "TAIR-GO" 10 0.000000322578831369694 2 0.00264791062363402 "lipid metabolism" "TAIR-GO" 10 9.89614524183119E-015 1 0.000671223842121911 "phenylpropanoid metabolism" "TAIR-GO" 10 0.0000000000385003095454632 1 0.00326134321138527 "phospholipid metabolism" "TAIR-GO" 10 3.34571758005341E-017 1 0.000225891531560163 "porphyrin biosynthesis" "TAIR-GO" 10 0.00000000426454764142252 1 0.0158669570758625 "chlorophyll biosynthesis" "AraCyc" 10 0.0000198632063828438 1 0.082988144951427 "jasmonic acid biosynthesis" "AraCyc" 10 0.00000000874655295663561 2 0.000543240391194323 "lipoxygenase pathway" "AraCyc" 10 0.0000000000891625261039608 2 0.000152190078284779 "phospholipid biosynthesis II" "AraCyc" 10 0.00000000801713211772166 1 0.0171777138781857 "triacylglycerol biosynthesis" "AraCyc" 10 0.000000000000632638106124355 1 0.00122441277767683 "aerobic respiration" "FunCat" 10 0.000000000851982349868 1 0.00760728679659544 "biogenesis of cell wall" "FunCat" 10 0.0000121732428139857 2 0.0187773819759147 "biogenesis of chloroplast" "FunCat" 10 0.000235714238059174 1 0.103019481703747 "respiration" "FunCat" 10 0.000000000851982349868 1 0.00760728679659544 "Benzoate degradation via CoA ligation" "KEGG" 10 0.000022409512258019 4 0.000919779737806519 "Diterpenoid biosynthesis" "KEGG" 10 0.000000000416667272155174 1 0.00462654427165653 "Inositol phosphate metabolism" "KEGG" 10 0.0000546035135014851 4 0.00135843654243838 "Nicotinate and nicotinamide metabolism" "KEGG" 10 0.00000600421063403808 4 0.00063165803232326 "Synthesis of membrane lipids in plastids" "AcylLipid" 10 0.000210591213730067 1 0.0591459754036076 "chlorophyll and phyochromobilin biosynthesis" "LitPath" 10 0.00000113104725739839 1 0.0161787003604264 "Gibberellin metabolism" "LitPath" 10 0.00004453163498799 1 0.0236115736548236 "giberelin catabolism" "LitPath" 10 0.0000000000000109787667687868 1 0.000195498325231014 "phytochromobilin biosynthesis" "LitPath" 10 0.0000000243326613543171 1 0.0039462467666891 "calcium ion transport" "TAIR-GO" 9 8.48015406455122E-016 1 0.000225891531560163 "metal ion transport" "TAIR-GO" 9 0 1 0 "Membrane Transport" "KEGG" 9 0.000000000344166352702159 1 0.0153328793380479 "Other ion-coupled transporters" "KEGG" 9 0.00000000000470484366330141 1 0.00462654427165653 "cellulose biosynthesis" "BioPath" 8 0.000930077824435497 1 0.0805548410722835 "hemicellulose biosynthesis" "BioPath" 8 0.00000180685230005006 1 0.0117750464814863 "alanine biosynthesis II" "AraCyc" 8 0.000000594542816676348 2 0.00146427225696695 "phenylalanine biosynthesis II" "AraCyc" 8 0.000000121816089336577 2 0.000999374511201173 "triacylglycerol degradation" "AraCyc" 6.5 0.000101759956814122 3 0.00132152816884858 "MUTANT DATA SET" "quantDE" 3.320227 "maxDE" 9.658413519 "MUTANT DATA SET" "Benzoate degradation via CoA ligation" "KEGG" 21 0.0000000000185466193751511 7 0.0000113896027920857 "Inositol phosphate metabolism" "KEGG" 21 0.000000000122981048528783 7 0.0000215995687428649 "Nicotinate and nicotinamide metabolism" "KEGG" 21 0.00000000000114136357815046 7 0.00000614309526927576 "Biosynthesis of Amino Acids and Derivatives" "BioPath" 20 0.00690860453991909 3 0.103719473163701 "Methionin/SAM/ethylene metabolism from cysteine and aspartate" "BioPath" 20 5.62263765557215E-015 3 0.000259904671366022 "secondary metabolism" "FunCat" 20 0.000000000000311366978074507 3 0.00234204861450703 "Miscellaneous acyl lipid metabolism" "AcylLipid" 16 0.0205492399563619 3 0.339436030429373 "Nucleotide sugars metabolism" "KEGG" 15 1.03208180342368E-015 2 0.00157624771606332 "Aromatic amino acid (Phe, Tyr, Trp) metabolism" "BioPath" 14 0.00000539939826521478 3 0.00267641926413192 "response to wounding" "TAIR-GO" 14 0.00000000400334072211384 3 0.000234177131507852 "Phenylpropanoid pathway" "LitPath" 14 0.00334613011185103 3 0.0405707169068552 "colanic acid building blocks biosynthesis" "AraCyc" 12 0.00000613953967325733 2 0.0289609701352282 "phospholipid biosynthesis II" "AraCyc" 12 0.00000000252379828095955 2 0.00213890317678705 "C-compound and carbohydrate utilization " "FunCat" 12 2.18718433292552E-025 2 0 "nucleotide metabolism" "FunCat" 12 0 2 0 "Chlorophyll biosynthesis and breakdown" "BioPath" 10 0.000298713865966097 1 0.0494614397923621 "Gluconeogenesis from lipids in seeds" "BioPath" 10 0.00502653453522982 1 0.16931990523974 "Leaf Glycerolipid Biosynthesis in Plastid" "BioPath" 10 0.00552466406087482 1 0.127496977287836 "defense response" "TAIR-GO" 10 0.0000045316886595905 2 0.00279299486234104 "fatty acid biosynthesis" "TAIR-GO" 10 0.000000339942643596381 1 0.0196477184605708 "gibberellic acid catabolism" "TAIR-GO" 10 0.00000000000788450071060378 1 0.00205083982820306 "growth" "TAIR-GO" 10 0.0000106283310070448 2 0.00476538797762225 "jasmonic acid biosynthesis" "TAIR-GO" 10 0.000000862527866448657 2 0.00239779356986304 "lipid metabolism" "TAIR-GO" 10 0.0000000000000295871052437708 1 0.000626690611065736 "methionine biosynthesis" "TAIR-GO" 10 0.000000000000305444515896847 1 0.00124188538865604 "phenylpropanoid metabolism" "TAIR-GO" 10 0.000000000111630184048947 1 0.00304808894896742 "phospholipid metabolism" "TAIR-GO" 10 1.01094139198876E-016 1 0.000210832096122819 "biosynthesis of proto- and siroheme" "AraCyc" 10 0.0000407992575212857 1 0.0863035101128617 "fatty acid oxidation pathway" "AraCyc" 10 0.000000801449147404327 1 0.0212450542089532 "jasmonic acid biosynthesis" "AraCyc" 10 0.000000267726485085383 2 0.00117226035452893 "lipoxygenase pathway" "AraCyc" 10 0.00000000311423434826485 2 0.000332502710522612 "methionine biosynthesis II" "AraCyc" 10 0.00000000311423434826485 1 0.0101447106122569 "octane oxidation" "AraCyc" 10 0.0000000247060447627598 1 0.00598874489542065 "triacylglycerol biosynthesis" "AraCyc" 10 0.0000000000241361134047326 1 0.00205852595968142 "aerobic respiration" "FunCat" 10 0.0000000221659832750152 1 0.00870590307892927 "biogenesis of chloroplast" "FunCat" 10 0.00300062625757729 1 0.115690347268352 "degradation " "FunCat" 10 0.00000004690902714004 1 0.0252382210613622 "degradation of lipids, fatty acids and isoprenoids" "FunCat" 10 0 1 0 "respiration" "FunCat" 10 0.0000000221659832750152 1 0.00870590307892927 "Diterpenoid biosynthesis" "KEGG" 10 0.0000000496680052522522 1 0.0094523824558579 "Fatty acid metabolism" "KEGG" 10 0.0000511302933510191 1 0.0674619744413843 "Methionine metabolism" "KEGG" 10 0.000000114429615342882 1 0.0255257702912427 "Porphyrin and chlorophyll metabolism" "KEGG" 10 0.00000834466141762727 1 0.0446058360700014 "Synthesis of membrane lipids in plastids" "AcylLipid" 10 0.000461075766562091 1 0.0591459754036076 "chlorophyll and phytochromobilin metabolism" "LitPath" 10 0.00809462912979114 1 0.111502700596013 "Gibberellin metabolism" "LitPath" 10 0.0000178290365347585 1 0.0336218561732317 "giberelin catabolism" "LitPath" 10 3.64754415094676E-015 1 0.000286730877005487 "phytochromobilin biosynthesis" "LitPath" 10 0.00000000868905568714186 1 0.00573074109038615 "arabinose biosynthesis" "TAIR-GO" 9 0 1 0 "cell wall biosynthesis (sensu Magnoliophyta)" "TAIR-GO" 9 0.00000102349425146568 1 0.0278570768326563 "N-terminal protein myristoylation" "TAIR-GO" 9 0.0000000816505876720305 1 0.0106750561502405 "Galactose metabolism" "KEGG" 9 0.0000249937515186205 1 0.0572546860559348 "cellulose biosynthesis" "BioPath" 8 0.00241034376505936 1 0.0856137166370773 "hemicellulose biosynthesis" "BioPath" 8 0.00000560195233011647 1 0.0126029234860376 "acetate fermentation" "AraCyc" 8 0.00725269956600723 2 0.0474029648665773 "fructose degradation (anaerobic)" "AraCyc" 8 0.00500132976583403 2 0.0391476816860494 "glycolysis IV" "AraCyc" 8 0.00524834728900007 2 0.040734228728668 "sorbitol fermentation" "AraCyc" 8 0.00758118793860633 2 0.0440044257470427 "biogenesis of cell wall" "FunCat" 8 0.00307805038669604 1 0.125247210845789 "intracellular signalling" "FunCat" 8 0.000349956594999782 3 0.00169380837845465 "Carbon fixation" "KEGG" 8 0.0127516595258034 2 0.0474854883248534 "Pyruvate metabolism" "KEGG" 8 0.0276238070753238 2 0.0610274693322232 "Shikimate pathway" "LitPath" 8 0.0442205996830885 2 0.0287738306951092