"Pathway" "Pathway.source" "V3" "V4" "V5" "V6" "IN THREE DATA SETS" "" "sum.of.scores" "sum.of.genes" "" "" "Phenylpropanoid Metabolism" "BioPath" "110" "11" "" "" "carotenoid biosynthesis" "AraCyc" "92" "10" "" "" "carotenoid biosynthesis" "AraCyc" "92" "10" "" "" "Glutathione metabolism" "KEGG" "86" "12" "" "" "Glucosyltransferases for benzoic acids" "BioPath" "80" "8" "" "" "vitamin E biosynthesis" "AraCyc" "54" "6" "" "" "vitamin E biosynthesis" "AraCyc" "54" "6" "" "" "plastoquinone biosynthesis" "AraCyc" "44" "5" "" "" "plastoquinone biosynthesis" "AraCyc" "44" "5" "" "" "C-compound and carbohydrate utilization " "FunCat" "36" "4" "" "" "ORGAN DATA SET" "quantDE" "4.348392" "maxDE" "5.8239938" "ORGAN DATA SET" "Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone)" "BioPath" "118" "3.27449112031527e-44" "14" "1.12016217044340e-07" "Carotenoid and abscisic acid metabolism" "LitPath" "75" "3.91259972601524e-59" "10" "1.53566712744933e-10" "Carotenoid biosynthesis" "BioPath" "64" "8.89964833637507e-68" "7" "3.05555283568317e-10" "carotenoid biosynthesis" "AraCyc" "64" "2.76919019026045e-84" "7" "4.27251602427437e-12" "carotenid biosynthesis" "LitPath" "64" "8.92579086747192e-64" "7" "1.92584306790802e-09" "Phenylpropanoid Metabolism" "BioPath" "60" "0.00134271952606859" "6" "0.420703731068136" "Glucosyltransferases for benzoic acids" "BioPath" "40" "4.2952570348874e-25" "4" "5.4429562979189e-05" "Biosynthesis of steroids" "KEGG" "36" "3.38487333422551e-18" "5" "6.63096856145782e-05" "Folding, Sorting and Degradation" "KEGG" "35" "5.84121288355977e-12" "4" "0.0250936537241267" "ATP-dependent proteolysis" "TAIR-GO" "30" "4.01249969365804e-32" "6" "1.9594283387829e-08" "transport " "FunCat" "30" "0" "4" "0" "Miscellaneous acyl lipid metabolism" "AcylLipid" "30" "5.91740916689304e-07" "6" "0.0341147726681375" "Biosynthesis of prenyl diphosphates" "BioPath" "28" "0.000108553948586304" "5" "0.00423150470209201" "Chloroplastic protein turnover" "BioPath" "26" "1.05102130336839e-21" "5" "1.40256226988702e-06" "biogenesis of chloroplast" "FunCat" "26" "3.82798855587042e-05" "4" "0.0219849720649345" "energy" "FunCat" "26" "0" "5" "0" "Protein export" "KEGG" "26" "7.932115351308e-21" "3" "0.000966875020548919" "vitamin E biosynthesis" "AraCyc" "24" "2.85952384404648e-25" "3" "1.12910641154133e-05" "Tryptophan metabolism" "KEGG" "23" "3.11827487994915e-16" "3" "0.00178065994241396" "biosynthesis of derivatives of homoisopentenyl pyrophosphate " "FunCat" "22" "4.62959899388348e-14" "3" "0.000510895635781299" "photorespiration" "AraCyc" "21" "7.1295296183331e-13" "5" "0.000144522134640558" "Pathway for nuclear-encoded, thylakoid-localized proteins" "BioPath" "20" "8.62438899008413e-10" "2" "0.00980939517926372" "Tocopherol biosynthesis" "BioPath" "20" "2.07280802156946e-16" "2" "0.000422861369458771" "carotene metabolism" "TAIR-GO" "20" "0" "2" "0" "starch metabolism" "BioPath" "18" "0.000234750443132938" "4" "0.0037137898558969" "Thylakoid biogenesis and photosystem assembly" "BioPath" "18" "2.78900399202603e-11" "2" "0.00140419785248932" "carotene biosynthesis" "TAIR-GO" "18" "2.92419058658639e-21" "2" "4.73796653440296e-05" "carotenoid biosynthesis" "TAIR-GO" "18" "3.50813079460936e-12" "2" "0.0023218969510467" "phenylalanine degradation I" "AraCyc" "18" "1.20593397954498e-09" "4" "0.000422650874426574" "tyrosine degradation" "AraCyc" "18" "1.20067377495374e-18" "4" "1.83877584076344e-06" "xanthophyll cycle" "AraCyc" "18" "0" "2" "0" "glycine biosynthesis I" "AraCyc" "17" "1.96672105809336e-08" "4" "0.00369512132598577" "superpathway of serine and glycine biosynthesis II" "AraCyc" "17" "4.59532795778549e-13" "4" "0.000151973868916984" "degradation " "FunCat" "17" "9.91115087970106e-09" "3" "0.00447539360268050" "protein degradation " "FunCat" "17" "2.63436666662150e-11" "3" "0.00133728016995217" "ClpP protease complex " "BioPath" "16" "1.39600484853938e-14" "4" "5.97602417077906e-06" "C-compound and carbohydrate utilization " "FunCat" "16" "0" "2" "0" "photosynthesis" "FunCat" "16" "0.00254879415036869" "4" "0.0057055381869594" "response to water deprivation" "TAIR-GO" "14" "0" "2" "0" "plastoquinone biosynthesis" "AraCyc" "14" "1.73587732654426e-17" "2" "5.63549574511979e-05" "starch degradation" "AraCyc" "14" "1.93200901010111e-09" "3" "0.000378389388170687" "metabolism of energy reserves (e.g. glycogen, trehalose)" "FunCat" "14" "0" "3" "0" "polyprenyl diphosphate biosynthesis" "LitPath" "14" "2.61913384357085e-10" "2" "0.00496812181585841" "Chloroplastic protein import via envelope membrane" "BioPath" "13" "4.76883103714292e-05" "2" "0.0284567438041499" "chloroplastic endopeptidase Clp complex" "TAIR-GO" "12" "5.55370930648566e-12" "3" "5.36524754353636e-05" "jasmonic acid biosynthesis" "TAIR-GO" "12" "0.00178695574760200" "2" "0.0300649000369759" "response to ethylene stimulus" "TAIR-GO" "12" "4.12111809616616e-08" "3" "0.00126111647229425" "jasmonic acid biosynthesis" "AraCyc" "12" "1.02525509149139e-05" "2" "0.00895094340788678" "Carbon fixation" "KEGG" "12" "0.0120537704178199" "3" "0.0181308735843237" "Glyoxylate and dicarboxylate metabolism" "KEGG" "12" "6.40010077868075e-06" "3" "0.000843329956405377" "Phenylalanine metabolism" "KEGG" "12" "0.00237600018186467" "2" "0.154699515038555" "Phenylalanine, tyrosine and tryptophan biosynthesis" "KEGG" "12" "0.00130946232550889" "2" "0.0289761058493636" "Tyrosine metabolism" "KEGG" "12" "0.000177027789884084" "2" "0.0239752815411233" "calmodulin binding" "TAIR-GO" "11" "2.05273064089483e-05" "2" "0.0103875637586008" "histidine biosynthesis" "AraCyc" "11" "1.01039478524253e-06" "2" "0.00636492690482879" "histidine biosynthesis I" "AraCyc" "11" "2.85589857883208e-07" "2" "0.00526432915012098" "channel / pore class transport" "FunCat" "11" "1.38457147003484e-07" "2" "0.00657951996559913" "nitrogen and sulfur utilization " "FunCat" "11" "5.49708406448298e-06" "2" "0.00257705563076207" "transport facilitation" "FunCat" "11" "0" "2" "1.82390769415583e-05" "Ion channels" "KEGG" "11" "8.4131758458653e-06" "2" "0.0405066365841019" "Ligand-Receptor Interaction" "KEGG" "11" "1.12219452255367e-05" "2" "0.0447958284370878" "Delta-pH pathway" "BioPath" "10" "1.04226567018767e-09" "1" "0.00372141294675501" "ERD1 protease (ClpC-like)" "BioPath" "10" "0" "1" "0" "salycilic acid biosynthesis" "BioPath" "10" "8.11951295949276e-08" "1" "0.00726916460259595" "SRP (signal recognition particle)-dependent pathway for integral membrane proteins" "BioPath" "10" "1.81368918540685e-05" "1" "0.0173381704532205" "aromatic amino acid family biosynthesis" "TAIR-GO" "10" "0.00276147343003838" "1" "0.0908662352833046" "aromatic amino acid family biosynthesis, shikimate pathway" "TAIR-GO" "10" "0.00052663041525472" "1" "0.0690575820277148" "cell plate formation (sensu Magnoliophyta)" "TAIR-GO" "10" "2.28389713231179e-11" "1" "0.00132730748199489" "chlorophyll catabolism" "TAIR-GO" "10" "5.27914427431863e-09" "1" "0.0038871631152966" "chloroplast inner membrane" "TAIR-GO" "10" "0" "1" "0" "chloroplast thylakoid membrane protein import" "TAIR-GO" "10" "6.50838160218202e-08" "1" "0.00758981144203658" "cytochrome b6f complex" "TAIR-GO" "10" "2.74837226913211e-07" "1" "0.0180881040753458" "cytochrome b6f complex assembly" "TAIR-GO" "10" "0" "1" "0" "galactolipid biosynthesis" "TAIR-GO" "10" "1.82718467698472e-06" "1" "0.0123502692873399" "glucosinolate catabolism" "TAIR-GO" "10" "1.06349790602354e-11" "1" "0.00132730748199489" "lipid biosynthesis" "TAIR-GO" "10" "1.82718467698472e-06" "1" "0.0123502692873399" "lipid transport" "TAIR-GO" "10" "1.47445332833019e-06" "1" "0.0247272216501852" "photosystem I" "TAIR-GO" "10" "1.18297604898573e-06" "1" "0.0247272216501852" "photosystem II" "TAIR-GO" "10" "4.73196393454095e-08" "1" "0.0123502692873399" "photosystem II (sensu Viridiplantae)" "TAIR-GO" "10" "7.90824038138423e-09" "1" "0.00758981144203658" "plastoquinone biosynthesis" "TAIR-GO" "10" "2.28389713231179e-11" "1" "0.00132730748199489" "thylakoid membrane organization and biogenesis" "TAIR-GO" "10" "0" "1" "0" "vitamin E biosynthesis" "TAIR-GO" "10" "1.58887639706647e-07" "1" "0.00758981144203658" "vitamin E metabolism" "TAIR-GO" "10" "0" "1" "0" "xanthophyll cycle" "TAIR-GO" "10" "0" "1" "0" "xanthophyll metabolism" "TAIR-GO" "10" "0" "1" "0" "glycosylglyceride biosynthesis" "AraCyc" "10" "7.99789890336887e-07" "1" "0.0115545943004813" "biosynthesis of glycosides" "FunCat" "10" "4.00190353220552e-13" "1" "0.00206709538670994" "electron transport and membrane-associated energy conservation " "FunCat" "10" "7.8636869829072e-08" "1" "0.0223500205632797" "metabolismn of primary metabolic sugars derivatives " "FunCat" "10" "4.00190353220552e-13" "1" "0.00206709538670994" "stress response" "FunCat" "10" "0" "1" "0" "Glutathione metabolism" "KEGG" "10" "0.00401164680479016" "1" "0.139776920440219" "Synthesis of membrane lipids in plastids" "AcylLipid" "10" "0.00389026840784001" "1" "0.0802066566222338" "abscisic acid biosynthesis" "LitPath" "10" "4.54382519836344e-05" "2" "0.00496812181585841" "chlorophyll catabolism" "LitPath" "10" "1.72019450008587e-07" "1" "0.0066714693863965" "chorismate biosynthesis" "LitPath" "10" "0.0105653712675055" "1" "0.144786621585702" "MEP (methylerythritol P) pathway, plastids" "LitPath" "10" "0.000699127643916934" "2" "0.00720560826759991" "Toc apparatus" "BioPath" "9" "0.000320268206908753" "1" "0.0565885547102359" "cation transport" "TAIR-GO" "9" "1.29882921540303e-12" "1" "0.00132730748199489" "ethylene biosynthesis" "TAIR-GO" "9" "3.20979478483272e-05" "1" "0.0321956632165648" "histidine biosynthesis" "TAIR-GO" "9" "9.87751961288555e-09" "1" "0.0038871631152966" "hypersensitive response" "TAIR-GO" "9" "1.92043466920898e-05" "1" "0.0180881040753458" "phenylpropanoid metabolism" "TAIR-GO" "9" "6.02784097752775e-05" "1" "0.0180881040753458" "photorespiration" "TAIR-GO" "9" "2.92155996668125e-07" "1" "0.0123502692873399" "protein-chloroplast targeting" "TAIR-GO" "9" "9.20058110191082e-07" "1" "0.0123502692873399" "acrylonitrile degradation" "AraCyc" "9" "5.3876267190018e-13" "1" "0.00346442100931239" "aldoxime degradation" "AraCyc" "9" "5.3876267190018e-13" "1" "0.00346442100931239" "IAA biosynthesis" "AraCyc" "9" "9.93196817550225e-05" "1" "0.0335304999487643" "IAA biosynthesis I" "AraCyc" "9" "4.69482484123625e-06" "1" "0.0191841160192731" "C-compound, carbohydrate catabolism" "FunCat" "9" "0.0141341974119373" "3" "0.0224198476534441" "chloroplast transport " "FunCat" "9" "5.37617443818561e-06" "1" "0.0274598324511572" "protein targeting, sorting and translocation" "FunCat" "9" "9.94726281115665e-07" "1" "0.0223500205632797" "transport routes " "FunCat" "9" "0.000264510101255072" "1" "0.0814374692993416" "Cyanoamino acid metabolism" "KEGG" "9" "3.61041073806749e-05" "1" "0.0575310634430882" "Glycine, serine and threonine metabolism" "KEGG" "9" "0.00310843501532733" "1" "0.108425829962697" "Histidine metabolism" "KEGG" "9" "3.89520241049454e-06" "1" "0.0348074402185231" "Nitrogen metabolism" "KEGG" "9" "0.0146371865450317" "1" "0.0887742951605844" "Protein folding and associated processing" "KEGG" "9" "7.97875469104562e-05" "1" "0.0617115813678588" "abscisic acid biosynthesis" "TAIR-GO" "8" "0.00128159130615796" "1" "0.0493522024777135" "response to osmotic stress" "TAIR-GO" "8" "2.40601252310203e-07" "1" "0.00758981144203658" "sugar mediated signaling" "TAIR-GO" "8" "0.000138447755159233" "1" "0.0180881040753458" "xanthophyll biosynthesis " "TAIR-GO" "8" "0" "1" "0" "alanine biosynthesis II" "AraCyc" "8" "0.00195868517134817" "3" "0.00290435208580812" "sucrose biosynthesis" "AraCyc" "8" "0.00162512562424170" "2" "0.0120695593686523" "threonine degradation" "AraCyc" "8" "4.82325253185955e-05" "3" "0.00148148139405101" "biosynthesis of vitamins, cofactors, and prosthetic groups" "FunCat" "8" "0.00051761040617075" "1" "0.0518469621887588" "secondary biosynthesis of derivatives of homoisopentenyl pyrophosphate " "FunCat" "8" "0" "1" "0" "Methane metabolism" "KEGG" "8" "0.0144653115747290" "2" "0.13274103966995" "STRESS DATA SET" "quantDE" "2.12675" "maxDE" "5.740124" "STRESS DATA SET" "Biosynthesis of Amino Acids and Derivatives" "BioPath" "16" "1.78412879083264e-07" "2" "0.0106762715217057" "Glutathione metabolism" "BioPath" "16" "1.69704294513869e-13" "2" "0.000860026373464203" "sulfate assimilation III" "AraCyc" "16" "7.42677739529795e-25" "2" "2.04671829922862e-06" "Glucosyltransferases for benzoic acids" "BioPath" "10" "2.11500315818298e-12" "1" "0.000611054055091855" "Phenylpropanoid Metabolism" "BioPath" "10" "0.00111466030370503" "1" "0.0904418948805069" "cysteine biosynthesis I" "AraCyc" "10" "5.6561794613492e-15" "1" "0.000550967737155873" "C-compound and carbohydrate utilization " "FunCat" "10" "4.42741427149522e-34" "1" "2.06050890448923e-07" "HORMONE DATA SET" "quantDE" "2.042557" "maxDE" "4.2454255" "HORMONE DATA SET" "Phenylpropanoid Metabolism" "BioPath" "40" "6.35289070967847e-13" "4" "0.0094001329664592" "Glutathione metabolism" "KEGG" "32" "1.68259869299629e-23" "5" "3.70435380367635e-06" "Glucosyltransferases for benzoic acids" "BioPath" "30" "3.80164796007711e-32" "3" "1.98671718170519e-06" "toxin catabolism" "TAIR-GO" "30" "8.84856721178994e-37" "7" "8.3429651721394e-10" "Biosynthesis of Amino Acids and Derivatives" "BioPath" "28" "9.38135426931578e-06" "4" "0.00810230078367056" "Glutathione metabolism" "BioPath" "28" "1.01474985797948e-14" "4" "0.000151728713920935" "Tryptophan metabolism" "KEGG" "17" "3.34297893694334e-12" "2" "0.00517400063663644" "lignin biosynthesis" "AraCyc" "16" "8.21127689291017e-11" "4" "1.76790153025466e-05" "stress response" "FunCat" "16" "0" "2" "0" "Phenylpropanoid pathway" "LitPath" "16" "9.65098862889404e-09" "4" "0.000798983275154588" "phenylalanine degradation I" "AraCyc" "12" "2.63732239593434e-10" "2" "0.00109277832227542" "tyrosine degradation" "AraCyc" "12" "1.87539362005813e-16" "2" "4.90292737407739e-05" "Stilbene, coumarine and lignin biosynthesis" "KEGG" "12" "0.00105386550544105" "2" "0.0849299399134356" "detoxification" "FunCat" "11" "0" "3" "0" "nitrogen and sulfur utilization " "FunCat" "11" "5.93659388480412e-12" "2" "4.86232534022778e-05" "Cyanoamino acid metabolism" "KEGG" "11" "5.44169360548937e-08" "2" "0.00212362544491618" "Chloroplastic protein turnover" "BioPath" "10" "9.40688606723718e-11" "1" "0.0037586477207704" "core phenylpropanoid metabolism" "BioPath" "10" "0.0005938727930521" "1" "0.0482008947087981" "ERD1 protease (ClpC-like)" "BioPath" "10" "0" "1" "0" "Tocopherol biosynthesis" "BioPath" "10" "1.13559929639309e-11" "1" "0.000588878209976018" "ATP-dependent proteolysis" "TAIR-GO" "10" "2.47757376998792e-13" "1" "0.00370979929804542" "carotenoid biosynthesis" "TAIR-GO" "10" "8.96709509655016e-12" "1" "0.00191776065234240" "cell plate formation (sensu Magnoliophyta)" "TAIR-GO" "10" "1.37361189963932e-18" "1" "7.06235592923726e-05" "gibberellic acid biosynthesis" "TAIR-GO" "10" "6.6244404179855e-10" "1" "0.00370979929804542" "lignin biosynthesis" "TAIR-GO" "10" "1.26186836484963e-10" "1" "0.00245313844861899" "plastoquinone biosynthesis" "TAIR-GO" "10" "1.37361189963932e-18" "1" "7.06235592923726e-05" "vitamin E biosynthesis" "TAIR-GO" "10" "1.64425704006305e-14" "1" "0.000419431245256882" "gibberellin biosynthesis" "AraCyc" "10" "2.26679702798956e-10" "1" "0.00366849558101416" "plastoquinone biosynthesis" "AraCyc" "10" "3.52060330757098e-16" "1" "0.000346678871691742" "vitamin E biosynthesis" "AraCyc" "10" "2.97090397834718e-12" "1" "0.00119584982219711" "biosynthesis of phenylpropanoids" "FunCat" "10" "3.39888016138061e-07" "1" "0.0232916673893527" "biosynthesis of secondary products derived from L-phenylalanine and L-tyrosine" "FunCat" "10" "3.39888016138061e-07" "1" "0.0232916673893527" "C-compound and carbohydrate utilization " "FunCat" "10" "5.32673057398887e-21" "1" "4.75977556937012e-05" "plant / fungal specific systemic sensing and response " "FunCat" "10" "8.47208859506854e-09" "1" "0.00756796814933141" "plant hormonal regulation" "FunCat" "10" "8.47208859506854e-09" "1" "0.00756796814933141" "secondary metabolism" "FunCat" "10" "1.26856116930372e-05" "1" "0.065833656697739" "Diterpenoid biosynthesis" "KEGG" "10" "8.08076648666587e-07" "1" "0.00668188731086791" "Phenylalanine metabolism" "KEGG" "10" "0.00251129782919211" "1" "0.232894450188765" "Tyrosine metabolism" "KEGG" "10" "0.000255754938402891" "1" "0.0656466177224715" "Gibberellin metabolism" "LitPath" "10" "1.07692866014015e-08" "1" "0.0151330908699267" "giberelin biosynthesis" "LitPath" "10" "2.29730154645217e-10" "1" "0.00888838610858189" "ethylene biosynthesis" "TAIR-GO" "9" "2.42865520294515e-11" "1" "0.00191776065234240" "acrylonitrile degradation" "AraCyc" "9" "1.71492281804291e-17" "1" "0.000346678871691742" "aldoxime degradation" "AraCyc" "9" "1.71492281804291e-17" "1" "0.000346678871691742" "IAA biosynthesis" "AraCyc" "9" "9.64383558766125e-09" "1" "0.00366849558101416" "IAA biosynthesis I" "AraCyc" "9" "3.09087707119967e-10" "1" "0.00203026077127460" "Benzoate degradation via CoA ligation" "KEGG" "9" "0.0242447960355339" "1" "0.240742149564709" "Nitrogen metabolism" "KEGG" "9" "0.00252761609659881" "1" "0.0439908397974237" "4-hydroxyproline degradation" "AraCyc" "8" "1.67430529376918e-09" "1" "0.0030719037184151" "arginine degradation IX" "AraCyc" "8" "1.67430529376918e-09" "1" "0.00366849558101416" "proline degradation I" "AraCyc" "8" "5.79187707314111e-07" "1" "0.0122348322915482" "proline degradation II" "AraCyc" "8" "1.20136458744201e-09" "1" "0.0030719037184151" "energy" "FunCat" "8" "1.03060497339284e-14" "1" "0.000142181863668211" "energy conversion and regeneration " "FunCat" "8" "4.37063186158862e-16" "1" "0.000142181863668211" "1,2-Dichloroethane degradation" "KEGG" "8" "7.0185879352306e-13" "1" "0.000640790837528698" "Arginine and proline metabolism" "KEGG" "8" "0.00341451902275083" "1" "0.0715238671997305" "Ascorbate and aldarate metabolism" "KEGG" "8" "0.000516535623847113" "1" "0.0278629381216103" "beta-Alanine metabolism" "KEGG" "8" "3.62122048492257e-05" "1" "0.0182399369589203" "Bile acid biosynthesis" "KEGG" "8" "7.31287426026093e-06" "1" "0.0118298164062968" "Butanoate metabolism" "KEGG" "8" "0.000171223267471881" "1" "0.0278629381216103" "Fatty acid metabolism" "KEGG" "8" "0.00669563912104059" "1" "0.0491066536197488" "Glycerolipid metabolism" "KEGG" "8" "0.00266382312454261" "1" "0.0465223799148599" "Histidine metabolism" "KEGG" "8" "3.54755569666639e-06" "1" "0.0165251204756625" "Limonene and pinene degradation" "KEGG" "8" "1.75544048614917e-11" "1" "0.00158067408966704" "Lysine degradation" "KEGG" "8" "3.22323269471433e-06" "1" "0.0218841704615938" "Propanoate metabolism" "KEGG" "8" "0.000360165400721199" "1" "0.0390913908606677" "Valine, leucine and isoleucine degradation" "KEGG" "8" "0.00120544546126700" "1" "0.0517423299120131" "MUTANT DATA SET" "quantDE" "2.563334" "maxDE" "3.765963769" "MUTANT DATA SET"