"Pathway" "Pathway.source" "V3" "V4" "V5" "V6" "IN THREE DATA SETS" "sum.of.scores" "sum.of.genes" "ORGAN DATA SET" "quantDE" 4.710949 "maxDE" 5.8448125 "ORGAN DATA SET" "Photosystems " "BioPath" 335 8.98040294069872E-154 48 3.11534756576863E-025 "Photosynthesis" "KEGG" 143 2.60555452107533E-164 23 1.25135370418189E-029 "additional photosystem II components" "BioPath" 132 2.88476893053991E-058 17 0.00000000092381741016561 "Photosystem I" "BioPath" 127 1.71539830266293E-038 21 0.000000000794521876047765 "Chlorophyll a/b binding proteins" "BioPath" 122 1.1807932666185E-092 15 8.95711484507147E-015 "biogenesis of chloroplast" "FunCat" 109 5.47148546691E-042 17 0.000000000336302573500948 "photosynthesis" "FunCat" 102 1.05004291835874E-053 15 0.0000000000992923228668256 "Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone)" "BioPath" 91 0.00118763838057935 10 0.122262957733536 "Photosystem II" "BioPath" 69 0.000000000000159519424491297 9 0.00177554087093775 "photosystem I" "TAIR-GO" 67 0 8 0 "glycolysis and gluconeogenesis" "FunCat" 65 0.0000177962469611749 10 0.0316246968847914 "transport " "FunCat" 63 0 10 0 "Carbon fixation" "KEGG" 55 6.71737659893326E-018 7 0.00126644478424642 "Chlorophyll biosynthesis and breakdown" "BioPath" 53 0.00000162629595366668 6 0.0246246557244216 "Porphyrin and chlorophyll metabolism" "KEGG" 53 4.25366650549911E-029 7 0.00000162204194280057 "chlorophyll and phytochromobilin metabolism" "LitPath" 53 1.28915904238727E-019 6 0.00014811689392424 "chlorophyll binding" "TAIR-GO" 52 3.30876319472594E-031 6 0.00000967930829714075 "photosystem II" "TAIR-GO" 51 0 6 0 "chlorophyll biosynthesis" "TAIR-GO" 49 1.1196256602449E-021 5 0.00022054971350714 "respiration" "FunCat" 44 2.17890870959429E-025 6 0.00000330410186728913 "light harvesting complex" "BioPath" 40 8.92697901335267E-034 5 0.000000505750038959454 "chlorophyll biosynthesis" "AraCyc" 40 0.0000000111983844485706 5 0.0402380920907314 "aerobic respiration" "FunCat" 40 2.08242004509457E-021 5 0.0000510050602652474 "chlorophyll biosynthesis" "LitPath" 39 1.37065595361523E-029 4 0.00000768612112914642 "photosystem II type I chlorophyll a /b binding protein" "BioPath" 36 0 4 0 "energy" "FunCat" 34 0 5 0 "photosystem I reaction center" "BioPath" 32 5.53528535632133E-024 7 0.0000000324263312794894 "photosynthesis" "TAIR-GO" 30 0.000000076473159021762 4 0.0111122644404841 "acetate fermentation" "AraCyc" 30 0.000532045116141371 4 0.240039954047081 "fructose degradation (anaerobic)" "AraCyc" 30 0.000190622998743546 4 0.195119140928112 "glycolysis IV" "AraCyc" 30 0.000218146400937711 4 0.203859273868158 "serine-isocitrate lyase pathway" "AraCyc" 30 0.0000150898552167705 5 0.0213279507472822 "sorbitol fermentation" "AraCyc" 30 0.000600006992295118 4 0.221720519164089 "Glucosinolate Metabolism" "LitPath" 30 0.00000000147137944309096 3 0.00511896813636621 "lipid, fatty acid and isoprenoid metabolism" "FunCat" 29 0.000792786552083112 4 0.0527658302607724 "transport facilitation" "FunCat" 28 0 4 0 "Pentose phosphate pathway" "KEGG" 28 0.00000000445600192723002 4 0.010976403981084 "photosystem I subunit precursor" "BioPath" 26 0 5 0 "pentose-phosphate shunt" "TAIR-GO" 26 0.000000000016137511686818 3 0.0078157649646943 "Calvin cycle" "AraCyc" 26 0.00000457304454335387 3 0.113606406077887 "photorespiration" "AraCyc" 26 0.00000000484056997593977 6 0.00106956735561531 "Lipid signaling" "AcylLipid" 25 0.014250939143754 4 0.255167337825217 "Oxygen-evolving enhancer protein" "BioPath" 24 4.064820548403E-018 3 0.000299440995516381 "protein biosynthesis" "TAIR-GO" 24 0 4 0 "gluconeogenesis" "AraCyc" 24 0.00169422655264181 4 0.0674218989828449 "cysteine biosynthesis I" "AraCyc" 23 0.000194291643831266 5 0.0108910387081702 "glycine biosynthesis I" "AraCyc" 23 0.00000362757195053909 5 0.0173064569208564 "lipoxygenase pathway" "AraCyc" 23 0.0000000000142766975871874 3 0.00204178869209905 "electron transport" "TAIR-GO" 22 0.000344733180942717 3 0.0490196167861086 "photosynthetic electron transport" "TAIR-GO" 22 7.12178218676932E-015 3 0.000332583824787498 "wax biosynthesis" "TAIR-GO" 22 0.00000000000550127658431236 3 0.000733105990155231 "formaldehyde assimilation I (serine pathway)" "AraCyc" 22 0.0000395628631480713 4 0.0209389343830552 "Fatty acid elongation and wax and cutin metabolism" "AcylLipid" 22 0.00000182948116163213 3 0.0657170955273076 "Miscellaneous acyl lipid metabolism" "AcylLipid" 22 0.0278984634838701 6 0.0530744952211838 "Glycan Biosynthesis and Metabolism" "KEGG" 21 0.00841729102015224 4 0.0577657462485917 "ATP synthase components" "BioPath" 20 0.00000465794428557972 3 0.00873201373274815 "Cytochrome b6/f complex" "BioPath" 20 0.0000000467866137123242 2 0.0403375824360115 "Pathway for nuclear-encoded, thylakoid-localized proteins" "BioPath" 20 0.00119317311779211 2 0.105216391306432 "Plastocyanin" "BioPath" 20 0 2 0 "SRP (signal recognition particle)-dependent pathway for integral membrane proteins" "BioPath" 20 0.0000000676045193909828 2 0.0117718244010724 "photosynthetic water oxidation" "TAIR-GO" 20 0 2 0 "response to UV" "TAIR-GO" 20 0.0000693439193995381 2 0.0598596734375656 "metabolism of energy reserves (e.g. glycogen, trehalose)" "FunCat" 20 0 3 0 "pentose-phosphate pathway " "FunCat" 20 0.0000211513980578585 2 0.0858099439000678 "Glutamate metabolism" "KEGG" 19 0.0152024025002037 2 0.172021238048136 "nonphotochemical quenching" "TAIR-GO" 18 0 2 0 "photosynthesis light harvesting" "TAIR-GO" 18 0.0000000460728628032974 2 0.0152400534356798 "photosynthesis light harvesting in photosystem I" "TAIR-GO" 18 0.00000000120262299830051 2 0.0100445154550912 "acetyl-CoA assimilation" "AraCyc" 18 0.00699406182752536 3 0.069178020926974 "Ascorbate and aldarate metabolism" "KEGG" 18 0.0000675776906082726 3 0.0087086905407043 "Fructose and mannose metabolism" "KEGG" 18 0.01277857161017 3 0.0658686652918384 "Membrane Transport" "KEGG" 18 0.00000000299668424893652 2 0.0352400628404017 "Other ion-coupled transporters" "KEGG" 18 0.00000000000103977041679718 2 0.00641705695297019 "calmodulin binding" "TAIR-GO" 17 0.0000154315211139026 2 0.0598596734375656 "chloroplast thylakoid membrane protein import" "TAIR-GO" 17 0.0000000000510087363436839 2 0.00134771888196923 "photosystem II assembly" "TAIR-GO" 17 1.30182182915724E-017 2 0.000355569929823621 "photosystem II stabilization" "TAIR-GO" 17 0 2 0 "cysteine biosynthesis II" "AraCyc" 17 0.000000637092113693549 4 0.00441546803627684 "serine biosynthesis" "AraCyc" 17 0.000000000000190279406865735 4 0.00000525293420746433 "starch degradation" "AraCyc" 17 0.00000136518797689955 3 0.00501296697604882 "Protein export" "KEGG" 17 0.0000133513400664114 2 0.0707260618998724 "Ferredoxin" "BioPath" 16 0.000000730688353589371 3 0.00563317110126906 "photosystem II type II chlorophyll a /b binding protein" "BioPath" 16 0.00000000202568907419649 2 0.0027009751097518 "photorespiration" "TAIR-GO" 16 0.000000000101210848613347 3 0.000117366395456181 "PSII associated light-harvesting complex II" "TAIR-GO" 16 0 2 0 "ascorbate glutathione cycle" "AraCyc" 16 0.0000332001863027648 3 0.0064309509245236 "glycine degradation I" "AraCyc" 16 0.00000000000296078053638087 3 0.000584071376933557 "mannitol degradation" "AraCyc" 16 0.0000438000165366576 2 0.121475823838814 "sorbitol degradation" "AraCyc" 16 0.0000743169813120982 2 0.132618616940339 "transported compounds (substrates)" "FunCat" 16 0 3 0 "galactose degradation I" "AraCyc" 15 0.000000000000268785115313747 4 0.00000525293420746433 "glucose conversion" "AraCyc" 15 0.0230392071173154 4 0.0441078255949106 "lactose degradation IV" "AraCyc" 15 0.000000000000268785115313747 4 0.00000525293420746433 "UDP-glucose conversion" "AraCyc" 15 0.0185544474246054 4 0.0401322914498515 "cuticle biosynthesis" "TAIR-GO" 14 0.0003010932500604 2 0.0485089620753756 "photosystem II antenna complex" "TAIR-GO" 14 0.000000000000277133012936523 2 0.000355569929823621 "glyceraldehyde 3-phosphate degradation" "AraCyc" 14 0.00141121684437391 2 0.100317958839061 "glyoxylate cycle" "AraCyc" 14 0.0193525052765282 2 0.100317958839061 "oxidative branch of the pentose phosphate pathway" "AraCyc" 14 0.000000296613151314747 3 0.00283706584089287 "superpathway of serine and glycine biosynthesis II" "AraCyc" 14 0.0000398922817644667 4 0.00359652408919557 "accessory proteins of electron transport and membrane-associated energy conservation" "FunCat" 14 1.07487521636415E-015 2 0.000125597744601096 "electron transport and membrane-associated energy conservation " "FunCat" 14 0.000000117996002119711 2 0.00842036362172292 "ATP synthesis" "KEGG" 14 0.0157144001853543 2 0.147642717032868 "glutamate degradation I" "AraCyc" 13 0.000000379481734011471 2 0.00543061371217662 "jasmonic acid biosynthesis" "AraCyc" 13 0.0120414944233712 2 0.0551599746680225 "glycine decarboxylation via glycine cleavage system" "TAIR-GO" 12 0 2 0 "formylTHF biosynthesis" "AraCyc" 12 0.00143381276985062 2 0.0551599746680225 "thiamine biosynthesis" "AraCyc" 12 0.0000000041790638117497 2 0.00208698646404223 "accessory proteins of photosynthetic electron transport " "FunCat" 12 0 2 0 "C-compound, carbohydrate anabolism" "FunCat" 12 0.00379525420020974 2 0.0672149463125358 "transcription" "FunCat" 11 0.000185395330935689 2 0.0303153429912992 "transcriptional control" "FunCat" 11 0.0023282418047595 2 0.019726692714119 "Regulatory enzymes" "BioPath" 10 0.000118541370636469 1 0.0228252230037245 "aging" "TAIR-GO" 10 0.00664551335559068 1 0.106500807529496 "ATP synthesis coupled proton transport" "TAIR-GO" 10 0.000306155089272249 1 0.0437815062700768 "chlorophyll catabolism" "TAIR-GO" 10 0.00000941685614745918 1 0.0144469608443554 "chloroplast ATP synthase complex" "TAIR-GO" 10 0.0000000605701450095471 1 0.00505270023466755 "chloroplast-nucleus signaling pathway" "TAIR-GO" 10 0.00000941685614745918 1 0.0144469608443554 "cytochrome b6f complex" "TAIR-GO" 10 0.000306155089272249 1 0.0626453037057701 "enzyme binding" "TAIR-GO" 10 0 1 0 "extrinsic to photosynthetic water oxidation" "TAIR-GO" 10 0 1 0 "glucose metabolism" "TAIR-GO" 10 0.000306155089272249 1 0.0437815062700768 "glucosinolate biosynthesis" "TAIR-GO" 10 0.0488415415084105 1 0.106500807529496 "glucosinolate catabolism" "TAIR-GO" 10 0.0000000293512218597033 1 0.00505270023466755 "pentacyclic triterpenoid biosynthesis" "TAIR-GO" 10 0.0121211908056254 1 0.106500807529496 "pentose-phosphate shunt, oxidative branch" "TAIR-GO" 10 0.000306155089272249 1 0.0437815062700768 "photosynthesis light harvesting in photosystem II" "TAIR-GO" 10 0.0000666535617228755 1 0.0437815062700768 "photosynthetic electron transport in cytochrome b6/f" "TAIR-GO" 10 0.000000000204804325629491 1 0.00505270023466755 "proton transport" "TAIR-GO" 10 0.000306155089272249 1 0.0437815062700768 "response to chemical substance" "TAIR-GO" 10 0 1 0 "response to stress" "TAIR-GO" 10 0.000149264192257364 1 0.0275462028067416 "tetrapyrrole binding" "TAIR-GO" 10 0 1 0 "ammonia assimilation cycle" "AraCyc" 10 0.00237343589024546 1 0.0687372346353792 "glucose and glucose-1-phosphate degradation" "AraCyc" 10 0.00040509644496962 1 0.131156664083911 "glucosinolate biosynthesis from homomethionine" "AraCyc" 10 0.000119410162870542 1 0.021729765813307 "glucosinolate biosynthesis from phenylalanine" "AraCyc" 10 0.000012668772445878 1 0.0134708934838533 "glutamine biosynthesis I" "AraCyc" 10 0.00085399791808976 1 0.042763354445315 "isopentenyl diphosphate biosynthesis -- mevalonate-independent" "AraCyc" 10 0.0000338670862055158 1 0.0315511554879393 "nitrate assimilation pathway" "AraCyc" 10 0.0115076126313104 1 0.0832168967572197 "octane oxidation" "AraCyc" 10 0.026282483016115 1 0.0832168967572197 "peptidoglycan biosynthesis" "AraCyc" 10 0.000002996401364306 1 0.0552076013563611 "pyridoxal 5'-phosphate biosynthesis" "AraCyc" 10 0.0000000325658063060623 1 0.021729765813307 "starch biosynthesis" "AraCyc" 10 0 1 0 "sucrose degradation III" "AraCyc" 10 0.0081325044799518 1 0.183710694101428 "TCA cycle variation II" "AraCyc" 10 0.00970761199685543 2 0.0476352103236369 "UDP-N-acetylglucosamine biosynthesis" "AraCyc" 10 0.0000654318502387394 1 0.042763354445315 "biosynthesis of glycosides" "FunCat" 10 0.00000000187518582627617 1 0.00731870212411034 "electron / hydrogen transport " "FunCat" 10 0.00000873391861425608 1 0.0330979207343112 "lipid, fatty acid and isoprenoid metabolism of energy reserves (e.g. glycogen, trehalose)" "FunCat" 10 0 1 0 "metabolismn of primary metabolic sugars derivatives " "FunCat" 10 0.00000000187518582627617 1 0.00731870212411034 "Cyanoamino acid metabolism" "KEGG" 10 0.00767664172132851 2 0.048974859022909 "Fluorene degradation" "KEGG" 10 0.00354774271299366 1 0.0875170821848509 "gamma-Hexachlorocyclohexane degradation" "KEGG" 10 0.0104889132908953 1 0.108615448736665 "Peptidoglycan biosynthesis" "KEGG" 10 0.000000826547109652696 1 0.0103576403526595 "Reductive carboxylate cycle (CO2 fixation)" "KEGG" 10 0.0092823447434729 2 0.0273752967664211 "chlorophyll catabolism" "LitPath" 10 0.0000000931067187502865 1 0.00446203991403926 "MEP (methylerythritol P) pathway, plastids" "LitPath" 10 0.000421154228130939 1 0.0461580536153287 "oxylipin pathway" "LitPath" 10 0.000000000447891184254716 1 0.00152488693680191 "phytol biosynthesis" "LitPath" 10 0 1 0 "triterpene biosynthesis" "LitPath" 10 0.000546980049779089 1 0.0562985126795202 "calcium ion transport" "TAIR-GO" 9 0.000000218265769722726 1 0.00505270023466755 "carbohydrate biosynthesis" "TAIR-GO" 9 0 1 0 "glutamate metabolism" "TAIR-GO" 9 0 1 0 "L-serine biosynthesis" "TAIR-GO" 9 0.0000000462672244455894 1 0.00505270023466755 "nitrogen compound metabolism" "TAIR-GO" 9 0.0000097634428824639 1 0.0144469608443554 "phosphate transport" "TAIR-GO" 9 0.0000147478575416299 1 0.0275462028067416 "starch biosynthesis" "TAIR-GO" 9 0.0331639422149501 1 0.0836856190060417 "sucrose biosynthesis" "TAIR-GO" 9 0 1 0 "beta-Alanine metabolism" "KEGG" 9 0.0247437236098048 1 0.142391900918839 "Taurine and hypotaurine metabolism" "KEGG" 9 0.000000428639226179484 1 0.0103576403526595 "photosynthetic electron transport in photosystem I" "TAIR-GO" 8 0.0000733534569574001 1 0.0144469608443554 "photosystem I (sensu Viridiplantae)" "TAIR-GO" 8 0 1 0 "photosystem I antenna complex" "TAIR-GO" 8 0 1 0 "response to high light intensity" "TAIR-GO" 8 0.000104379950765749 1 0.0144469608443554 "epicuticular wax biosynthesis" "AraCyc" 8 0.0000030339290496521 1 0.00696009472452714 "N-Glycan biosynthesis" "KEGG" 8 0.00658902540606426 1 0.119621606113572 "carotenid biosynthesis" "LitPath" 8 0.0446622592371805 1 0.0671446439489759 "auxin metabolism" "TAIR-GO" 7 0.00341920278052219 1 0.0437815062700768 "photomorphogenesis" "TAIR-GO" 7 0.0000312389976603291 1 0.0144469608443554 "regulation of transcription" "TAIR-GO" 7 0.0000000122675319988626 1 0 "regulation of transcription, DNA-dependent" "TAIR-GO" 7 0 1 0 "response to pest, pathogen or parasite" "TAIR-GO" 7 0.0000000122675319988626 1 0.00505270023466755 "response to water deprivation" "TAIR-GO" 7 0 1 0 "signal sequence binding" "TAIR-GO" 7 0 1 0 "chloroplast transport " "FunCat" 7 0.0285322119471143 1 0.087026636580505 "protein targeting, sorting and translocation" "FunCat" 7 0.0105657301765922 1 0.0719391386758024 "stress response" "FunCat" 7 0 1 0 "STRESS DATA SET" "quantDE" 1.973006 "maxDE" 3.611809 "STRESS DATA SET" "HORMONE DATA SET" "quantDE" 1.092508 "maxDE" 3.2917007 "HORMONE DATA SET" "Aromatic amino acid (Phe, Tyr, Trp) metabolism" "BioPath" 10 0.000000000000039703173548874 1 0.000422447945025441 "Phenylpropanoid Metabolism" "BioPath" 10 0.00000000551269011412817 1 0.00418351480103982 "aromatic amino acid family biosynthesis" "TAIR-GO" 10 0.0000000000000454413506821048 1 0.00046679557527372 "aromatic amino acid family biosynthesis, anthranilate pathway" "TAIR-GO" 10 0 1 0 "aromatic amino acid family biosynthesis, shikimate pathway" "TAIR-GO" 10 4.6440079712328E-015 1 0.000339248522138489 "response to biotic stimulus" "TAIR-GO" 10 0 1 0 "alanine biosynthesis II" "AraCyc" 10 2.25651108274439E-015 1 0.000555992045376726 "phenylalanine biosynthesis II" "AraCyc" 10 2.76761395160496E-016 1 0.000428975064738143 "tyrosine biosynthesis I" "AraCyc" 10 1.61334855653653E-019 1 0.0000674374779021592 "Phenylalanine, tyrosine and tryptophan biosynthesis" "KEGG" 10 4.58813429332217E-017 1 0.00116703036915658 "Phe/Tyr biosynthesis" "LitPath" 10 0 1 0 "Shikimate pathway" "LitPath" 10 0.000000487058243060173 1 0.00978550455095267 "Tyr biosynthesis" "LitPath" 10 0 1 0 "MUTANT DATA SET" "quantDE" 2.296623 "maxDE" 3.642308209 "MUTANT DATA SET" "Ribosome" "KEGG" 30 0.00000816599909356111 5 0.0204574883470545 "Photosystems " "BioPath" 22 0.0000000159171834349517 3 0.00712218925711483 "additional photosystem II components" "BioPath" 16 0.000000000182137466600213 2 0.00282052442566755 "ATP synthase components" "BioPath" 16 1.08529583637229E-020 2 0.0000425933336653016 "ATP synthesis coupled proton transport" "TAIR-GO" 16 6.62284739349257E-023 2 0.000015821855067405 "proton transport" "TAIR-GO" 16 6.62284739349257E-023 2 0.000015821855067405 "Carbon fixation" "KEGG" 16 0.0000000815617928636188 2 0.0183883152905259 "protein synthesis" "FunCat" 12 0.00126765439468416 2 0.0494557799066479 "ribosome biogenesis" "FunCat" 12 0.0347656204002167 2 0.0963348402333737 "Branched-chain amino acids from aspartate" "BioPath" 10 0.0000000856130875568143 1 0.0146128067870479 "starch metabolism" "BioPath" 10 0.000000386509520804661 1 0.0207166836438686 "glucosinolate biosynthesis" "TAIR-GO" 10 0.00000000144848264746917 1 0.00383657134631592 "proton-transporting ATP synthase, catalytic core (sensu Eukaryota)" "TAIR-GO" 10 0 1 0 "starch catabolism" "TAIR-GO" 10 3.24731777268666E-016 1 0.000426757003132605 "Calvin cycle" "AraCyc" 10 0.0000000271500134320151 1 0.0230543441154862 "homomethionine biosynthesis" "AraCyc" 10 0 1 0 "leucine biosynthesis" "AraCyc" 10 0.000000000000555204104196561 1 0.00428038961115786 "starch degradation" "AraCyc" 10 0.00000000000868964347465766 1 0.00375972958265529 "C-compound and carbohydrate utilization " "FunCat" 10 2.01689645495528E-021 1 0.0000432706869942739 "energy" "FunCat" 10 1.71649578468184E-019 1 0.000129284030762596 "glycolysis and gluconeogenesis" "FunCat" 10 0.00847712583566375 1 0.185255761509219 "metabolism of energy reserves (e.g. glycogen, trehalose)" "FunCat" 10 0 1 0 "photosynthesis" "FunCat" 10 0.00000905270410827002 1 0.0345277866897977 "Glyoxylate and dicarboxylate metabolism" "KEGG" 10 0.0000005170190340209 1 0.0242852551673143 "Pyruvate metabolism" "KEGG" 10 0.00226177247818706 1 0.129718936423891 "Starch and sucrose metabolism" "KEGG" 10 0.00298734454744625 1 0.138617840512906 "Valine, leucine and isoleucine biosynthesis" "KEGG" 10 0.00000094521807422216 1 0.0293927666140969 "Glucosinolate Metabolism" "LitPath" 10 0.00000000467988964319957 1 0.00706242724540631 "Phenylalanine metabolism" "KEGG" 8 0.00234454413696204 2 0.0391936276589369 "pentacyclic triterpenoid biosynthesis" "TAIR-GO" 7 0.000000650873742380094 1 0.00383657134631592 "isoprenoid biosynthesis " "FunCat" 7 0.00655666359737254 1 0.0623844608142481 "lipid, fatty acid and isoprenoid biosynthesis " "FunCat" 7 0.00295740642053454 1 0.0485074535596423 "Biosynthesis of steroids" "KEGG" 7 0.0225916967955611 1 0.0603372062429491 "triterpene biosynthesis" "LitPath" 7 0.00000000453674727755325 1 0.0019091377856178 "triterpene, sterol, and brassinosteroid metabolism" "LitPath" 7 0.00194593230091679 1 0.0788871368815812