"Pathway" "Pathway.source" "V3" "V4" "V5" "V6" "IN ALL DATA SETS" "sum.of.scores" "sum.of.genes" "chlorophyll biosynthesis" "AraCyc" 314 38 "photosynthesis" "FunCat" 305 48 "chlorophyll biosynthesis" "TAIR-GO" 261 30 "chlorophyll biosynthesis" "LitPath" 235 27 "Literature annotations" "Carotenoid and abscisic acid metabolism | carotenoid degradation" "photosynthesis" "TAIR-GO" 189 28 "mRNA processing in chloroplast" "BioPath" 116 23 "photorespiration" "AraCyc" 87 21 "carotenoid biosynthesis" "AraCyc" 85 9 "photorespiration" "TAIR-GO" 73 16 "Carotenoid and abscisic acid metabolism" "LitPath" 60 7 "carotenoid biosynthesis" "TAIR-GO" 47 4 "carotenoid degradation" "LitPath" 36 4 "ORGAN DATA SET" "quantDE" 2.565025 "maxDE" 3.6632394 "ORGAN DATA SET" "Photosystems " "BioPath" 312 2.54863009856634E-079 50 4.34073774592475E-018 "Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone)" "BioPath" 301 2.38918215360783E-079 37 0.000000000000831611799975127 "biogenesis of chloroplast" "FunCat" 185 4.9068937922242E-088 29 1.60005100714276E-017 "Chlorophyll biosynthesis and breakdown" "BioPath" 183 2.62911552681974E-084 22 0.000000000000261565121838148 "C-compound and carbohydrate metabolism" "FunCat" 178 0.0000000133378095489457 29 0.0396502667174462 "chlorophyll and phytochromobilin metabolism" "LitPath" 177 2.67931977881565E-098 21 0.0000000000000156398990566676 "photosynthesis" "FunCat" 152 2.87504120550831E-087 25 5.92769249288396E-018 "Intermediary Carbon Metabolism" "BioPath" 146 0.0491183682942426 23 0.33922920044796 "Porphyrin and chlorophyll metabolism" "KEGG" 141 1.17128004456187E-114 17 4.94098394049835E-016 "additional photosystem II components" "BioPath" 129 8.3959538297396E-035 20 0.00000000342407485898938 "chlorophyll biosynthesis" "AraCyc" 128 1.71694837345108E-059 16 0.00000125911674033792 "Photosynthesis" "KEGG" 127 1.70660725481543E-100 23 1.72606571498119E-022 "glycolysis and gluconeogenesis" "FunCat" 117 9.84190416652537E-015 19 0.00118533428534902 "Carbon fixation" "KEGG" 113 5.67800412329746E-043 18 0.00000000900032951677237 "Photosystem I" "BioPath" 103 0.000000000179674811594336 18 0.000134436426887183 "Leaf Glycerolipid Biosynthesis in Plastid" "BioPath" 81 0.00351779209605458 9 0.262692938310925 "biosynthesis of proto- and siroheme" "AraCyc" 80 1.11881638950294E-029 12 0.0000335495945066683 "chlorophyll biosynthesis" "TAIR-GO" 75 4.32040660381499E-037 8 0.00000178244123762829 "Glycolysis / Gluconeogenesis" "KEGG" 74 0.000000000000208201481428523 11 0.0031557899343022 "Calvin cycle" "AraCyc" 73 4.25899455357377E-029 14 0.000000331088338183892 "Chlorophyll a/b binding proteins" "BioPath" 70 5.11551398828419E-019 9 0.0000692875248775043 "chlorophyll and phyochromobilin biosynthesis" "LitPath" 68 2.28779356394939E-043 10 0.000000008662185753046 "porphyrin biosynthesis" "TAIR-GO" 66 1.7939864608258E-044 9 0.0000000313629502236252 "acetate fermentation" "AraCyc" 66 0.00000000000534410559457305 11 0.0162249343955794 "fructose degradation (anaerobic)" "AraCyc" 66 0.000000000000291395833607865 11 0.00892988823631096 "glycolysis I" "AraCyc" 66 0.0241073498630222 11 0.480775182186322 "glycolysis IV" "AraCyc" 66 0.000000000000426336822375206 11 0.0101305687533265 "sorbitol fermentation" "AraCyc" 66 0.00000000000752958766622084 11 0.012904109247125 "Synthesis of membrane lipids in plastids" "AcylLipid" 65 5.69815062586486E-046 7 0.0000000811861361171943 "transport " "FunCat" 64 0 11 0 "Photosystem II" "BioPath" 59 0.00284560421304418 9 0.0361652899864676 "gluconeogenesis" "AraCyc" 58 0.00000000000179024709594406 9 0.00543272252638534 "starch metabolism" "BioPath" 57 0.000000034436094284628 9 0.00540245500809421 "Pentose phosphate pathway" "KEGG" 55 1.2853413062731E-018 9 0.000183131765532432 "photosystem I" "TAIR-GO" 54 0 7 0 "Pathway for nuclear-encoded, thylakoid-localized proteins" "BioPath" 52 7.0522497610588E-018 7 0.000088820403386159 "Folding, Sorting and Degradation" "KEGG" 52 0.0166654287223112 8 0.243570507940216 "mRNA processing in chloroplast" "BioPath" 50 7.65044522852214E-034 10 0.00000000349302880425447 "Carotenoid and abscisic acid metabolism" "LitPath" 40 0.000000000120128744916791 5 0.00716514238372674 "chlorophyll biosynthesis" "LitPath" 49 1.18498303376855E-022 5 0.000140931961199781 "Transcription (chloroplast)" "BioPath" 44 2.59494038847606E-024 5 0.0000432714147489122 "transcription initiation" "TAIR-GO" 44 5.31258410300703E-028 5 0.0000308563164891003 "transport facilitation" "FunCat" 43 0 7 0 "Fructose and mannose metabolism" "KEGG" 42 0.000000640118683844122 6 0.0252116487792463 "Carotenoid biosynthesis" "BioPath" 40 0.000000000123484282697994 5 0.00173735098448416 "Biosynthesis of steroids" "KEGG" 40 0.00305854422617501 4 0.168100206500862 "carotenid biosynthesis" "LitPath" 40 0.000000000000100796697106953 5 0.000636347374186037 "photosystem II" "TAIR-GO" 39 0 5 0 "photorespiration" "AraCyc" 39 0.0000000000170959895905646 9 0.00054522501931556 "response to light" "TAIR-GO" 38 0.0000831618645272054 5 0.19113728199204 "carotenoid biosynthesis" "AraCyc" 38 3.17035732690793E-016 4 0.000971767691056899 "glycerol degradation II" "AraCyc" 38 0.0000263464582794703 6 0.103163983220377 "glycosylglyceride desaturation pathway" "AraCyc" 37 0 4 0 "Protein export" "KEGG" 37 0.000000000000442543134842222 6 0.00185854243930912 "photosynthesis" "TAIR-GO" 36 0.000000402829710205841 5 0.014270741938629 "protein biosynthesis" "TAIR-GO" 36 0 6 0 "respiration" "FunCat" 36 0.00000000000187760098906781 5 0.000802410343713032 "electron transport" "TAIR-GO" 35 0.000000663994761230698 5 0.014270741938629 "pentose-phosphate pathway " "FunCat" 33 0.00000000218000075889755 5 0.0056896054770909 "light harvesting complex" "BioPath" 32 2.66199585172456E-016 4 0.000270631466413573 "protein folding" "TAIR-GO" 32 0 4 0 "glyceraldehyde 3-phosphate degradation" "AraCyc" 32 0.00000000144842022040475 5 0.0134850498530994 "aerobic respiration" "FunCat" 32 0.000000000900296626110259 4 0.00562404224863306 "Glycine, serine and threonine metabolism" "KEGG" 32 0.0000114276243794245 6 0.00677089612661246 "Translation factors" "KEGG" 32 0.0427397555265357 9 0.0459647537645136 "Protein folding / chaperonins (chloroplast)" "BioPath" 30 0.00000105523255572997 4 0.0346849027058786 "Translation (chloroplast)" "BioPath" 30 7.22635405650846E-016 5 0.0000432714147489122 "pentose-phosphate shunt" "TAIR-GO" 30 0.000000000101984550361304 4 0.005407088222447 "phospholipid desaturation pathway" "AraCyc" 30 2.50356371810914E-019 3 0.000295578657666506 "1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradatio" "KEGG" 30 8.31236960340884E-021 3 0.00159352740035614 "1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation" "KEGG" 30 1.87456383538136E-025 3 0.000221327359662022 "Androgen and estrogen metabolism" "KEGG" 30 1.59451294581874E-024 3 0.000490507960062489 "Benzoate degradation via hydroxylation" "KEGG" 30 6.55156704011058E-016 3 0.00252340144475051 "IPP (isopentenyl diphosphate) and DMAPP (dimethylallyl diphosphat) biosynthesis" "LitPath" 30 0.00769484187980467 3 0.200833486133659 "MEP (methylerythritol P) pathway, plastids" "LitPath" 30 0.0000000000174026227136837 3 0.0142026604822551 "phytochromobilin biosynthesis" "LitPath" 30 0.00000000000380262138585609 3 0.00475482748437765 "photosynthetic electron transport" "TAIR-GO" 29 3.05983920343929E-019 4 0.000070114197478708 "Ferredoxin" "BioPath" 28 0.000000000000095011878537773 6 0.0000268143847510968 "Oxygen-evolving enhancer protein" "BioPath" 28 5.89431485943687E-019 4 0.0000509430729339162 "photosystem I reaction center" "BioPath" 28 0.000000000000095011878537773 6 0.0000268143847510968 "formaldehyde assimilation I (serine pathway)" "AraCyc" 28 0.000616868792976859 5 0.0695257657815698 "mannitol degradation" "AraCyc" 28 0.0000000306846595532833 5 0.0203133324619636 "sorbitol degradation" "AraCyc" 28 0.0000000822370824364096 5 0.0244756603546892 "carotenoid biosynthesis" "TAIR-GO" 18 0.000000000306582439448609 2 0.00608281275863822 "chloroplast thylakoid membrane protein import" "TAIR-GO" 27 1.31521635402616E-019 3 0.000122829248342305 "glycine biosynthesis I" "AraCyc" 27 0.00040351267850762 7 0.0344949143960851 "superpathway of serine and glycine biosynthesis II" "AraCyc" 27 0.000000000516954308200582 7 0.000400980644810908 "Early light-inducible proteins" "BioPath" 26 0.000000000499965480180077 4 0.000839031595575225 "photorespiration" "TAIR-GO" 25 1.71709400237792E-018 4 0.0000127907946206382 "oxidative branch of the pentose phosphate pathway" "AraCyc" 25 0.000000000000732956037723884 7 0.00000333341899992069 "energy" "FunCat" 25 0 4 0 "Delta-pH pathway" "BioPath" 24 0 3 0 "chlorophyll binding" "TAIR-GO" 24 0.000201850654512406 3 0.0406136504312734 "Aminoacyl-tRNA biosynthesis" "KEGG" 24 0.00000238011233416017 10 0.0000332931032093111 "tRNA charging pathway" "AraCyc" 22 0.00499034648183691 9 0.00750409766060526 "ATP synthase components" "BioPath" 20 0.0020084412099037 3 0.0388636047870981 "Cytochrome b6/f complex" "BioPath" 20 0.0000474624823692685 2 0.118114679912495 "Plastocyanin" "BioPath" 20 0 2 0 "SRP (signal recognition particle)-dependent pathway for integral membrane proteins" "BioPath" 20 0.0000647443323129032 2 0.0386311686181177 "Thylakoid biogenesis and photosystem assembly" "BioPath" 20 0.00134158965079797 2 0.0607590762738435 "chlorophyll catabolism" "TAIR-GO" 20 0.0000000000000681805495776513 2 0.00117436744756546 "chloroplast-nucleus signaling pathway" "TAIR-GO" 20 0.0000000000000681805495776513 2 0.00117436744756546 "phytochromobilin biosynthesis" "TAIR-GO" 20 0.0000000000000681805495776513 2 0.00117436744756546 "isopentenyl diphosphate biosynthesis -- mevalonate-independent" "AraCyc" 20 0.000000000147189236702666 2 0.0116388648180239 "starch biosynthesis" "AraCyc" 20 0 2 0 "transported compounds (substrates)" "FunCat" 20 0 4 0 "metabolism of acyl-lipids in mitochondria" "AcylLipid" 20 0.0000696307965006118 2 0.064393960928247 "chlorophyll catabolism" "LitPath" 20 0.000000000000734124815245398 2 0.00158169792230232 "hypersensitive response" "TAIR-GO" 19 0.000000400477540510493 2 0.0184072402417581 "starch biosynthesis" "TAIR-GO" 19 0.0000269281025369486 2 0.0297266549343466 "starch degradation" "AraCyc" 19 0.0001530404017524 3 0.0391516290955001 "metabolism of energy reserves (e.g. glycogen, trehalose)" "FunCat" 19 0 3 0 "psbP family of thylakoid proteins" "BioPath" 18 0.0000000000103534925136319 5 0.0000070053942379847 "nonphotochemical quenching" "TAIR-GO" 18 0 2 0 "formylTHF biosynthesis" "AraCyc" 18 0.000609184774163824 3 0.0710089879735357 "glycine degradation I" "AraCyc" 18 0.000000000118881064506414 4 0.000524224052924384 "calmodulin binding" "TAIR-GO" 17 0.0015316087851759 2 0.151585244407258 "photoinhibition" "TAIR-GO" 17 0.0000000000157867309725403 2 0.00117436744756546 "photosystem I subunit precursor" "BioPath" 16 0.0000000164133190419533 3 0.00164413534016858 "photosystem II type II chlorophyll a /b binding protein" "BioPath" 16 0.00000114292419512764 2 0.0095909435452604 "magnesium chelatase complex" "TAIR-GO" 16 0 2 0 "photosystem II (sensu Viridiplantae)" "TAIR-GO" 16 0.00000000454151564933387 2 0.00432898204523491 "plastid organization and biogenesis" "TAIR-GO" 16 0.000000000093704594678724 3 0.000122829248342305 "response to high light intensity" "TAIR-GO" 16 0.000000000093704594678724 2 0.00117436744756546 "RNA processing" "TAIR-GO" 16 0 3 0 "ascorbate glutathione cycle" "AraCyc" 16 0.011172905831206 3 0.0486288253620982 "cysteine biosynthesis II" "AraCyc" 16 0.00181394870977472 6 0.00303573858394529 "serine biosynthesis" "AraCyc" 16 0.0000000103199428202051 6 0.0000000441306512772082 "TCA cycle variation II" "AraCyc" 16 0.0031296800861336 3 0.0592548115747857 "C-compound and carbohydrate utilization " "FunCat" 16 0 3 0 "nucleotide metabolism" "FunCat" 16 0 5 0 "translation" "FunCat" 16 0.000726182590748353 4 0.0206218448376905 "photosynthetic electron transport in photosystem I" "TAIR-GO" 15 0.000000000545424099126466 2 0.00117436744756546 "galactose degradation I" "AraCyc" 15 0.000000000735773232333 4 0.000101755832836927 "lactose degradation IV" "AraCyc" 15 0.000000000735773232333 4 0.000101755832836927 "Membrane Transport" "KEGG" 15 0.000755555711336493 3 0.0480112806256159 "Protein folding and associated processing" "KEGG" 15 0.0227727470229283 2 0.229593104494709 "Chloroplastic protein turnover" "BioPath" 14 0.0428618843545892 2 0.227160996493062 "transcription" "FunCat" 14 0.000149286015286893 2 0.103361506100151 "transcriptional control" "FunCat" 14 0.00306626728451344 2 0.0705311573152653 "one-carbon compound metabolism" "TAIR-GO" 13 0.000000272570710369076 2 0.00432898204523491 "phosphate transport" "TAIR-GO" 13 0.000000146581422612839 2 0.00432898204523491 "folate biosynthesis" "AraCyc" 13 0.00148782643447733 2 0.124110021768237 "ribose degradation" "AraCyc" 13 0.0000078348511909045 5 0.000288588577550128 "Other ion-coupled transporters" "KEGG" 13 0.0000724822853226903 2 0.0369677944604835 "Plastoquinone biosynthesis" "BioPath" 12 0 2 0 "chloroplast organization and biogenesis" "TAIR-GO" 12 0.00000364609843181579 2 0.0184072402417581 "glycine decarboxylation via glycine cleavage system" "TAIR-GO" 12 0 2 0 "plastid large ribosomal subunit" "TAIR-GO" 12 0 2 0 "cyanate degradation" "AraCyc" 12 0.0000103043417584342 2 0.1041212892443 "aminoacyl-tRNA-synthetases" "FunCat" 12 0.000671955866984551 5 0.00240561811646546 "biosynthesis of vitamins, cofactors, and prosthetic groups" "FunCat" 12 0.0339896882579742 2 0.103361506100151 "electron / hydrogen transport " "FunCat" 12 0.0000109704438144347 2 0.00929379327084685 "non-oxidative branch of the pentose phosphate pathway" "AraCyc" 11 0.00558861753215948 4 0.0039559663813393 "protein targeting, sorting and translocation" "FunCat" 11 0.00127336455873727 2 0.0323796487627124 "FtsH protease (many homologues / subcellular localization ambiguous)" "BioPath" 10 0 1 0 "Regulatory enzymes" "BioPath" 10 0.00436023250365392 1 0.0525946522518335 "ADPG pyrophosphorylase complex (sensu Eukaryota)" "TAIR-GO" 10 0 1 0 "ATP synthesis coupled proton transport" "TAIR-GO" 10 0.00602933762069026 1 0.0900968666281517 "carotene biosynthesis" "TAIR-GO" 10 0.000135116955067405 1 0.0311891471147117 "carotenoid biosynthesis/TAS" "TAIR-GO" 10 0 1 0 "cell death" "TAIR-GO" 10 0.00402630212147816 1 0.0580493121841885 "chaperone cofactor dependent protein folding" "TAIR-GO" 10 0 1 0 "chloroplast ATP synthase complex" "TAIR-GO" 10 0.00000251113484812642 1 0.0111792940032809 "chloroplast envelope" "TAIR-GO" 10 0 1 0 "cytochrome b6f complex" "TAIR-GO" 10 0.00602933762069026 1 0.125941679821348 "enzyme binding" "TAIR-GO" 10 0 1 0 "etioplast organization and biogenesis" "TAIR-GO" 10 0 1 0 "extrinsic to photosynthetic water oxidation" "TAIR-GO" 10 0 1 0 "galactolipid biosynthesis" "TAIR-GO" 10 0.0226407242226373 1 0.0900968666281517 "glucose metabolism" "TAIR-GO" 10 0.00602933762069026 1 0.0900968666281517 "glycolipid biosynthesis" "TAIR-GO" 10 0.00259275710067264 1 0.0580493121841885 "heme biosynthesis" "TAIR-GO" 10 0 1 0 "isoprenoid biosynthesis" "TAIR-GO" 10 0.0226407242226373 1 0.0900968666281517 "lipid biosynthesis" "TAIR-GO" 10 0.0226407242226373 1 0.0900968666281517 "lipoic acid metabolism" "TAIR-GO" 10 0 1 0 "pentose-phosphate shunt, oxidative branch" "TAIR-GO" 10 0.00602933762069026 1 0.0900968666281517 "photosynthesis, dark reaction" "TAIR-GO" 10 0 1 0 "photosynthetic electron transport in cytochrome b6/f" "TAIR-GO" 10 0.0000000104586620790462 1 0.0111792940032809 "photosynthetic water oxidation" "TAIR-GO" 10 0 1 0 "plastoquinone biosynthesis" "TAIR-GO" 10 0.00000251113484812642 1 0.0111792940032809 "protein binding" "TAIR-GO" 10 0.000711525159811645 1 0.0900968666281517 "protein complex assembly" "TAIR-GO" 10 0 1 0 "proton transport" "TAIR-GO" 10 0.00602933762069026 1 0.0900968666281517 "response to chemical substance" "TAIR-GO" 10 0 1 0 "response to stress" "TAIR-GO" 10 0.00324658847549332 1 0.0580493121841885 "response to temperature" "TAIR-GO" 10 0.000195461713733886 1 0.0311891471147117 "RNA binding" "TAIR-GO" 10 0 1 0 "systemic acquired resistance" "TAIR-GO" 10 0.0104097939711219 1 0.164427689776149 "tetrapyrrole binding" "TAIR-GO" 10 0 1 0 "thylakoid membrane organization and biogenesis" "TAIR-GO" 10 0 1 0 "vitamin E biosynthesis" "TAIR-GO" 10 0.00402630212147816 1 0.0580493121841885 "xanthophyll cycle" "TAIR-GO" 10 0 1 0 "xanthophyll metabolism" "TAIR-GO" 10 0 1 0 "glucose and glucose-1-phosphate degradation" "AraCyc" 10 0.0221165757647415 1 0.327590827011909 "peptidoglycan biosynthesis" "AraCyc" 10 0.000374489305298946 1 0.156564751478951 "plastoquinone biosynthesis" "AraCyc" 10 0.0000369289966959964 1 0.0425767563766807 "UDP-N-acetylglucosamine biosynthesis" "AraCyc" 10 0.0051811020119979 1 0.124536328867397 "vitamin E biosynthesis" "AraCyc" 10 0.024937237146661 1 0.124536328867397 "xanthophyll cycle" "AraCyc" 10 0.000000139479734145186 1 0.00801791411523273 "protein modification " "FunCat" 10 0.0261678068078661 1 0.387029526160962 "chlorophyll a biosynthesis" "LitPath" 10 0 1 0 "phytol biosynthesis" "LitPath" 10 0 1 0 "plastochinone and phylloquinone biosynthesis" "LitPath" 10 0.00264848412463418 4 0.00524107240802516 "carbohydrate biosynthesis" "TAIR-GO" 9 0 1 0 "circadian rhythm" "TAIR-GO" 9 0 1 0 "sucrose biosynthesis" "TAIR-GO" 9 0 1 0 "alanine degradation III" "AraCyc" 9 0.00000344037474198171 1 0.0226233352171475 "superpathway of gluconate degradation" "AraCyc" 9 0.00306462039049312 5 0.00183281518742606 "carotenoid degradation" "LitPath" 9 0.00000000122294660015244 1 0.0137283268384445 "Sec (secretory) pathway" "BioPath" 8 0.00190341432818233 2 0.0095909435452604 "photosystem I (sensu Viridiplantae)" "TAIR-GO" 8 0 1 0 "PSII associated light-harvesting complex II" "TAIR-GO" 8 0.0000168577025338304 1 0.0111792940032809 "regulation of transcription" "TAIR-GO" 8 0.00000000311686655331618 1 0 "C-compound and carbohydrate transport " "FunCat" 8 0.000000869752658718596 2 0.00210834952163943 "One carbon pool by folate" "KEGG" 8 0.0368495863805512 2 0.0556730194318525 "Other translation factors" "KEGG" 8 0.0249045176365392 2 0.117506764931583 "Thiamine metabolism" "KEGG" 8 0.00161262946667865 2 0.0113811447131684 "Ubiquinone biosynthesis" "KEGG" 8 0.00546635486163339 3 0.00376797735200438 "proton gradient regulation" "BioPath" 7 0 1 0 "fatty acid desaturation" "TAIR-GO" 7 0.0050179698584597 1 0.0311891471147117 "photosystem II assembly" "TAIR-GO" 7 0.00142885237261219 1 0.0311891471147117 "photosystem II stabilization" "TAIR-GO" 7 0.000259117459011827 1 0.0111792940032809 "signal sequence binding" "TAIR-GO" 7 0 1 0 "STRESS DATA SET" "quantDE" 1.6795 "maxDE" 3.861818 "STRESS DATA SET" "Photosystems " "BioPath" 146 1.03047946447361E-027 24 0.000000084161562131056 "Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone)" "BioPath" 145 5.16767816276954E-030 18 0.0000054780340466922 "C-compound and carbohydrate metabolism" "FunCat" 123 0.00000000000311819675610826 20 0.0197203433892171 "photosynthesis" "FunCat" 112 2.54114829859594E-074 17 0.000000000000495097819028627 "biogenesis of chloroplast" "FunCat" 111 5.24647886928931E-053 18 0.0000000000320117565213667 "Intermediary Carbon Metabolism" "BioPath" 98 0.0000809356290768372 14 0.184115592652355 "Chlorophyll biosynthesis and breakdown" "BioPath" 89 3.78238933587223E-032 11 0.00000179390397242675 "Porphyrin and chlorophyll metabolism" "KEGG" 85 1.81158563979131E-067 10 0.000000000599292988282023 "chlorophyll and phytochromobilin metabolism" "LitPath" 83 2.30080739155729E-036 10 0.000000734566309168471 "chlorophyll biosynthesis" "AraCyc" 76 9.18463190785005E-037 10 0.0000640889289737522 "glycolysis and gluconeogenesis" "FunCat" 67 0.00000000162838431161727 10 0.0303520944885796 "Ribosome" "KEGG" 66 0.0326376478010608 16 0.00733509200056575 "Carbon fixation" "KEGG" 65 2.00836473900138E-026 10 0.0000129361470511621 "additional photosystem II components" "BioPath" 61 0.000000000000277407303181357 11 0.0000132519949799198 "chlorophyll biosynthesis" "TAIR-GO" 55 1.16089160716625E-034 6 0.00000314130651529306 "protein synthesis" "FunCat" 52 0.000290986714226947 14 0.00118059996358397 "Photosynthesis" "KEGG" 49 4.29462307777493E-028 11 0.000000000458296252477149 "Calvin cycle" "AraCyc" 48 9.52563184346538E-023 9 0.0000183614229075875 "Glycolysis / Gluconeogenesis" "KEGG" 44 0.000000000418296303307882 6 0.0183552207837952 "Pentose phosphate pathway" "KEGG" 44 6.27452206889701E-022 7 0.0000722500848849616 "mRNA processing in chloroplast" "BioPath" 42 1.35630922723824E-034 8 0.0000000104631464015352 "gluconeogenesis" "AraCyc" 42 0.000000000000102909725147982 6 0.00870743371328083 "Leaf Glycerolipid Biosynthesis in Plastid" "BioPath" 41 0.0487631014038866 5 0.245859972115513 "Photosystem I" "BioPath" 39 0.0356246835862327 6 0.12611837710163 "chlorophyll biosynthesis" "LitPath" 39 1.9540012362306E-024 4 0.0000664109166699958 "biosynthesis of proto- and siroheme" "AraCyc" 36 0.0000000000277271137700656 6 0.00516348951290097 "Photosystem II" "BioPath" 35 0.00280893891347298 5 0.064817548843155 "Synthesis of membrane lipids in plastids" "AcylLipid" 35 2.17647426701236E-028 4 0.00000493907362402918 "Translation factors" "KEGG" 32 0.000000610525627137385 9 0.000800053052071083 "Protein folding / chaperonins (chloroplast)" "BioPath" 30 0.000000000000119146757593582 4 0.00247307342265369 "Translation (chloroplast)" "BioPath" 30 3.68730726270747E-024 5 0.00000102752913007071 "Carotenoid and abscisic acid metabolism" "LitPath" 20 0.0000000662093692753931 2 0.0323824253749304 "oxidative branch of the pentose phosphate pathway" "AraCyc" 28 1.8621904562157E-023 6 0.00000140855365369397 "Glycine, serine and threonine metabolism" "KEGG" 28 0.00000000106252511535283 6 0.000212984521349458 "transport " "FunCat" 27 0 6 0 "Chlorophyll a/b binding proteins" "BioPath" 26 0.000150304711059932 3 0.0473301876671683 "protein folding" "TAIR-GO" 26 0 3 0 "ascorbic acid biosynthesis" "BioPath" 24 0.0000429203418503152 3 0.0651270042926125 "Early light-inducible proteins" "BioPath" 24 0.0000000000000118779578653994 3 0.000865418434726367 "Transcription (chloroplast)" "BioPath" 24 0.00000000000216519935324265 3 0.000865418434726367 "photosystem I" "TAIR-GO" 24 3.8099748847356E-019 3 0.000267028083312289 "porphyrin biosynthesis" "TAIR-GO" 24 0.0000000000147851245703335 4 0.00041522785390472 "protein biosynthesis" "TAIR-GO" 24 0 4 0 "transcription initiation" "TAIR-GO" 24 3.20062760024285E-015 3 0.000511473005428417 "photorespiration" "AraCyc" 24 0.00000000863419570403115 7 0.000302854740467513 "chlorophyll and phyochromobilin biosynthesis" "LitPath" 24 0.000000000682177384241507 4 0.000840494671342025 "pentose-phosphate pathway " "FunCat" 22 0.0000000412202805994234 3 0.0185584286615925 "Carotenoid biosynthesis" "BioPath" 20 0.0000216226145731378 2 0.0426914560681203 "Pathway for nuclear-encoded, thylakoid-localized proteins" "BioPath" 20 0.0000573977661642603 2 0.066340054625951 "Thylakoid biogenesis and photosystem assembly" "BioPath" 20 0.00000006867435092367 2 0.0112981054966398 "photosynthesis" "TAIR-GO" 20 0.0000298776405008768 3 0.0211937285211627 "carotenoid biosynthesis" "AraCyc" 20 0.00000000737376445699615 2 0.0134142518764014 "fructose degradation (anaerobic)" "AraCyc" 20 0.0364769842229721 4 0.241175755670952 "glycolysis IV" "AraCyc" 20 0.0390541575285664 4 0.2512816856072 "serine biosynthesis" "AraCyc" 20 2.31768933075033E-018 7 0 "Biosynthesis of steroids" "KEGG" 20 0.0387798805947354 2 0.222158742072878 "Fructose and mannose metabolism" "KEGG" 20 0.00148876725090493 3 0.078399788453467 "carotenid biosynthesis" "LitPath" 20 0.000000647596726546879 2 0.0240458744349726 "Ferredoxin" "BioPath" 18 0.000000000459440600262691 4 0.000211934792646961 "light harvesting complex" "BioPath" 18 0.00000000272906106307984 2 0.00682695389867687 "psbP family of thylakoid proteins" "BioPath" 18 6.94326027707171E-017 5 0.000000156471114074994 "formaldehyde assimilation I (serine pathway)" "AraCyc" 18 0.000482169799979601 3 0.0949243716491046 "serine-isocitrate lyase pathway" "AraCyc" 18 0.0339601849687408 3 0.214635434294613 "tRNA charging pathway" "AraCyc" 18 0.0000524232071488199 5 0.0362813089253444 "Aminoacyl-tRNA biosynthesis" "KEGG" 18 0.000000230532477145245 5 0.00287549967128822 "electron transport" "TAIR-GO" 17 0.000578105818164526 2 0.0934206377121646 "photoinhibition" "TAIR-GO" 17 8.09110777986398E-017 2 0.000162187172333597 "photosystem II" "TAIR-GO" 17 0.0000000000000966593783232169 2 0.00149431032365629 "glycosylglyceride desaturation pathway" "AraCyc" 17 0.0000000000000455861241701469 2 0.000567440435762969 "chlorophyll binding" "TAIR-GO" 16 0.0000673503320546542 2 0.0309248331091501 "fatty acid biosynthesis" "TAIR-GO" 16 0.000589121967843209 2 0.045425645485203 "magnesium chelatase complex" "TAIR-GO" 16 0 2 0 "photorespiration" "TAIR-GO" 16 0.000000000000475286260091681 3 0.0000415979405304311 "response to high light intensity" "TAIR-GO" 16 9.76692371352316E-016 2 0.000162187172333597 "response to light" "TAIR-GO" 16 0.031124347614908 2 0.333121720145667 "cysteine biosynthesis I" "AraCyc" 16 0.0155816977987287 6 0.00386571404405181 "cysteine biosynthesis II" "AraCyc" 16 0.000000588104699600036 6 0.000127331874058437 "non-oxidative branch of the pentose phosphate pathway" "AraCyc" 16 0.000000000981142447828461 4 0.00036491780975096 "translation" "FunCat" 16 0.000000348457272417533 4 0.00247902250004888 "Citrate cycle (TCA cycle)" "KEGG" 16 0.00707820925543649 2 0.176280378213531 "Oxygen-evolving enhancer protein" "BioPath" 14 0.0000000222902525481006 2 0.0036103505467982 "embryonic development" "TAIR-GO" 14 0.0133530515496896 2 0.0825866013335143 "pentose-phosphate shunt" "TAIR-GO" 14 0.0000254993002516845 2 0.0247606918529327 "glyceraldehyde 3-phosphate degradation" "AraCyc" 14 0.000418047639407038 2 0.119795202593646 "transport facilitation" "FunCat" 14 0 4 0 "Chloroplastic protein import via envelope membrane" "BioPath" 13 0.0262577619336775 2 0.162889031442261 "chloroplast transport " "FunCat" 13 0.000000895103751971477 2 0.0113873137171663 "transport routes " "FunCat" 13 0.000181044691109151 2 0.0577853093495665 "chloroplast organization and biogenesis" "TAIR-GO" 12 0.000000000907307939776834 2 0.00286911933587907 "plastid large ribosomal subunit" "TAIR-GO" 12 0 2 0 "plastid organization and biogenesis" "TAIR-GO" 12 0.00000000028009869391087 2 0.000622682893780774 "RNA processing" "TAIR-GO" 12 0 2 0 "aspartate degradation II" "AraCyc" 12 0.00182353543499202 2 0.0495241200478661 "biosynthesis of pyrimidine ribonucleotides" "AraCyc" 12 0.00112678300217347 3 0.0308723800496918 "glycine biosynthesis I" "AraCyc" 12 0.0390400485097093 5 0.0245261439563098 "glycine degradation I" "AraCyc" 12 0.0000000141278380915527 3 0.000788118235291856 "glyoxylate cycle" "AraCyc" 12 0.0337994938606681 2 0.119795202593646 "phenylalanine degradation I" "AraCyc" 12 0.0262195748049571 2 0.17021654066989 "ribose degradation" "AraCyc" 12 0.0000000300416039593282 4 0.00023463443534345 "superpathway of serine and glycine biosynthesis II" "AraCyc" 12 0.000177330128977158 5 0.000760015394756615 "TCA cycle variation II" "AraCyc" 12 0.000377514435417543 2 0.0578565456946843 "biosynthesis of vitamins, cofactors, and prosthetic groups" "FunCat" 12 0.000213042135939691 2 0.0298158506294725 "aspartate/ornithin cycle / nitric oxid from glutamate" "BioPath" 10 0.0188555074340195 1 0.279308670302375 "Cytochrome b6/f complex" "BioPath" 10 0.00482041587917737 1 0.139984763967451 "Delta-pH pathway" "BioPath" 10 0.00000109005226288941 1 0.0156680508230883 "Plastoquinone biosynthesis" "BioPath" 10 0.0000000000133615426629776 1 0.00549210776206138 "Sec (secretory) pathway" "BioPath" 10 0.000000100131258921513 1 0.0298083476927147 "Tocopherol biosynthesis" "BioPath" 10 0.0022015033965285 1 0.0472736791233257 "carotene biosynthesis" "TAIR-GO" 10 0.000000152755951872855 1 0.00867701371984743 "cell death" "TAIR-GO" 10 0.00000881320364555994 1 0.0167313445459141 "chaperone cofactor dependent protein folding" "TAIR-GO" 10 0 1 0 "chloroplast thylakoid membrane protein import" "TAIR-GO" 10 0.00000380846640417587 1 0.0167313445459141 "glucose metabolism" "TAIR-GO" 10 0.0000147116172749508 1 0.0268893673607526 "pentose-phosphate shunt, oxidative branch" "TAIR-GO" 10 0.0000147116172749508 1 0.0268893673607526 "photosynthesis light harvesting" "TAIR-GO" 10 0.000342559283853279 1 0.0675726115373815 "photosystem II (sensu Viridiplantae)" "TAIR-GO" 10 0.000000515205696687265 1 0.0167313445459141 "plastoquinone biosynthesis" "TAIR-GO" 10 0.0000000018136867335433 1 0.00300046268817154 "protein binding" "TAIR-GO" 10 0.00000106124853021857 1 0.0268893673607526 "protein complex assembly" "TAIR-GO" 10 0 1 0 "RNA binding" "TAIR-GO" 10 0 1 0 "systemic acquired resistance" "TAIR-GO" 10 0.0000298666722006157 1 0.0525310128123434 "vitamin E biosynthesis" "TAIR-GO" 10 0.00000881320364555994 1 0.0167313445459141 "xanthophyll cycle" "TAIR-GO" 10 0 1 0 "xanthophyll metabolism" "TAIR-GO" 10 0 1 0 "ascorbate biosynthesis" "AraCyc" 10 0.0000111501878349326 1 0.0789474140073424 "ascorbate glutathione cycle" "AraCyc" 10 0.0102260242334375 1 0.207324390511655 "de novo biosynthesis of pyrimidine ribonucleotides" "AraCyc" 10 0.00809604104982658 2 0.108196573566174 "phospholipid desaturation pathway" "AraCyc" 10 0.0000407931894539077 1 0.0252238212504322 "plastoquinone biosynthesis" "AraCyc" 10 0.0000000671790853700342 1 0.0156794972454504 "starch degradation" "AraCyc" 10 0.00406672736134042 3 0.00663352269441232 "vitamin E biosynthesis" "AraCyc" 10 0.000169977124180481 1 0.0493742455308719 "xanthophyll cycle" "AraCyc" 10 0.000000000161073379888206 1 0.00280626366682777 "aminoacyl-tRNA-synthetases" "FunCat" 10 0.0000483971919062445 3 0.0106634594588397 "protein modification " "FunCat" 10 0.00027367817130326 1 0.189380304839541 "transported compounds (substrates)" "FunCat" 10 0 3 0 "1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradatio" "KEGG" 10 0.00000979245700993643 1 0.0381400646186174 "1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation" "KEGG" 10 0.000000776437274351663 1 0.0170392211281651 "Androgen and estrogen metabolism" "KEGG" 10 0.00000125678550554519 1 0.023305313090232 "Benzoate degradation via hydroxylation" "KEGG" 10 0.000184122133854536 1 0.046586262910105 "Diterpenoid biosynthesis" "KEGG" 10 0.00739548983409806 1 0.0652548153895686 "Protein export" "KEGG" 10 0.01793531113175 1 0.274676676901866 "metabolism of acyl-lipids in mitochondria" "AcylLipid" 10 0.00115735109994518 1 0.0643683726178581 "chlorophyll a biosynthesis" "LitPath" 10 0 1 0 "giberelin biosynthesis" "LitPath" 10 0.0493423298609597 1 0.18224426905255 "MEP (methylerythritol P) pathway, plastids" "LitPath" 10 0.00459298782174697 1 0.0978256278026524 "phytochromobilin biosynthesis" "LitPath" 10 0.00318370053326689 1 0.0616046114309406 "phytol biosynthesis" "LitPath" 10 0 1 0 "Toc apparatus" "BioPath" 9 0.036597467516963 1 0.194355514856721 "carbohydrate biosynthesis" "TAIR-GO" 9 0 1 0 "protein-chloroplast targeting" "TAIR-GO" 9 0.0000344591270895378 1 0.0268893673607526 "starch biosynthesis" "TAIR-GO" 9 0.00368847644222862 1 0.0525310128123434 "sucrose biosynthesis" "TAIR-GO" 9 0 1 0 "carbon monoxide dehydrogenase pathway" "AraCyc" 9 0.00638674019814838 4 0.0145292532193079 "protein targeting, sorting and translocation" "FunCat" 9 0.000143311204392684 1 0.0711299823056868 "carotenoid degradation" "LitPath" 9 0.00000000000165854622946288 1 0.00356241392643181 "lipid transport" "TAIR-GO" 8 0.00148437757475668 1 0.0525310128123434 "nonphotochemical quenching" "TAIR-GO" 8 0.000000170034970265194 1 0.00300046268817154 "PSII associated light-harvesting complex II" "TAIR-GO" 8 0.0000000443357995769209 1 0.00300046268817154 "regulation of transcription" "TAIR-GO" 8 0.00000000000555648964021386 1 0 "C-compound and carbohydrate transport " "FunCat" 8 0.00000000498138402612168 2 0.000474626105962353 "nucleotide metabolism" "FunCat" 8 0 2 0 "Cell division" "KEGG" 8 0.00000474329882450212 2 0.00312935579883314 "Cell Growth and Death" "KEGG" 8 0.00000474329882450212 2 0.00312935579883314 "Other translation factors" "KEGG" 8 0.000361749414950727 2 0.0278587598635379 "Ubiquinone biosynthesis" "KEGG" 8 0.0000543347799455785 3 0.000410957030339528 "phylloquinone biosynthesis" "LitPath" 8 0.0312011007463701 3 0.0323824253749304 "plastochinone and phylloquinone biosynthesis" "LitPath" 8 0.000294047895935755 3 0.0027832691718162 "proton gradient regulation" "BioPath" 7 0 1 0 "fatty acid desaturation" "TAIR-GO" 7 0.0000454179382544427 1 0.00867701371984743 "one-carbon compound metabolism" "TAIR-GO" 7 0.0000842918377271274 1 0.0167313445459141 "photosynthetic electron transport" "TAIR-GO" 7 0.00247272490186496 1 0.0388994913731894 "photosynthetic electron transport in photosystem I" "TAIR-GO" 7 0.0000454179382544427 1 0.00867701371984743 "photosystem II assembly" "TAIR-GO" 7 0.0000104569554681459 1 0.00867701371984743 "photosystem II stabilization" "TAIR-GO" 7 0.00000152960185648961 1 0.00300046268817154 "folate biosynthesis" "AraCyc" 7 0.0109187927961071 1 0.168163288359137 "HORMONE DATA SET" "quantDE" 0.9312801 "maxDE" 2.0907959 "HORMONE DATA SET" "biogenesis of chloroplast" "FunCat" 35 2.30524994732993E-027 5 0.00000448750913942237 "protein folding" "TAIR-GO" 32 0 4 0 "Leaf Glycerolipid Biosynthesis" "BioPath" 27 0.00363724805430684 3 0.193833269113074 "Leaf Glycerolipid Biosynthesis in Plastid" "BioPath" 27 0.00000000000148013274840068 3 0.00611638120513553 "glycosylglyceride desaturation pathway" "AraCyc" 27 1.35608704287228E-052 3 0.00000000224568415687666 "Synthesis of membrane lipids in plastids" "AcylLipid" 27 0 3 0 "Ribosome" "KEGG" 24 0.00192963727443586 5 0.0233898851093791 "C-compound and carbohydrate metabolism" "FunCat" 21 0.00105994859788387 3 0.138644675669264 "photosynthesis" "FunCat" 21 8.92591984743294E-016 3 0.000299324914008979 "Protein folding / chaperonins (chloroplast)" "BioPath" 20 4.44109809469189E-021 2 0.000694260788583212 "phospholipid desaturation pathway" "AraCyc" 20 1.06395104210626E-031 2 0.00000341266063915748 "1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradatio" "KEGG" 20 2.5709745946692E-028 2 0.0000539142658412203 "1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation" "KEGG" 20 4.2521023112476E-031 2 0.0000130770825549839 "Androgen and estrogen metabolism" "KEGG" 20 1.44239587905217E-030 2 0.0000227437910554034 "Benzoate degradation via hydroxylation" "KEGG" 20 4.68568724897368E-025 2 0.000076545790951283 "Chlorophyll biosynthesis and breakdown" "BioPath" 16 0.000000303660204337282 2 0.00876377794997217 "Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone)" "BioPath" 16 0.0110481161753388 2 0.0944890547580097 "chlorophyll biosynthesis" "AraCyc" 16 0.0000000000396319072114297 2 0.0059955152272085 "Folding, Sorting and Degradation" "KEGG" 16 0.0000198570760617798 3 0.0146673676574668 "Porphyrin and chlorophyll metabolism" "KEGG" 16 0.0000000000141720957389685 2 0.00168005101559864 "chlorophyll and phytochromobilin metabolism" "LitPath" 16 0.00000000734302640581398 2 0.00496812181585841 "mRNA processing in chloroplast" "BioPath" 14 1.86100286671518E-015 4 0.000000220910115525935 "plastid large ribosomal subunit" "TAIR-GO" 12 0 2 0 "protein biosynthesis" "TAIR-GO" 12 0 2 0 "biosynthesis of vitamins, cofactors, and prosthetic groups" "FunCat" 12 0.000000000000118611081249941 2 0.000138314540878806 "protein synthesis" "FunCat" 12 0.00255262275587504 4 0.00220493396368527 "Protein folding and associated processing" "KEGG" 12 0.000000000303803676695618 2 0.00150260260954306 "ascorbic acid biosynthesis" "BioPath" 10 0.00000195443753549972 1 0.0303723948804744 "Thylakoid biogenesis and photosystem assembly" "BioPath" 10 0.00000000257905528330916 1 0.00340963857462499 "cell death" "TAIR-GO" 10 0.000000000041303847807182 1 0.00161063734897204 "chaperone cofactor dependent protein folding" "TAIR-GO" 10 0 1 0 "chloroplast organization and biogenesis" "TAIR-GO" 10 0.000000000000459288449422205 1 0.00394236978202865 "development" "TAIR-GO" 10 0.00448157277828866 1 0.121212107907583 "embryonic development" "TAIR-GO" 10 0.0000290395151227623 1 0.0392132754366375 "response to temperature" "TAIR-GO" 10 0.000000000000728951536286512 1 0.000813887954833953 "systemic acquired resistance" "TAIR-GO" 10 0.000000000168263781583529 1 0.0054613734251367 "ascorbate biosynthesis" "AraCyc" 10 0.0000000000000340415498103331 1 0.00177681521439337 "chlorophyll a biosynthesis" "LitPath" 10 0 1 0 "carbohydrate biosynthesis" "TAIR-GO" 9 0 1 0 "starch biosynthesis" "TAIR-GO" 9 0.00000015475825395998 1 0.0054613734251367 "sucrose biosynthesis" "TAIR-GO" 9 0 1 0 "glycolysis and gluconeogenesis" "FunCat" 9 0.0346436859287988 1 0.226993256161348 "Carbon fixation" "KEGG" 9 0.00290460558134431 1 0.114987612632937 "carotenoid degradation" "LitPath" 9 2.32150798977355E-020 1 0.000121643402365964 "additional photosystem II components" "BioPath" 8 0.0169358956094464 1 0.092546072865761 "Early light-inducible proteins" "BioPath" 8 0.0000000283298415139365 1 0.00340963857462499 "regulation of transcription" "TAIR-GO" 8 1.03204703144395E-016 1 0 "photorespiration" "AraCyc" 8 0.000000853239537408565 2 0.00177220203745035 "Aminoacyl-tRNA biosynthesis" "KEGG" 8 0.00000306057919558409 4 0.0000259458609363887 "fatty acid desaturation" "TAIR-GO" 7 0.00000000528011917462738 1 0.000813887954833953 "photoinhibition" "TAIR-GO" 7 0.0000000105240138527566 1 0.000813887954833953 "MUTANT DATA SET" "quantDE" 0.91987 "maxDE" 3.164501047 "MUTANT DATA SET" "Cell Wall Carbohydrate Metabolism" "BioPath" 10 0.00477155139737412 1 0.168444161176948 "mRNA processing in chloroplast" "BioPath" 10 1.39109798155402E-017 1 0.000278808745800613 "pectin metabolism" "BioPath" 10 0.0000000551327135154742 1 0.0405088941950963 "Translation (chloroplast)" "BioPath" 10 4.83089980538583E-019 1 0.0000891600668287881 "protein modification " "FunCat" 10 0 1 0 "Pentose and glucuronate interconversions" "KEGG" 10 5.38562069733909E-017 1 0.000287832708898011 "Starch and sucrose metabolism" "KEGG" 10 0.00000000349866248769583 1 0.00722438568707305 "carotenoid biosynthesis" "TAIR-GO" 9 2.11170413408368E-015 1 0.00030224077631844 "Carotenoid and abscisic acid metabolism" "LitPath" 9 0.00000000193749815422473 1 0.00268576773539919 "carotenoid degradation" "LitPath" 9 1.90260584448404E-024 1 0.0000130332216820676