"Pathway"	"Pathway.source"	"V3"	"V4"	"V5"	"V6"
"IN THREE DATA SETS"		"sum.of.scores"	"sum.of.genes"		
"ORGAN DATA SET"	"quantDE"	5.986086	"maxDE"	6.8785709	"ORGAN DATA SET"
"Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone)"	"BioPath"	92	9.29986257800686E-024	12	0.000029639525160057
"Phenylpropanoid Metabolism"	"BioPath"	63	0.00156273018641323	8	0.300045552349325
"Carotenoid and abscisic acid metabolism"	"LitPath"	55	2.33335670896177E-034	8	0.000000168601764311796
"Folding, Sorting and Degradation"	"KEGG"	51	5.87259023537597E-019	7	0.00118933736860938
"biogenesis of chloroplast"	"FunCat"	46	1.95961650125294E-017	7	0.00023479460289367
"Biosynthesis of steroids"	"KEGG"	46	1.14615243957421E-022	6	0.0000282167265791875
"Carotenoid biosynthesis"	"BioPath"	44	1.16067980930192E-035	5	0.00000193204822793165
"carotenoid biosynthesis"	"AraCyc"	44	3.393928900335E-046	5	0.000000052180131647967
"carotenid biosynthesis"	"LitPath"	44	7.18314215508065E-034	5	0.00000466589107303083
"Glucosyltransferases for benzoic acids"	"BioPath"	40	5.12522072004088E-024	4	0.000120607094205933
"ATP-dependent proteolysis"	"TAIR-GO"	38	5.14550865876571E-049	8	0.00000000000164845094781646
"Biosynthesis of prenyl diphosphates"	"BioPath"	34	0.00000138509096838012	5	0.0094318545473542
"Chloroplastic protein turnover"	"BioPath"	34	5.6515254965157E-032	7	0.00000000339981144432121
"Pathway for nuclear-encoded, thylakoid-localized proteins"	"BioPath"	34	2.16991110439638E-022	4	0.000120607094205933
"Protein export"	"KEGG"	34	4.31415948855652E-027	4	0.000231279832360611
"ClpP protease complex "	"BioPath"	24	5.26691382392698E-026	6	0.00000000669113427968474
"Miscellaneous acyl lipid metabolism"	"AcylLipid"	24	0.0000306386345672214	5	0.0270695644874992
"C-compound and carbohydrate utilization "	"FunCat"	22	0	3	0
"degradation "	"FunCat"	21	0.0000000000012746208880822	4	0.000625946886578818
"protein degradation "	"FunCat"	21	5.67595072029546E-016	4	0.00012912385113017
"IPP (isopentenyl diphosphate) and DMAPP (dimethylallyl diphosphat) biosynthesis"	"LitPath"	20	0.0000476664241073718	3	0.0159103331719959
"MEP (methylerythritol P) pathway, plastids"	"LitPath"	20	0.0000000000085447872389225	3	0.000623341866361914
"carotene biosynthesis"	"TAIR-GO"	18	1.98528762471286E-022	2	0.0000363530094926693
"xanthophyll cycle"	"AraCyc"	18	0	2	0
"Glyoxylate and dicarboxylate metabolism"	"KEGG"	18	0.0000000054133283864915	4	0.000194428233598099
"Tryptophan metabolism"	"KEGG"	18	0.0000000020339583130027	3	0.00438292045320038
"photorespiration"	"AraCyc"	17	0.00000000941909799577262	4	0.00166000757136401
"transport "	"FunCat"	17	9.90489986333851E-029	4	0
"Protein folding and associated processing"	"KEGG"	17	0.000000000516757272819961	3	0.00159503089633669
"chloroplastic endopeptidase Clp complex"	"TAIR-GO"	16	5.92408228241676E-019	4	0.000000736812675821404
"Methane metabolism"	"KEGG"	16	0.00000896961091461079	4	0.0222361163292076
"Delta-pH pathway"	"BioPath"	14	4.83968258062906E-015	2	0.0000734014374920514
"mRNA processing in chloroplast"	"BioPath"	14	0.0000000263585094225067	2	0.0122048309238182
"response to water deprivation"	"TAIR-GO"	14	0	2	0
"isopentenyl diphosphate biosynthesis -- mevalonate-independent"	"AraCyc"	14	0.000000000000243077715011883	2	0.000324327456530694
"Carbon fixation"	"KEGG"	14	0.0182162459854921	3	0.0401989754909064
"Chloroplastic protein import via envelope membrane"	"BioPath"	13	0.0000954368496284193	2	0.043388270844763
"glycine biosynthesis I"	"AraCyc"	13	0.0000363857925300001	3	0.0246087402424529
"superpathway of serine and glycine biosynthesis II"	"AraCyc"	13	0.0000000175931045524643	3	0.00221310321343801
"transport routes "	"FunCat"	13	0.000000144007451694873	2	0.0126663750879597
"jasmonic acid biosynthesis"	"TAIR-GO"	12	0.000492172261709906	2	0.02393147144078
"response to ethylene stimulus"	"TAIR-GO"	12	0.00000000772049201554137	3	0.000905794101877121
"jasmonic acid biosynthesis"	"AraCyc"	12	0.0000242704989601493	2	0.0105368952253326
"phenylalanine degradation I"	"AraCyc"	12	0.0000820726094467255	3	0.00480490890111947
"biosynthesis of derivatives of homoisopentenyl pyrophosphate "	"FunCat"	12	0.00000834364544675083	2	0.00750243563624037
"Synthesis of membrane lipids in plastids"	"AcylLipid"	12	0.0000627330775344784	2	0.00450285022331858
"ascorbic acid biosynthesis"	"BioPath"	10	0.0294976752763681	2	0.0560490361743336
"ERD1 protease (ClpC-like)"	"BioPath"	10	0	1	0
"salycilic acid biosynthesis"	"BioPath"	10	0.000000156433510479431	1	0.0100316935262417
"Sec (secretory) pathway"	"BioPath"	10	0.000000000163730558191317	1	0.0100316935262417
"SRP (signal recognition particle)-dependent pathway for integral membrane proteins"	"BioPath"	10	0.0000329746545940643	1	0.0237215345382726
"Transcriptional regulators (chloroplast)"	"BioPath"	10	0.000000000163730558191317	1	0.00176830735776306
"aromatic amino acid family biosynthesis"	"TAIR-GO"	10	0.00090248712263447	1	0.0781274135622317
"aromatic amino acid family biosynthesis, shikimate pathway"	"TAIR-GO"	10	0.000157491132035414	1	0.0591438941990954
"cell plate formation (sensu Magnoliophyta)"	"TAIR-GO"	10	0.00000000000495887495817637	1	0.00111387893148632
"chloroplast thylakoid membrane protein import"	"TAIR-GO"	10	0.0000000152910136353	1	0.00639595498174908
"chloroplast-nucleus signaling pathway"	"TAIR-GO"	10	0.00000000120075264019445	1	0.00326893077547362
"fatty acid biosynthesis"	"TAIR-GO"	10	0.00238747155779534	1	0.0882443095709696
"glucosinolate catabolism"	"TAIR-GO"	10	0.00000000000229837056596629	1	0.00111387893148632
"isoprenoid biosynthesis"	"TAIR-GO"	10	0.000000455776252982135	1	0.010429108543697
"photoinhibition"	"TAIR-GO"	10	0.000000000313090530809402	1	0.00326893077547362
"photosystem I"	"TAIR-GO"	10	0.000000292385476328144	1	0.0209663719874844
"photosystem II"	"TAIR-GO"	10	0.0000000110661645499339	1	0.010429108543697
"photosystem II (sensu Viridiplantae)"	"TAIR-GO"	10	0.00000000180710423293866	1	0.00639595498174908
"phytochromobilin biosynthesis"	"TAIR-GO"	10	0.00000000120075264019445	1	0.00326893077547362
"positive regulation of transcription"	"TAIR-GO"	10	0.000000000783231298670064	1	0.00326893077547362
"regulation of transcription"	"TAIR-GO"	10	0	1	0
"RNA binding"	"TAIR-GO"	10	0	1	0
"RNA processing"	"TAIR-GO"	10	0	1	0
"thylakoid membrane organization and biogenesis"	"TAIR-GO"	10	0	1	0
"xanthophyll cycle"	"TAIR-GO"	10	0	1	0
"xanthophyll metabolism"	"TAIR-GO"	10	0	1	0
"glycosylglyceride desaturation pathway"	"AraCyc"	10	0.0000000020982406022839	1	0.00389600979493148
"phospholipid desaturation pathway"	"AraCyc"	10	0.0000000668892276303175	1	0.00638315300525842
"threonine degradation"	"AraCyc"	10	0.00000206274850905528	4	0.000158896974217775
"biosynthesis of glycosides"	"FunCat"	10	0.000000000000223349763763342	1	0.00227042751704751
"metabolismn of primary metabolic sugars derivatives "	"FunCat"	10	0.000000000000223349763763342	1	0.00227042751704751
"stress response"	"FunCat"	10	0	1	0
"1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradatio"	"KEGG"	10	0.0000000502188116279116	1	0.0130244970123481
"1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation"	"KEGG"	10	0.00000000331718930628305	1	0.00564287406070637
"Androgen and estrogen metabolism"	"KEGG"	10	0.00000000553573396500424	1	0.0077977568264658
"Ascorbate and aldarate metabolism"	"KEGG"	10	0.00165577327341437	2	0.0129604241613576
"Benzoate degradation via hydroxylation"	"KEGG"	10	0.00000127696780997456	1	0.0160708116287095
"Fluorene degradation"	"KEGG"	10	0.0000232331632853856	2	0.00296014592813563
"Fructose and mannose metabolism"	"KEGG"	10	0.0383225191591077	2	0.063521078048315
"gamma-Hexachlorocyclohexane degradation"	"KEGG"	10	0.0000897950548299908	2	0.00429819374772886
"Glutathione metabolism"	"KEGG"	10	0.0231806895725447	1	0.205241830712275
"abscisic acid biosynthesis"	"LitPath"	10	0.0000404760079748261	2	0.00589217323138198
"chorismate biosynthesis"	"LitPath"	10	0.00966544600696564	1	0.159390032811761
"phytochromobilin biosynthesis"	"LitPath"	10	0.000418819546096208	1	0.04606701238966
"polyprenyl diphosphate biosynthesis"	"LitPath"	10	0.00000228890686066214	1	0.0594586254424194
"Toc apparatus"	"BioPath"	9	0.00053355498066579	1	0.0758079928947017
"histidine biosynthesis"	"TAIR-GO"	9	0.00000000254565935602093	1	0.00326893077547362
"phenylpropanoid metabolism"	"TAIR-GO"	9	0.000018135868657374	1	0.0153057638337438
"photorespiration"	"TAIR-GO"	9	0.0000000784693128156932	1	0.010429108543697
"protein-chloroplast targeting"	"TAIR-GO"	9	0.000000251675079302346	1	0.010429108543697
"histidine biosynthesis"	"AraCyc"	9	0.0000818768979107381	1	0.0635997625563693
"histidine biosynthesis I"	"AraCyc"	9	0.0000304758483201346	1	0.0565884604604715
"C-compound, carbohydrate catabolism"	"FunCat"	9	0.0100119876619934	3	0.0261534059528588
"chloroplast transport "	"FunCat"	9	0.00000335072263354461	1	0.0299806769626047
"protein targeting, sorting and translocation"	"FunCat"	9	0.000000612074079646886	1	0.024422398861779
"Glycine, serine and threonine metabolism"	"KEGG"	9	0.0167800282278201	1	0.161735746512191
"Histidine metabolism"	"KEGG"	9	0.0000345590472796961	1	0.0543892152964132
"biosynthesis of extracellular lipids"	"LitPath"	9	0	1	0
"Thylakoid biogenesis and photosystem assembly"	"BioPath"	8	0.00328114839876579	1	0.0323033102900261
"abscisic acid biosynthesis"	"TAIR-GO"	8	0.000470012273763242	1	0.0420998855673721
"carotenoid biosynthesis"	"TAIR-GO"	8	0.00033892631327589	1	0.027354331632009
"hydrogen peroxide catabolism"	"TAIR-GO"	8	0	2	0
"response to osmotic stress"	"TAIR-GO"	8	0.0000000721991007083722	1	0.00639595498174908
"sugar mediated signaling"	"TAIR-GO"	8	0.0000469026124917738	1	0.0153057638337438
"xanthophyll biosynthesis "	"TAIR-GO"	8	0	1	0
"4-hydroxyproline degradation"	"AraCyc"	8	0.0000190668947719911	1	0.0317040739962292
"acetyl-CoA assimilation"	"AraCyc"	8	0.0465815324586709	2	0.0493065432179616
"arginine degradation IX"	"AraCyc"	8	0.0000190668947719911	1	0.0374084339181312
"methylglyoxal degradation"	"AraCyc"	8	0.0000103283573812202	3	0.000355599258749108
"proline degradation I"	"AraCyc"	8	0.00282207371646175	1	0.110823992656323
"proline degradation II"	"AraCyc"	8	0.0000141312839289415	1	0.0317040739962292
"starch degradation"	"AraCyc"	8	0.00041193812268294	2	0.00621779013994264
"biosynthesis of vitamins, cofactors, and prosthetic groups"	"FunCat"	8	0.000351400285272903	1	0.0564178959215907
"secondary biosynthesis of derivatives of homoisopentenyl pyrophosphate "	"FunCat"	8	0	1	0
"Photosynthesis"	"KEGG"	8	0.0279348432096777	3	0.00392623482090944
"protein modification "	"FunCat"	7	0.000274896413886778	2	0.00904951007534988
"STRESS DATA SET"	"quantDE"	1.173229	"maxDE"	9.518386	"STRESS DATA SET"
"cell death"	"TAIR-GO"	10	3.831005495192E-024	1	0.00000311574526289879
"fatty acid alpha-oxidation"	"TAIR-GO"	10	0	1	0
"jasmonic acid biosynthesis"	"AraCyc"	10	1.12966531291748E-018	1	0.000114566708796863
"lipoxygenase pathway"	"AraCyc"	10	8.6611332215901E-021	1	0.0000495202955826085
"Lipid signaling"	"AcylLipid"	10	0.0000169820653333815	1	0.0619469026548673
"HORMONE DATA SET"	"quantDE"	3.595618	"maxDE"	5.0887684	"HORMONE DATA SET"
"Transporters required for plastid development"	"BioPath"	10	0	1	0
"iron ion homeostasis"	"TAIR-GO"	10	0	1	0
"cation transport (Na, K, Ca , NH4, etc.) "	"FunCat"	10	1.49592279030172E-021	1	0.00000926434976613799
"heavy metal ion transport (Cu, Fe, etc.)"	"FunCat"	10	1.39341918871144E-023	1	0.00000309076335673385
"ion transport "	"FunCat"	10	0	1	0
"transport "	"FunCat"	10	3.57265188301642E-023	1	0.00000926434976613799
"transport facilitation"	"FunCat"	10	0	1	0.00000926434976613799
"transported compounds (substrates)"	"FunCat"	10	0	1	0
"MUTANT DATA SET"	"quantDE"	2.883799	"maxDE"	6.651088631	"MUTANT DATA SET"