Pathway Hierarchy1	Pathway Hierarchy2	KEGG Pathway	Pathway ID	Gene Number	Background number	P-Value	Q-Value	Gene IDs
Metabolism	Energy metabolism	Photosynthesis - antenna proteins	ko00196	21	26	6.154366e-23	6.585171e-21	AT1G15820,AT1G29930,AT1G30000,AT4G10340,AT1G61520,AT3G27690,AT2G08665,AT2G40100,AT2G34430,AT5G54270,AT1G05207,AT3G47470,AT1G29910,AT3G54890,AT5G01530,AT2G05100,AT3G61470,AT3G08940,AT1G29920,AT2G05070,AT2G34420
Metabolism	Energy metabolism	Photosynthesis	ko00195	17	84	1.565713e-06	8.376563e-05	AT2G30790,AT1G30380,AT1G31330,AT1G06680,AT2G30570,AT1G03600,AT1G55670,AT1G30510,AT5G66570,AT1G55673,AT4G28750,AT4G12800,AT2G27510,AT1G08380,AT4G28755,AT3G50820,AT1G03130
Metabolism	Energy metabolism	Nitrogen metabolism	ko00910	12	45	2.616015e-06	9.330454e-05	AT1G37130,AT3G45060,AT3G01500,AT5G14740,AT2G41220,AT5G18170,AT3G17820,AT3G44300,AT1G77760,AT5G16570,AT3G03910,AT1G12940
Metabolism	Biosynthesis of other secondary metabolites	Flavonoid biosynthesis	ko00941	7	25	2.417596e-04	6.318589e-03	AT5G66230,AT4G22880,AT5G42800,AT5G08640,AT5G07990,AT3G51240,AT1G67980
Metabolism	Lipid metabolism	Cutin, suberine and wax biosynthesis	ko00073	9	42	2.952612e-04	6.318589e-03	AT1G72970,AT1G65450,AT1G01600,AT3G56700,AT1G02205,AT4G33790,AT1G57750,AT1G63710,AT5G37300
Metabolism	Amino acid metabolism	Alanine, aspartate and glutamate metabolism	ko00250	9	52	1.517038e-03	2.268009e-02	AT3G17820,AT5G18170,AT5G16570,AT1G23310,AT5G65010,AT2G13360,AT5G10240,AT3G03910,AT3G47340
Metabolism	Biosynthesis of other secondary metabolites	Flavone and flavonol biosynthesis	ko00944	3	5	1.384963e-03	2.268009e-02	AT5G17050,AT1G30530,AT5G07990
Metabolism	Carbohydrate metabolism	Starch and sucrose metabolism	ko00500	18	157	1.695708e-03	2.268009e-02	AT3G43190,AT1G45191,AT1G60140,AT1G61820,AT4G21760,AT1G73370,AT4G09020,AT2G22190,AT3G60130,AT1G23870,AT4G17770,AT5G10100,AT3G13790,AT2G18700,AT4G39210,AT5G55700,AT3G20440,AT1G78580
Metabolism	Biosynthesis of other secondary metabolites	Anthocyanin biosynthesis	ko00942	2	2	2.830585e-03	3.028726e-02	AT4G14090,AT5G54060
Metabolism	Biosynthesis of other secondary metabolites	Phenylpropanoid biosynthesis	ko00940	20	190	2.707274e-03	3.028726e-02	AT2G37130,AT2G22990,AT3G21560,AT5G64120,AT1G65060,AT3G49110,AT1G67980,AT1G77520,AT1G21100,AT3G21770,AT5G42180,AT4G37520,AT2G18150,AT1G05260,AT4G21760,AT1G61820,AT3G60130,AT5G66690,AT4G39330,AT1G45191
Genetic Information Processing	Translation	Ribosome biogenesis in eukaryotes	ko03008	12	98	5.677035e-03	5.522207e-02	AT3G07050,AT4G02400,AT1G56110,AT5G27120,AT4G25630,AT5G66540,AT1G63810,AT3G57150,AT1G67120,AT3G57940,AT1G06720,AT3G06530
Metabolism	Metabolism of other amino acids	Glutathione metabolism	ko00480	11	100	1.703575e-02	1.519021e-01	AT5G17220,AT2G25080,AT5G62480,AT1G78370,AT5G53120,AT4G39640,AT1G10360,AT2G02930,AT1G07890,AT5G41670,AT4G08390
Organismal Systems	Environmental adaptation	Circadian rhythm - plant	ko04712	6	46	3.399429e-02	2.797992e-01	AT1G56650,AT1G65480,AT2G46830,AT5G15850,AT1G01060,AT5G52250
Metabolism	Amino acid metabolism	Arginine biosynthesis	ko00220	5	36	4.047400e-02	3.019711e-01	AT5G16570,AT3G17820,AT5G18170,AT3G03910,AT1G23310
Metabolism	Metabolism of cofactors and vitamins	Vitamin B6 metabolism	ko00750	3	15	4.233240e-02	3.019711e-01	AT1G73010,AT4G35630,AT2G38230
Metabolism	Amino acid metabolism	Valine, leucine and isoleucine degradation	ko00280	6	50	4.835743e-02	3.233903e-01	AT5G09300,AT3G13450,AT1G50110,AT4G31810,AT5G65770,AT1G03090
Metabolism	Amino acid metabolism	Glycine, serine and threonine metabolism	ko00260	8	79	5.839487e-02	3.658525e-01	AT5G14060,AT4G34200,AT1G08630,AT1G17745,AT4G35630,AT2G13360,AT1G23310,AT1G68010
Metabolism	Biosynthesis of other secondary metabolites	Tropane, piperidine and pyridine alkaloid biosynthesis	ko00960	5	41	6.496446e-02	3.658525e-01	AT4G23600,AT2G29300,AT2G29340,AT2G29370,AT2G29290
Metabolism	Lipid metabolism	alpha-Linolenic acid metabolism	ko00592	5	41	6.496446e-02	3.658525e-01	AT1G77120,AT1G18020,AT3G25760,AT1G17420,AT3G25780
Metabolism	Carbohydrate metabolism	Glyoxylate and dicarboxylate metabolism	ko00630	8	82	6.966930e-02	3.727308e-01	AT5G16570,AT2G41220,AT3G17820,AT2G13360,AT1G68010,AT1G23310,AT4G35090,AT4G18360
Metabolism	Carbohydrate metabolism	Pentose and glucuronate interconversions	ko00040	9	98	7.663848e-02	3.904913e-01	AT4G13210,AT1G04680,AT5G57655,AT2G45220,AT1G53830,AT3G10720,AT3G53190,AT1G67750,AT3G43270
Metabolism	Amino acid metabolism	Cysteine and methionine metabolism	ko00270	10	116	8.957682e-02	4.356691e-01	AT4G23600,AT2G19590,AT1G50110,AT1G55920,AT5G53120,AT5G14060,AT5G65770,AT3G03780,AT1G12010,AT5G28020
Metabolism	Metabolism of other amino acids	Cyanoamino acid metabolism	ko00460	7	75	1.034603e-01	4.813154e-01	AT1G61820,AT5G22300,AT4G21760,AT3G44300,AT3G60130,AT1G45191,AT4G39640
Metabolism	Carbohydrate metabolism	Galactose metabolism	ko00052	6	62	1.109822e-01	4.947958e-01	AT3G47800,AT3G13790,AT1G63180,AT5G20250,AT1G56600,AT1G12780
Metabolism	Metabolism of cofactors and vitamins	Porphyrin and chlorophyll metabolism	ko00860	5	50	1.256145e-01	5.376300e-01	AT4G25080,AT5G13630,AT1G74470,AT3G56940,AT1G44446
Metabolism	Amino acid metabolism	Valine, leucine and isoleucine biosynthesis	ko00290	3	25	1.455183e-01	5.988638e-01	AT1G50110,AT2G31810,AT5G65770
Metabolism	Metabolism of cofactors and vitamins	Riboflavin metabolism	ko00740	2	14	1.690825e-01	6.461365e-01	AT5G59750,AT1G25230
Metabolism	Overview	Biosynthesis of amino acids	ko01230	18	263	1.642141e-01	6.461365e-01	AT1G08630,AT1G17745,AT3G03780,AT2G39800,AT5G14060,AT1G55920,AT1G23310,AT1G50110,AT4G23600,AT4G34200,AT5G28020,AT4G35630,AT2G31810,AT5G65770,AT1G79530,AT3G17820,AT3G55610,AT5G16570
Metabolism	Lipid metabolism	Fatty acid biosynthesis	ko00061	4	44	2.053217e-01	7.575663e-01	AT1G49430,AT3G04000,AT2G47240,AT1G43800
Metabolism	Biosynthesis of other secondary metabolites	Stilbenoid, diarylheptanoid and gingerol biosynthesis	ko00945	5	62	2.336775e-01	7.576816e-01	AT2G30750,AT5G25140,AT1G13710,AT3G48360,AT1G67980
Metabolism	Lipid metabolism	Arachidonic acid metabolism	ko00590	2	17	2.283460e-01	7.576816e-01	AT2G25080,AT4G39640
Metabolism	Metabolism of terpenoids and polyketides	Carotenoid biosynthesis	ko00906	3	31	2.270740e-01	7.576816e-01	AT4G19170,AT5G52570,AT2G29090
Metabolism	Overview	Carbon metabolism	ko01200	18	278	2.269460e-01	7.576816e-01	AT5G18170,AT5G41670,AT1G79530,AT5G28020,AT4G35630,AT4G34200,AT3G14940,AT5G50950,AT1G13700,AT1G68010,AT4G35090,AT4G31810,AT1G23310,AT3G03910,AT2G13360,AT1G55920,AT1G17745,AT4G18360
Cellular Processes	Transport and catabolism	Peroxisome	ko04146	7	98	2.664534e-01	7.823357e-01	AT4G35090,AT4G18360,AT2G13360,AT2G47240,AT1G49430,AT3G56700,AT4G33790
Genetic Information Processing	Transcription	RNA polymerase	ko03020	4	48	2.514907e-01	7.823357e-01	AT3G57660,AT5G45140,AT3G13940,ATCG00190
Metabolism	Carbohydrate metabolism	Amino sugar and nucleotide sugar metabolism	ko00520	10	149	2.705273e-01	7.823357e-01	AT1G31070,AT1G74910,AT3G10740,AT3G02230,AT1G63180,AT1G65590,AT4G39210,AT2G43620,AT1G12780,AT2G28760
Metabolism	Metabolism of cofactors and vitamins	Pantothenate and CoA biosynthesis	ko00770	3	33	2.559785e-01	7.823357e-01	AT1G50110,AT5G65770,AT2G31810
Metabolism	Glycan biosynthesis and metabolism	Glycosphingolipid biosynthesis - ganglio series	ko00604	1	6	2.799470e-01	7.882719e-01	AT1G65590
Metabolism	Carbohydrate metabolism	Propanoate metabolism	ko00640	3	37	3.149672e-01	8.641409e-01	AT4G31810,AT3G13450,AT5G09300
Genetic Information Processing	Replication and repair	Non-homologous end-joining	ko03450	1	9	3.890413e-01	8.856897e-01	AT2G31970
Metabolism	Amino acid metabolism	Arginine and proline metabolism	ko00330	4	55	3.362665e-01	8.856897e-01	AT3G55610,AT2G39800,AT5G53120,AT3G30775
Metabolism	Biosynthesis of other secondary metabolites	Isoquinoline alkaloid biosynthesis	ko00950	2	25	3.875279e-01	8.856897e-01	AT4G23600,AT4G28680
Metabolism	Carbohydrate metabolism	Ascorbate and aldarate metabolism	ko00053	3	42	3.888968e-01	8.856897e-01	AT4G08390,AT1G14520,AT1G07890
Metabolism	Lipid metabolism	Fatty acid degradation	ko00071	3	42	3.888968e-01	8.856897e-01	AT1G77120,AT2G47240,AT1G49430
Metabolism	Lipid metabolism	Linoleic acid metabolism	ko00591	1	9	3.890413e-01	8.856897e-01	AT1G17420
Metabolism	Metabolism of terpenoids and polyketides	Brassinosteroid biosynthesis	ko00905	1	9	3.890413e-01	8.856897e-01	AT5G05690
Metabolism	Nucleotide metabolism	Pyrimidine metabolism	ko00240	8	129	3.811023e-01	8.856897e-01	AT5G45140,AT3G57660,AT5G14580,AT1G14250,ATCG00190,AT4G20320,AT3G13940,AT1G08260
Environmental Information Processing	Membrane transport	ABC transporters	ko02010	2	28	4.439123e-01	8.965044e-01	AT1G02520,AT3G28345
Metabolism	Amino acid metabolism	Phenylalanine metabolism	ko00360	3	46	4.466358e-01	8.965044e-01	AT4G23600,AT1G65060,AT1G67980
Metabolism	Amino acid metabolism	Tyrosine metabolism	ko00350	3	45	4.323840e-01	8.965044e-01	AT4G23600,AT1G77120,AT4G28680
Metabolism	Glycan biosynthesis and metabolism	Glycosphingolipid biosynthesis - globo and isoglobo series	ko00603	1	11	4.524414e-01	8.965044e-01	AT1G65590
Metabolism	Lipid metabolism	Glycerolipid metabolism	ko00561	4	63	4.341087e-01	8.965044e-01	AT2G38110,AT1G73480,AT2G11810,AT4G01950
Metabolism	Metabolism of terpenoids and polyketides	Terpenoid backbone biosynthesis	ko00900	4	63	4.341087e-01	8.965044e-01	AT4G34350,AT1G76490,AT5G58780,AT1G74470
Metabolism	Overview	2-Oxocarboxylic acid metabolism	ko01210	5	79	4.127315e-01	8.965044e-01	AT2G31810,AT5G14060,AT5G65770,AT1G23310,AT1G50110
Metabolism	Carbohydrate metabolism	C5-Branched dibasic acid metabolism	ko00660	1	12	4.816346e-01	9.202660e-01	AT2G31810
Metabolism	Glycan biosynthesis and metabolism	Glycosaminoglycan degradation	ko00531	1	12	4.816346e-01	9.202660e-01	AT1G65590
Cellular Processes	Transport and catabolism	Phagosome	ko04145	5	98	6.036642e-01	9.572972e-01	AT2G29550,AT1G64740,AT5G61790,AT4G17730,AT1G75780
Metabolism	Amino acid metabolism	Lysine biosynthesis	ko00300	1	16	5.836753e-01	9.572972e-01	AT5G14060
Metabolism	Amino acid metabolism	Tryptophan metabolism	ko00380	3	52	5.287171e-01	9.572972e-01	AT2G30766,AT4G35090,AT3G44300
Metabolism	Biosynthesis of other secondary metabolites	Monobactam biosynthesis	ko00261	1	14	5.354427e-01	9.572972e-01	AT5G14060
Metabolism	Lipid metabolism	Biosynthesis of unsaturated fatty acids	ko01040	2	32	5.143538e-01	9.572972e-01	AT1G43800,AT3G04000
Metabolism	Lipid metabolism	Fatty acid elongation	ko00062	2	38	6.083758e-01	9.572972e-01	AT5G04530,AT2G28630
Metabolism	Lipid metabolism	Steroid biosynthesis	ko00100	2	37	5.937145e-01	9.572972e-01	AT3G45130,AT5G24160
Metabolism	Metabolism of cofactors and vitamins	Biotin metabolism	ko00780	1	16	5.836753e-01	9.572972e-01	AT3G04000
Metabolism	Metabolism of cofactors and vitamins	Nicotinate and nicotinamide metabolism	ko00760	1	16	5.836753e-01	9.572972e-01	AT3G62040
Metabolism	Metabolism of cofactors and vitamins	Ubiquinone and other terpenoid-quinone biosynthesis	ko00130	2	36	5.786471e-01	9.572972e-01	AT1G65060,AT4G23600
Metabolism	Metabolism of other amino acids	Taurine and hypotaurine metabolism	ko00430	1	16	5.836753e-01	9.572972e-01	AT4G39640
Metabolism	Overview	Fatty acid metabolism	ko01212	4	72	5.387586e-01	9.572972e-01	AT1G43800,AT2G47240,AT1G49430,AT3G04000
Metabolism	Carbohydrate metabolism	Butanoate metabolism	ko00650	1	19	6.468151e-01	9.934691e-01	AT2G31810
Metabolism	Energy metabolism	Sulfur metabolism	ko00920	2	41	6.499330e-01	9.934691e-01	AT5G28020,AT1G55920
Cellular Processes	Transport and catabolism	Autophagy - other eukaryotes	ko04136	1	40	8.884835e-01	1.000000e+00	AT2G45170
Cellular Processes	Transport and catabolism	Endocytosis	ko04144	3	181	9.970598e-01	1.000000e+00	AT3G17660,AT4G35730,AT5G44560
Environmental Information Processing	Signal transduction	MAPK signaling pathway - plant	ko04016	4	135	9.341550e-01	1.000000e+00	AT4G35090,AT1G07430,AT4G36450,AT3G11410
Environmental Information Processing	Signal transduction	Plant hormone signal transduction	ko04075	14	312	7.840558e-01	1.000000e+00	AT2G46690,AT1G66350,AT3G50750,AT3G11410,AT4G27260,AT5G13370,AT1G28130,AT4G38860,AT5G17490,AT1G77920,AT1G07430,AT5G54510,AT2G36270,AT2G41370
Genetic Information Processing	Folding, sorting and degradation	Protein export	ko03060	2	58	8.225556e-01	1.000000e+00	AT5G28540,AT5G42020
Genetic Information Processing	Folding, sorting and degradation	Protein processing in endoplasmic reticulum	ko04141	8	227	9.225337e-01	1.000000e+00	AT5G61790,AT1G30000,AT5G28540,AT5G56010,AT3G53800,AT1G02620,AT5G42020,AT4G03510
Genetic Information Processing	Folding, sorting and degradation	RNA degradation	ko03018	4	124	9.028713e-01	1.000000e+00	AT5G14580,AT3G13470,AT5G56500,AT2G33210
Genetic Information Processing	Folding, sorting and degradation	SNARE interactions in vesicular transport	ko04130	2	51	7.634122e-01	1.000000e+00	AT1G08560,AT4G17730
Genetic Information Processing	Folding, sorting and degradation	Ubiquitin mediated proteolysis	ko04120	5	155	9.214667e-01	1.000000e+00	AT4G33260,AT5G13840,AT5G52250,AT4G33270,AT5G22920
Genetic Information Processing	Replication and repair	Base excision repair	ko03410	2	47	7.224396e-01	1.000000e+00	AT1G13635,AT1G08260
Genetic Information Processing	Replication and repair	DNA replication	ko03030	1	61	9.648820e-01	1.000000e+00	AT1G08260
Genetic Information Processing	Replication and repair	Homologous recombination	ko03440	3	81	8.133714e-01	1.000000e+00	AT1G05490,AT2G31970,AT5G20420
Genetic Information Processing	Replication and repair	Nucleotide excision repair	ko03420	1	80	9.876826e-01	1.000000e+00	AT1G08260
Genetic Information Processing	Transcription	Spliceosome	ko03040	1	217	9.999940e-01	1.000000e+00	AT5G61030
Genetic Information Processing	Translation	mRNA surveillance pathway	ko03015	3	128	9.699932e-01	1.000000e+00	AT5G03470,AT5G43620,AT1G66500
Genetic Information Processing	Translation	Ribosome	ko03010	2	369	1.000000e+00	1.000000e+00	AT1G64880,AT3G28500
Genetic Information Processing	Translation	RNA transport	ko03013	3	199	9.987169e-01	1.000000e+00	AT1G79280,AT2G44070,AT1G53870
Metabolism	Amino acid metabolism	Phenylalanine, tyrosine and tryptophan biosynthesis	ko00400	1	58	9.585726e-01	1.000000e+00	AT4G23600
Metabolism	Carbohydrate metabolism	Citrate cycle (TCA cycle)	ko00020	1	65	9.718280e-01	1.000000e+00	AT5G50950
Metabolism	Carbohydrate metabolism	Fructose and mannose metabolism	ko00051	2	70	8.937596e-01	1.000000e+00	AT5G57655,AT1G74910
Metabolism	Carbohydrate metabolism	Glycolysis / Gluconeogenesis	ko00010	4	121	8.923175e-01	1.000000e+00	AT1G79530,AT1G77120,AT3G61610,AT3G47800
Metabolism	Carbohydrate metabolism	Inositol phosphate metabolism	ko00562	1	73	9.818755e-01	1.000000e+00	AT1G14520
Metabolism	Carbohydrate metabolism	Pentose phosphate pathway	ko00030	2	59	8.298291e-01	1.000000e+00	AT1G13700,AT5G41670
Metabolism	Carbohydrate metabolism	Pyruvate metabolism	ko00620	2	92	9.604635e-01	1.000000e+00	AT5G50950,AT3G14940
Metabolism	Energy metabolism	Carbon fixation in photosynthetic organisms	ko00710	3	73	7.540255e-01	1.000000e+00	AT3G14940,AT1G23310,AT1G79530
Metabolism	Energy metabolism	Oxidative phosphorylation	ko00190	1	181	9.999547e-01	1.000000e+00	AT2G18230
Metabolism	Glycan biosynthesis and metabolism	N-Glycan biosynthesis	ko00510	1	48	9.281695e-01	1.000000e+00	AT1G30000
Metabolism	Glycan biosynthesis and metabolism	Other glycan degradation	ko00511	1	22	7.003952e-01	1.000000e+00	AT1G65590
Metabolism	Lipid metabolism	Glycerophospholipid metabolism	ko00564	4	97	7.666398e-01	1.000000e+00	AT2G38110,AT3G18000,AT1G73600,AT4G01950
Metabolism	Lipid metabolism	Sphingolipid metabolism	ko00600	1	32	8.269377e-01	1.000000e+00	AT3G58490
Metabolism	Metabolism of other amino acids	beta-Alanine metabolism	ko00410	2	47	7.224396e-01	1.000000e+00	AT5G53120,AT4G31810
Metabolism	Metabolism of other amino acids	Selenocompound metabolism	ko00450	1	20	6.656611e-01	1.000000e+00	AT3G03780
Metabolism	Metabolism of terpenoids and polyketides	Diterpenoid biosynthesis	ko00904	1	22	7.003952e-01	1.000000e+00	AT1G30040
Metabolism	Metabolism of terpenoids and polyketides	Sesquiterpenoid and triterpenoid biosynthesis	ko00909	1	29	7.959514e-01	1.000000e+00	AT5G24160
Metabolism	Metabolism of terpenoids and polyketides	Zeatin biosynthesis	ko00908	1	22	7.003952e-01	1.000000e+00	AT5G05860
Metabolism	Nucleotide metabolism	Purine metabolism	ko00230	7	171	8.126221e-01	1.000000e+00	AT5G45140,AT3G57660,AT5G14580,ATCG00190,AT1G08260,AT3G13940,AT1G14250
Organismal Systems	Environmental adaptation	Plant-pathogen interaction	ko04626	4	209	9.965033e-01	1.000000e+00	AT1G12220,AT4G26090,AT5G56010,AT3G10190