darkorange

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Trait PCC P value
Silique 0.42 8.0⋅10-147
Seed 0.4 5.0⋅10-133
Endosperm 0.2 1.0⋅10-32
Replum 0.099 4.0⋅10-9
Embryo 0.098 6.0⋅10-9
Suspensor 0.064 2.0⋅10-4
Aerial tissue -0.06 4.0⋅10-4
Leaf -0.064 2.0⋅10-4
Rosette -0.069 4.0⋅10-5
Seedling -0.16 2.0⋅10-22
Module Enrichments

Gene Ontology: Biological Process
Rank Pvalue Hits Over-representation Accession Biological Process
1 1.5⋅10-2 10/407 (2.5%) 4.3 GO:0019748 secondary metabolic process
2 1.5⋅10-2 15/855 (1.8%) 3.1 GO:0006629 lipid metabolic process
Gene Ontology: Molecular Function
Rank Pvalue Hits Over-representation Accession Molecular Function
1 6.0⋅10-4 11/322 (3.4%) 5.4 GO:0052689 carboxylic ester hydrolase activity
2 1.2⋅10-3 5/54 (9.3%) 14.5 GO:0045735 nutrient reservoir activity
3 1.6⋅10-3 4/32 (12.5%) 19.6 GO:0030145 manganese ion binding
4 3.0⋅10-3 2/3 (66.7%) 104.7 GO:0052691 UDP-arabinopyranose mutase activity
5 3.9⋅10-2 7/278 (2.5%) 4 GO:0008289 lipid binding
6 4.1⋅10-2 14/945 (1.5%) 2.3 GO:0016788 hydrolase activity, acting on ester bonds
7 4.6⋅10-2 7/304 (2.3%) 3.6 GO:0005506 iron ion binding
Gene Ontology: Cellular Component
Rank Pvalue Hits Over-representation Accession Cellular Component
1 3.4⋅10-12 39/2023 (1.9%) 3.7 GO:0005576 extracellular region
Plant Ontology: Plant Anatomy
Rank Pvalue Hits Over-representation Accession Plant Anatomy
1 2.8⋅10-7 8/82 (9.8%) 23.1 PO:0009089 endosperm
2 1.1⋅10-6 16/667 (2.4%) 5.7 PO:0000019 gynoecium primordium
3 1.1⋅10-5 14/611 (2.3%) 5.4 PO:0009001 fruit
4 2.3⋅10-4 4/29 (13.8%) 32.7 PO:0009088 seed coat
5 9.3⋅10-4 2/3 (66.7%) 157.9 PO:0000010 cultured plant embryo
6 9.3⋅10-4 2/3 (66.7%) 157.9 PO:0000011 cultured somatic plant embryo
7 9.3⋅10-4 2/3 (66.7%) 157.9 PO:0006091 embryogenic callus
8 9.3⋅10-4 2/3 (66.7%) 157.9 PO:0025302 somatic plant embryo
9 1.7⋅10-3 2/4 (50.0%) 118.4 PO:0000009 cultured plant callus
10 2.5⋅10-3 2/5 (40.0%) 94.8 PO:0005052 plant callus
Plant Ontology: Plant Structure Development Stage
Rank Pvalue Hits Over-representation Accession Plant Structure Development Stage
1 1.3⋅10-3 4/58 (6.9%) 17.9 PO:0004505 fertilized ovule stage
2 1.3⋅10-3 4/57 (7.0%) 18.2 PO:0007633 endosperm development stage
3 1.3⋅10-3 4/55 (7.3%) 18.8 PO:0004506 developing seed stage
4 1.6⋅10-3 8/388 (2.1%) 5.3 PO:0001170 seed development stage
WikiPathways
Rank Pvalue Hits Over-representation WikiPathways Description
KEGG
Rank Pvalue Hits Over-representation Entry Name
1 3.0⋅10-2 3/136 (2.2%) 4.9 ath00940 Phenylpropanoid biosynthesis - Arabidopsis thaliana (thale cress)
2 3.0⋅10-2 2/50 (4.0%) 8.9 ath00460 Cyanoamino acid metabolism - Arabidopsis thaliana (thale cress)
3 3.0⋅10-2 3/122 (2.5%) 5.5 ath00520 Amino sugar and nucleotide sugar metabolism - Arabidopsis thaliana (thale cress)
4 3.0⋅10-2 9/945 (1.0%) 2.1 ath01110 Biosynthesis of secondary metabolites - Arabidopsis thaliana (thale cress)
5 3.0⋅10-2 4/187 (2.1%) 4.8 ath00500 Starch and sucrose metabolism - Arabidopsis thaliana (thale cress)
AraCyc
Rank Pvalue Hits Over-representation PathwayID Pathway Name
1 1.9⋅10-2 4/86 (4.7%) 4.7 LIPAS-PWY triacylglycerol degradation
2 1.9⋅10-2 2/13 (15.4%) 15.4 PWY-1782 superpathway of indole-3-acetate conjugate biosynthesis
3 3.9⋅10-2 2/27 (7.4%) 7.4 PWY-3301 sinapate ester biosynthesis
AtRegNet
Rank Pvalue Hits Over-representation TF Symbol TF Name TF Description
1 4.4⋅10-5 41/3670 (1.1%) 2.2 MYB119 myb domain protein 119 myb domain protein 119
2 4.5⋅10-5 39/3471 (1.1%) 2.2 MYB98 myb domain protein 98 myb domain protein 98
3 1.4⋅10-3 22/1621 (1.4%) 2.7 FUS3 FUSCA 3 AP2/B3-like transcriptional factor family protein
4 1.2⋅10-2 19/1542 (1.2%) 2.5 ANAC087 Arabidopsis NAC domain containing protein 87 NAC domain containing protein 87
5 1.2⋅10-2 35/3860 (0.9%) 1.8 CUC3 CUP SHAPED COTYLEDON3 NAC (No Apical Meristem) domain transcriptional regulator superfamily protein
6 1.3⋅10-2 39/4583 (0.9%) 1.7 NAC028 NAC domain containing protein 28 NAC domain containing protein 28
7 1.4⋅10-2 44/5500 (0.8%) 1.6 PC-MYB1 PC-MYB1 Homeodomain-like protein
8 1.7⋅10-2 27/2787 (1.0%) 1.9 NAC075 NAC domain containing protein 75 NAC domain containing protein 75
9 2.7⋅10-2 33/3846 (0.9%) 1.7 NAC038 NAC domain containing protein 38 NAC domain containing protein 38
10 4.3⋅10-2 46/6320 (0.7%) 1.5 NAC076 NAC domain containing protein 76 NAC domain containing protein 76
11 4.3⋅10-2 8/458 (1.7%) 3.5 NAC073 NAC domain containing protein 73 NAC domain containing protein 73
12 4.3⋅10-2 20/2007 (1.0%) 2 CUC1 CUP-SHAPED COTYLEDON1 NAC (No Apical Meristem) domain transcriptional regulator superfamily protein
13 4.3⋅10-2 10/661 (1.5%) 3 AT1G19040 AT1G19040 NAC (No Apical Meristem) domain transcriptional regulator superfamily protein
14 4.3⋅10-2 19/1823 (1.0%) 2.1 NAC6 NAC domain containing protein 6 NAC domain containing protein 6
Plant Cistrome Database
Rank Pvalue Hits Over-representation TF Symbol TF Name TF Description
1 3.1⋅10-6 36/2644 (1.4%) 2.7 MYB118 myb domain protein 118 myb domain protein 118
2 1.1⋅10-5 53/5419 (1.0%) 2 MYB119 myb domain protein 119 myb domain protein 119
3 3.9⋅10-5 39/3471 (1.1%) 2.2 MYB98 myb domain protein 98 myb domain protein 98
4 1.3⋅10-3 22/1620 (1.4%) 2.7 FUS3 FUSCA 3 AP2/B3-like transcriptional factor family protein
5 4.8⋅10-3 27/2472 (1.1%) 2.2 CUC2 CUP-SHAPED COTYLEDON 2 NAC (No Apical Meristem) domain transcriptional regulator superfamily protein
6 1.2⋅10-2 35/3860 (0.9%) 1.8 CUC3 CUP SHAPED COTYLEDON3 NAC (No Apical Meristem) domain transcriptional regulator superfamily protein
7 1.4⋅10-2 39/4583 (0.9%) 1.7 NAC028 NAC domain containing protein 28 NAC domain containing protein 28
8 2.2⋅10-2 27/2785 (1.0%) 1.9 NAC075 NAC domain containing protein 75 NAC domain containing protein 75
9 3.5⋅10-2 33/3846 (0.9%) 1.7 NAC038 NAC domain containing protein 38 NAC domain containing protein 38
10 4.4⋅10-2 53/7465 (0.7%) 1.4 NAC076 NAC domain containing protein 76 NAC domain containing protein 76
11 4.4⋅10-2 45/5982 (0.8%) 1.5 NAC096 NAC domain containing protein 96 NAC domain containing protein 96
12 4.9⋅10-2 51/7195 (0.7%) 1.4 NAC046 NAC domain containing protein 46 NAC domain containing protein 46
13 4.9⋅10-2 10/661 (1.5%) 3 AT1G19040 AT1G19040 NAC (No Apical Meristem) domain transcriptional regulator superfamily protein
14 4.9⋅10-2 23/2399 (1.0%) 1.9 NAC105 NAC domain containing protein 105 NAC domain containing protein 105
15 5.0⋅10-2 20/2007 (1.0%) 2 CUC1 CUP-SHAPED COTYLEDON1 NAC (No Apical Meristem) domain transcriptional regulator superfamily protein
16 5.0⋅10-2 59/8763 (0.7%) 1.3 SGR5 SHOOT GRAVITROPISM 5 C2H2-like zinc finger protein
Pfam
Rank Pvalue Hits Over-representation Family Summary
1 8.0⋅10-5 6/86 (7.0%) 12.3 Lipase_GDSL GDSL-like Lipase/Acylhydrolase
2 8.0⋅10-5 5/44 (11.4%) 20 LTP_2 Probable lipid transfer
3 1.6⋅10-4 4/31 (12.9%) 22.7 Cupin_1 Cupin
4 4.1⋅10-4 2/3 (66.7%) 117.2 RGP Reversibly glycosylated polypeptide
5 1.8⋅10-3 3/28 (10.7%) 18.8 AMP-binding_C AMP-binding enzyme C-terminal domain
6 3.7⋅10-3 3/40 (7.5%) 13.2 AMP-binding AMP-binding enzyme
7 3.7⋅10-3 3/38 (7.9%) 13.9 Abhydrolase_6 Alpha/beta hydrolase family
8 1.1⋅10-2 3/61 (4.9%) 8.6 Pectinesterase Pectinesterase
9 1.4⋅10-2 2/23 (8.7%) 15.3 CBFD_NFYB_HMF Histone-like transcription factor (CBF/NF-Y) and archaeal histone
10 1.6⋅10-2 2/26 (7.7%) 13.5 LOB Lateral organ boundaries (LOB) domain
11 1.8⋅10-2 3/88 (3.4%) 6 2OG-FeII_Oxy 2OG-Fe(II) oxygenase superfamily
12 1.8⋅10-2 3/88 (3.4%) 6 PMEI Plant invertase/pectin methylesterase inhibitor
13 1.8⋅10-2 3/85 (3.5%) 6.2 DIOX_N non-haem dioxygenase in morphine synthesis N-terminal
14 2.6⋅10-2 2/40 (5.0%) 8.8 EamA EamA-like transporter family
15 3.5⋅10-2 2/48 (4.2%) 7.3 PTR2 POT family
darkorange Module: 107 genes
Probeset Symbol Name Description Average Ranking
AT4G34520_at KCS18 3-ketoacyl-CoA synthase 18 3-ketoacyl-CoA synthase 18 21.01864172233
AT5G38160_at AT5G38160 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein 23.34773930862
AT3G58740_at CSY1 citrate synthase 1 citrate synthase 1 23.650238177609
AT2G44470_at BGLU29 beta glucosidase 29 beta glucosidase 29 23.984352130292
AT5G49190_at SUS2 sucrose synthase 2 sucrose synthase 2 24.369481331666
AT5G50750_at RGP4 reversibly glycosylated polypeptide 4 reversibly glycosylated polypeptide 4 25.737552226096
AT5G22810_at AT5G22810 GDSL-like lipase/acylhydrolase superfamily protein 26.655647071347
AT5G38170_at AT5G38170 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein 26.801866833435
AT5G48100_at TT10 TRANSPARENT TESTA 10 Laccase/Diphenol oxidase family protein 27.590088351917
AT3G26790_at FUS3 FUSCA 3 AP2/B3-like transcriptional factor family protein 27.945758043484
AT5G07260_at AT5G07260 START (StAR-related lipid-transfer) lipid-binding domain-containing protein 27.961206323017
AT1G20500_at AT1G20500 AMP-dependent synthetase and ligase family protein 28.390704420257
AT1G04380_at AT1G04380 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein 29.393405540623
AT2G25540_at CESA10 cellulose synthase 10 cellulose synthase A catalytic subunit 3 UDP-forming-like protein 29.568007025574
AT5G47670_at NF-YB6 nuclear factor Y, subunit B6 nuclear factor Y, subunit B6 29.761110519733
AT2G34700_at AT2G34700 Pollen Ole e 1 allergen and extensin family protein 30.194740133592
AT4G33600_at AT4G33600 transmembrane protein 30.790756313703
AT5G44360_at AT5G44360 FAD-binding Berberine family protein 31.969316337121
AT3G12203_at scpl17 serine carboxypeptidase-like 17 serine carboxypeptidase-like 17 32.498509726695
AT5G38195_at AT5G38195 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein 32.71765973867
AT1G71691_at AT1G71691 GDSL-like Lipase/Acylhydrolase superfamily protein 33.528514782979
AT2G23550_at MES6 methyl esterase 6 methyl esterase 6 33.635215690449
AT1G62070_at AT1G62070 hypothetical protein 34.589416398329
AT3G62730_at AT3G62730 desiccation-like protein 35.013525560848
AT5G56300_at GAMT2 gibberellic acid methyltransferase 2 gibberellic acid methyltransferase 2 35.128669132714
AT4G25980_at AT4G25980 peroxidase superfamily protein 35.524755834686
AT1G71250_at AT1G71250 GDSL-like Lipase/Acylhydrolase superfamily protein 37.508781967693
AT2G23580_at MES4 methyl esterase 4 methyl esterase 4 38.22533065439
AT1G68380_at AT1G68380 Core-2/I-branching beta-1,6-N-acetylglucosaminyltransferase family protein 38.537888868191
AT1G25410_at IPT6 isopentenyltransferase 6 isopentenyltransferase 6 38.669738137691
AT1G27040_at AT1G27040 Major facilitator superfamily protein 39.285334113953
AT5G07200_at GA20OX3 gibberellin 20-oxidase 3 gibberellin 20-oxidase 3 40.144150677276
AT1G65880_at BZO1 benzoyloxyglucosinolate 1 benzoyloxyglucosinolate 1 40.880818053597
AT2G46960_at CYP709B1 cytochrome P450, family 709, subfamily B, polypeptide 1 cytochrome P450, family 709, subfamily B, polypeptide 1 41.372288900125
AT4G37360_at CYP81D2 cytochrome P450, family 81, subfamily D, polypeptide 2 cytochrome P450, family 81, subfamily D, polypeptide 2 41.746280969742
AT5G50770_at HSD6 hydroxysteroid dehydrogenase 6 hydroxysteroid dehydrogenase 6 41.898248928866
AT1G71120_at GLIP6 GDSL-motif lipase/hydrolase 6 GDSL-motif lipase/hydrolase 6 42.870053490167
AT3G25160_at AT3G25160 ER lumen protein retaining receptor family protein 43.654682385502
AT1G62210_at AT1G62210 hypothetical protein 43.735336775155
AT1G04660_at AT1G04660 glycine-rich protein 45.368902520159
AT4G37050_at PLP4 PATATIN-like protein 4 PATATIN-like protein 4 45.851212177662
AT4G11180_at AT4G11180 Disease resistance-responsive (dirigent-like protein) family protein 45.961505708279
AT5G47150_at AT5G47150 YDG/SRA domain-containing protein 47.131263804987
AT3G04200_at AT3G04200 RmlC-like cupins superfamily protein 47.674468424834
AT1G68510_at LBD42 LOB domain-containing protein 42 LOB domain-containing protein 42 49.094632354898
AT1G78500_at AT1G78500 Terpenoid cyclases family protein 49.667116853394
AT3G04280_at RR22 response regulator 22 response regulator 22 50.614850839609
AT4G33280_at AT4G33280 AP2/B3-like transcriptional factor family protein 50.68616440908
AT1G27080_at NRT1.6 nitrate transporter 1.6 nitrate transporter 1.6 51.019919099449
AT2G38900_at AT2G38900 Serine protease inhibitor, potato inhibitor I-type family protein 51.34199776459
AT5G27200_at ACP5 acyl carrier protein 5 acyl carrier protein 5 51.480313755755
AT1G11170_at AT1G11170 lysine ketoglutarate reductase trans-splicing-like protein (DUF707) 51.55881257152
AT3G11180_at AT3G11180 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein 52.172432605051
AT3G03240_at AT3G03240 alpha/beta-Hydrolases superfamily protein 53.251656598451
AT5G12460_at AT5G12460 fringe-like protein (DUF604) 53.884856428134
AT5G08460_at AT5G08460 GDSL-like Lipase/Acylhydrolase superfamily protein 54.796843814035
AT3G08900_at RGP3 reversibly glycosylated polypeptide 3 reversibly glycosylated polypeptide 3 55.199936131144
AT5G26120_at ASD2 alpha-L-arabinofuranosidase 2 alpha-L-arabinofuranosidase 2 55.366094951699
AT5G14995_at AT5G14995 ECA1 gametogenesis related family protein 55.423217659739
AT5G24316_at AT5G24316 proline-rich family protein 56.478191446896
AT1G43640_at TLP5 tubby like protein 5 tubby like protein 5 56.573216329138
AT5G13670_at UMAMIT15 Usually multiple acids move in and out Transporters 15 nodulin MtN21 /EamA-like transporter family protein 57.055166724326
AT1G71690_at AT1G71690 glucuronoxylan 4-O-methyltransferase-like protein (DUF579) 57.09702078399
AT1G09380_at UMAMIT25 Usually multiple acids move in and out Transporters 25 nodulin MtN21 /EamA-like transporter family protein 57.335930223275
AT2G47750_at GH3.9 putative indole-3-acetic acid-amido synthetase GH3.9 putative indole-3-acetic acid-amido synthetase GH3.9 58.795253745642
AT5G10220_at ANN6 annexin 6 annexin 6 59.536052638582
AT3G04170_at AT3G04170 RmlC-like cupins superfamily protein 59.836934827155
AT1G21970_at LEC1 LEAFY COTYLEDON 1 Histone superfamily protein 60.510192404929
AT3G44460_at DPBF2 Basic-leucine zipper (bZIP) transcription factor family protein 60.764909386061
AT1G60970_at AT1G60970 SNARE-like superfamily protein 60.768502009208
AT1G28590_at AT1G28590 GDSL-like Lipase/Acylhydrolase superfamily protein 61.083754690369
AT4G31060_at AT4G31060 Integrase-type DNA-binding superfamily protein 62.024123799132
AT1G23200_at AT1G23200 Plant invertase/pectin methylesterase inhibitor superfamily 62.907190568699
AT2G23510_at SDT spermidine disinapoyl acyltransferase spermidine disinapoyl acyltransferase 63.193343002368
AT3G24250_at AT3G24250 glycine-rich protein 63.796005535301
AT1G50650_at AT1G50650 Stigma-specific Stig1 family protein 64.468544588445
AT3G60730_at AT3G60730 Plant invertase/pectin methylesterase inhibitor superfamily 64.697753945232
AT4G09820_at TT8 TRANSPARENT TESTA 8 basic helix-loop-helix (bHLH) DNA-binding superfamily protein 65.052345849855
AT5G50260_at CEP1 cysteine endopeptidase 1 Cysteine proteinases superfamily protein 66.635974133113
AT3G04150_at AT3G04150 RmlC-like cupins superfamily protein 67.691846076057
AT1G62340_at ALE1 ABNORMAL LEAF-SHAPE 1 PA-domain containing subtilase family protein 68.058473268223
AT4G14730_at AT4G14730 Bax inhibitor-1 family protein 68.562877558081
AT1G53690_at AT1G53690 DNA directed RNA polymerase, 7 kDa subunit 69.874364637943
AT5G39130_at AT5G39130 RmlC-like cupins superfamily protein 70.316975809671
AT5G38180_at AT5G38180 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein 70.443256513293
AT5G51490_at AT5G51490 Plant invertase/pectin methylesterase inhibitor superfamily 70.466249301434
AT2G23260_at UGT84B1 UDP-glucosyl transferase 84B1 UDP-glucosyl transferase 84B1 71.657024243553
AT3G02590_at AT3G02590 Fatty acid hydroxylase superfamily protein 73.44399499694
AT2G01770_at VIT1 vacuolar iron transporter 1 vacuolar iron transporter 1 77.276425739149
AT1G71890_at SUC5 Major facilitator superfamily protein 78.121231072198
AT3G13640_at ABCE1 ATP-binding cassette E1 RNAse l inhibitor protein 1 78.869933736062
AT3G10200_at AT3G10200 S-adenosyl-L-methionine-dependent methyltransferases superfamily protein 79.269074167709
AT2G47120_at AT2G47120 NAD(P)-binding Rossmann-fold superfamily protein 79.842097559677
AT2G25940_at ALPHA-VPE alpha-vacuolar processing enzyme alpha-vacuolar processing enzyme 80.112083189185
AT5G45770_at RLP55 receptor like protein 55 receptor like protein 55 82.479082949677
AT5G07500_at PEI1 Zinc finger C-x8-C-x5-C-x3-H type family protein 82.605363653299
AT5G20940_at AT5G20940 Glycosyl hydrolase family protein 83.041687734518
AT1G76290_at AT1G76290 AMP-dependent synthetase and ligase family protein 83.432026239455
AT4G00220_at JLO JAGGED LATERAL ORGANS Lateral organ boundaries (LOB) domain family protein 84.958891076989
AT5G57920_at ENODL10 early nodulin-like protein 10 early nodulin-like protein 10 85.23606195279
AT3G52780_at PAP20 Purple acid phosphatases superfamily protein 85.812677967906
AT2G28650_at EXO70H8 exocyst subunit exo70 family protein H8 exocyst subunit exo70 family protein H8 88.841977805573
AT1G05450_at AT1G05450 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein 89.518828006493
AT5G60630_at AT5G60630 transmembrane protein 89.891742289166
AT3G52970_at CYP76G1 cytochrome P450, family 76, subfamily G, polypeptide 1 cytochrome P450, family 76, subfamily G, polypeptide 1 91.459203768263
AT5G18290_at SIP1;2 Aquaporin-like superfamily protein 96.101950661309
AT3G15510_at NAC2 NAC domain containing protein 2 NAC domain containing protein 2 104.16218032307

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