date generated: 2020-11-05

Background

Mitch performs unidimensional and multidimensional gene set enrichment analysis. The concept behind this dates to work by Cox and Mann (https://doi.org/10.1186/1471-2105-13-S16-S12). This implementation is suited to R based workflows of multi-omics datasets. This software was developed by Antony Kaspi and Mark Ziemann. Learn more about Mitch at the website: https://github.com/markziemann/Mitch

Input profiles

Here is the first few lines of the input profile.

##                   x
## ATCG00270  7.970979
## AT1G07550 -7.703160
## AT2G29380  7.630163
## AT1G08440  7.152272
## ATCG00550  7.151114
## AT3G12500  7.145171

Here are some metrics about the input data profile:

Profile metrics
Profile metrics
num_genesets 211
num_genes_in_profile 21066
duplicated_genes_present 0
num_profile_genes_in_sets 985
num_profile_genes_not_in_sets 20081

Here is a plot of the input profiles. Note the dynamic ranges.

Here is the contour plot of the profile including all detected genes.

Input genesets

Here are some metrics about the gene sets used: GMT file of genesets: plant_reactome.gmt

Gene sets metrics
Gene sets metrics
num_genesets 211
num_genesets_excluded 167
num_genesets_included 44

Differential pathway expression


Interactive enrichment scatterplot

Significance is calculated by -log10(p-value). All points shown are FDR<0.05.

Significance is calculated by -log10(p-value). Top N sets shown irrespective of FDR.

Results table

Top N= 43 gene sets

set setSize pANOVA s.dist p.adjustANOVA
R-ATH-1119610 Biotin biosynthesis II 10 0.001890 -0.56700 0.0272
R-ATH-1119494 Tryptophan biosynthesis 15 0.001710 0.46800 0.0272
R-ATH-6787011 Jasmonic acid signaling 20 0.000589 0.44400 0.0253
R-ATH-1119292 Cytokinins 7-N-glucoside biosynthesis 10 0.025400 -0.40800 0.1410
R-ATH-1119375 Cytokinins 9-N-glucoside biosynthesis 10 0.025400 -0.40800 0.1410
R-ATH-1119477 Starch biosynthesis 16 0.005720 -0.39900 0.0615
R-ATH-1119331 Cysteine biosynthesis I 11 0.026200 0.38700 0.1410
R-ATH-1119624 Methionine salvage pathway 10 0.097600 0.30300 0.2730
R-ATH-1119430 Chorismate biosynthesis 10 0.102000 0.29900 0.2730
R-ATH-9645850 Activation of pre-replication complex 27 0.010200 0.28600 0.0880
R-ATH-9618218 Arsenic uptake and detoxification 19 0.058700 0.25100 0.2520
R-ATH-1119486 IAA biosynthesis I 21 0.049400 0.24800 0.2360
R-ATH-8879007 Response to cold temperature 20 0.073500 -0.23100 0.2630
R-ATH-9608575 Reproductive meristem phase change 11 0.223000 0.21200 0.4560
R-ATH-9609573 Tricin biosynthesis 23 0.081900 -0.21000 0.2650
R-ATH-1119402 Phospholipid biosynthesis I 16 0.162000 -0.20200 0.3860
R-ATH-1119519 Calvin cycle 28 0.067500 0.20000 0.2630
R-ATH-1119620 GDP-L-fucose biosynthesis I (from GDP-D-mannose) 17 0.183000 0.18700 0.4130
R-ATH-5608118 Auxin signalling 30 0.086300 0.18100 0.2650
R-ATH-5679411 Gibberellin signaling 20 0.195000 -0.16700 0.4200
R-ATH-1119533 TCA cycle (plant) 25 0.158000 0.16300 0.3860
R-ATH-1119540 Leucine biosynthesis 13 0.336000 0.15400 0.6280
R-ATH-1119428 GDP-D-rhamnose biosynthesis 15 0.311000 0.15100 0.6080
R-ATH-1119325 Sphingolipid metabolism 13 0.359000 -0.14700 0.6430
R-ATH-9640760 G1 phase 10 0.475000 0.13000 0.7320
R-ATH-8933811 Circadian rhythm 17 0.384000 -0.12200 0.6600
R-ATH-1119334 Ethylene biosynthesis from methionine 10 0.566000 0.10500 0.7370
R-ATH-3899351 Abscisic acid (ABA) mediated signaling 13 0.520000 0.10300 0.7320
R-ATH-1119465 Sucrose biosynthesis 17 0.468000 -0.10200 0.7320
R-ATH-1119452 Galactose degradation II 17 0.525000 0.08900 0.7320
R-ATH-1119273 Lysine biosynthesis I 18 0.528000 0.08590 0.7320
R-ATH-1119283 Lysine biosynthesis II 18 0.528000 0.08590 0.7320
R-ATH-1119506 Tyrosine degradation I 10 0.640000 0.08540 0.7860
R-ATH-6788019 Salicylic acid signaling 17 0.546000 0.08450 0.7340
R-ATH-1119419 Lysine biosynthesis VI 12 0.682000 -0.06820 0.8150
R-ATH-1119312 Photorespiration 25 0.590000 0.06220 0.7460
R-ATH-1119473 Cytokinins-O-glucoside biosynthesis 25 0.731000 -0.03970 0.8500
R-ATH-1119479 Valine degradation 12 0.869000 0.02750 0.9740
R-ATH-9611432 Recognition of fungal and bacterial pathogens and immunity response 14 0.912000 -0.01700 0.9740
R-ATH-5632095 Brassinosteroid signaling 46 0.915000 0.00913 0.9740
R-ATH-5655101 Xyloglucan biosynthesis 13 0.965000 -0.00708 0.9740
R-ATH-1119460 Isoleucine biosynthesis from threonine 11 0.969000 -0.00686 0.9740
R-ATH-1119438 Secologanin and strictosidine biosynthesis 12 0.974000 -0.00538 0.9740


Results (complete table)


Click HERE to show results for all gene sets

Complete results
set setSize pANOVA s.dist p.adjustANOVA
R-ATH-1119610 Biotin biosynthesis II 10 0.001890 -0.56700 0.0272
R-ATH-1119494 Tryptophan biosynthesis 15 0.001710 0.46800 0.0272
R-ATH-6787011 Jasmonic acid signaling 20 0.000589 0.44400 0.0253
R-ATH-1119292 Cytokinins 7-N-glucoside biosynthesis 10 0.025400 -0.40800 0.1410
R-ATH-1119375 Cytokinins 9-N-glucoside biosynthesis 10 0.025400 -0.40800 0.1410
R-ATH-1119477 Starch biosynthesis 16 0.005720 -0.39900 0.0615
R-ATH-1119331 Cysteine biosynthesis I 11 0.026200 0.38700 0.1410
R-ATH-1119624 Methionine salvage pathway 10 0.097600 0.30300 0.2730
R-ATH-1119430 Chorismate biosynthesis 10 0.102000 0.29900 0.2730
R-ATH-9645850 Activation of pre-replication complex 27 0.010200 0.28600 0.0880
R-ATH-9618218 Arsenic uptake and detoxification 19 0.058700 0.25100 0.2520
R-ATH-1119486 IAA biosynthesis I 21 0.049400 0.24800 0.2360
R-ATH-8879007 Response to cold temperature 20 0.073500 -0.23100 0.2630
R-ATH-9608575 Reproductive meristem phase change 11 0.223000 0.21200 0.4560
R-ATH-9609573 Tricin biosynthesis 23 0.081900 -0.21000 0.2650
R-ATH-1119402 Phospholipid biosynthesis I 16 0.162000 -0.20200 0.3860
R-ATH-1119519 Calvin cycle 28 0.067500 0.20000 0.2630
R-ATH-1119620 GDP-L-fucose biosynthesis I (from GDP-D-mannose) 17 0.183000 0.18700 0.4130
R-ATH-5608118 Auxin signalling 30 0.086300 0.18100 0.2650
R-ATH-5679411 Gibberellin signaling 20 0.195000 -0.16700 0.4200
R-ATH-1119533 TCA cycle (plant) 25 0.158000 0.16300 0.3860
R-ATH-1119540 Leucine biosynthesis 13 0.336000 0.15400 0.6280
R-ATH-1119428 GDP-D-rhamnose biosynthesis 15 0.311000 0.15100 0.6080
R-ATH-1119325 Sphingolipid metabolism 13 0.359000 -0.14700 0.6430
R-ATH-9640760 G1 phase 10 0.475000 0.13000 0.7320
R-ATH-8933811 Circadian rhythm 17 0.384000 -0.12200 0.6600
R-ATH-1119334 Ethylene biosynthesis from methionine 10 0.566000 0.10500 0.7370
R-ATH-3899351 Abscisic acid (ABA) mediated signaling 13 0.520000 0.10300 0.7320
R-ATH-1119465 Sucrose biosynthesis 17 0.468000 -0.10200 0.7320
R-ATH-1119452 Galactose degradation II 17 0.525000 0.08900 0.7320
R-ATH-1119273 Lysine biosynthesis I 18 0.528000 0.08590 0.7320
R-ATH-1119283 Lysine biosynthesis II 18 0.528000 0.08590 0.7320
R-ATH-1119506 Tyrosine degradation I 10 0.640000 0.08540 0.7860
R-ATH-6788019 Salicylic acid signaling 17 0.546000 0.08450 0.7340
R-ATH-1119419 Lysine biosynthesis VI 12 0.682000 -0.06820 0.8150
R-ATH-1119312 Photorespiration 25 0.590000 0.06220 0.7460
R-ATH-1119473 Cytokinins-O-glucoside biosynthesis 25 0.731000 -0.03970 0.8500
R-ATH-1119479 Valine degradation 12 0.869000 0.02750 0.9740
R-ATH-9611432 Recognition of fungal and bacterial pathogens and immunity response 14 0.912000 -0.01700 0.9740
R-ATH-5632095 Brassinosteroid signaling 46 0.915000 0.00913 0.9740
R-ATH-5655101 Xyloglucan biosynthesis 13 0.965000 -0.00708 0.9740
R-ATH-1119460 Isoleucine biosynthesis from threonine 11 0.969000 -0.00686 0.9740
R-ATH-1119438 Secologanin and strictosidine biosynthesis 12 0.974000 -0.00538 0.9740


Detailed Gene set reports



R-ATH-1119610_Biotin_biosynthesis_II

R-ATH-1119610_Biotin_biosynthesis_II
26
set R-ATH-1119610_Biotin_biosynthesis_II
setSize 10
pANOVA 0.00189
s.dist -0.567
p.adjustANOVA 0.0272



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT3G04520 -9820
AT3G08860 -9350
AT5G46180 -8850
AT3G48780 -8359
AT3G22200 -7467
AT5G23670 -5982
AT2G38400 -3513
AT5G57590 -3186
AT4G36480 -1039
AT2G43360 -37

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT3G04520 -9820
AT3G08860 -9350
AT5G46180 -8850
AT3G48780 -8359
AT3G22200 -7467
AT5G23670 -5982
AT2G38400 -3513
AT5G57590 -3186
AT4G36480 -1039
AT2G43360 -37


R-ATH-1119494_Tryptophan_biosynthesis

R-ATH-1119494_Tryptophan_biosynthesis
21
set R-ATH-1119494_Tryptophan_biosynthesis
setSize 15
pANOVA 0.00171
s.dist 0.468
p.adjustANOVA 0.0272



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT1G25220 10722
AT3G54640 10721
AT5G17990 10625
AT5G05730 10535
AT5G05590 10499
AT2G04400 10472
AT4G27070 10414
AT5G54810 8503
AT5G38530 7673
AT5G57890 1347
AT4G02610 1141
AT1G70570 -2320
AT5G48220 -2455
AT1G29410 -2971
AT2G29690 -7875

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT1G25220 10722
AT3G54640 10721
AT5G17990 10625
AT5G05730 10535
AT5G05590 10499
AT2G04400 10472
AT4G27070 10414
AT5G54810 8503
AT5G38530 7673
AT5G57890 1347
AT4G02610 1141
AT1G70570 -2320
AT5G48220 -2455
AT1G29410 -2971
AT2G29690 -7875


R-ATH-6787011_Jasmonic_acid_signaling

R-ATH-6787011_Jasmonic_acid_signaling
34
set R-ATH-6787011_Jasmonic_acid_signaling
setSize 20
pANOVA 0.000589
s.dist 0.444
p.adjustANOVA 0.0253



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT2G06050 10598
AT5G17490 10530
AT3G29575 10449
AT1G32640 10111
AT1G69260 9982
AT2G46510 9591
AT4G28910 9404
AT3G03450 7871
AT1G14920 6856
AT2G39940 5346
AT4G17880 5097
AT2G46370 4884
AT1G66350 4515
AT1G13740 4442
AT2G01570 3698
AT5G63110 2544
AT5G27030 2280
AT3G16830 -3476
AT5G46760 -8277
AT4G38130 -8810

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT2G06050 10598
AT5G17490 10530
AT3G29575 10449
AT1G32640 10111
AT1G69260 9982
AT2G46510 9591
AT4G28910 9404
AT3G03450 7871
AT1G14920 6856
AT2G39940 5346
AT4G17880 5097
AT2G46370 4884
AT1G66350 4515
AT1G13740 4442
AT2G01570 3698
AT5G63110 2544
AT5G27030 2280
AT3G16830 -3476
AT5G46760 -8277
AT4G38130 -8810


R-ATH-1119292_Cytokinins_7-N-glucoside_biosynthesis

R-ATH-1119292_Cytokinins_7-N-glucoside_biosynthesis
3
set R-ATH-1119292_Cytokinins_7-N-glucoside_biosynthesis
setSize 10
pANOVA 0.0254
s.dist -0.408
p.adjustANOVA 0.141



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT2G36770 -9965
AT2G36780 -9617
AT3G55700 -9506
AT2G36800 -7772
AT3G53160 -7349
AT2G36790 -6293
AT3G46670 -977
AT3G11340 1238
AT3G53150 3962
AT5G05860 5414

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT2G36770 -9965
AT2G36780 -9617
AT3G55700 -9506
AT2G36800 -7772
AT3G53160 -7349
AT2G36790 -6293
AT3G46670 -977
AT3G11340 1238
AT3G53150 3962
AT5G05860 5414


R-ATH-1119375_Cytokinins_9-N-glucoside_biosynthesis

R-ATH-1119375_Cytokinins_9-N-glucoside_biosynthesis
8
set R-ATH-1119375_Cytokinins_9-N-glucoside_biosynthesis
setSize 10
pANOVA 0.0254
s.dist -0.408
p.adjustANOVA 0.141



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT2G36770 -9965
AT2G36780 -9617
AT3G55700 -9506
AT2G36800 -7772
AT3G53160 -7349
AT2G36790 -6293
AT3G46670 -977
AT3G11340 1238
AT3G53150 3962
AT5G05860 5414

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT2G36770 -9965
AT2G36780 -9617
AT3G55700 -9506
AT2G36800 -7772
AT3G53160 -7349
AT2G36790 -6293
AT3G46670 -977
AT3G11340 1238
AT3G53150 3962
AT5G05860 5414


R-ATH-1119477_Starch_biosynthesis

R-ATH-1119477_Starch_biosynthesis
18
set R-ATH-1119477_Starch_biosynthesis
setSize 16
pANOVA 0.00572
s.dist -0.399
p.adjustANOVA 0.0615



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT4G18240 -10039
AT2G21590 -9837
AT1G70820 -8975
AT3G20440 -7973
AT5G51820 -7392
AT1G27680 -6946
AT5G48300 -6733
AT5G03650 -6455
AT5G24300 -6267
AT2G36390 -5386
AT5G17530 -2068
AT1G23190 -1626
AT1G70730 539
AT5G19220 2217
AT4G39210 5924
AT3G01180 7214

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT4G18240 -10039
AT2G21590 -9837
AT1G70820 -8975
AT3G20440 -7973
AT5G51820 -7392
AT1G27680 -6946
AT5G48300 -6733
AT5G03650 -6455
AT5G24300 -6267
AT2G36390 -5386
AT5G17530 -2068
AT1G23190 -1626
AT1G70730 539
AT5G19220 2217
AT4G39210 5924
AT3G01180 7214


R-ATH-1119331_Cysteine_biosynthesis_I

R-ATH-1119331_Cysteine_biosynthesis_I
6
set R-ATH-1119331_Cysteine_biosynthesis_I
setSize 11
pANOVA 0.0262
s.dist 0.387
p.adjustANOVA 0.141



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT3G59760 9856
AT4G14880 9851
AT5G56760 9812
AT3G13110 7497
AT3G04940 7257
AT4G35640 6130
AT5G28020 3802
AT3G22460 -362
AT2G43750 -460
AT5G28030 -2711
AT2G17640 -3503

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT3G59760 9856
AT4G14880 9851
AT5G56760 9812
AT3G13110 7497
AT3G04940 7257
AT4G35640 6130
AT5G28020 3802
AT3G22460 -362
AT2G43750 -460
AT5G28030 -2711
AT2G17640 -3503


R-ATH-1119624_Methionine_salvage_pathway

R-ATH-1119624_Methionine_salvage_pathway
28
set R-ATH-1119624_Methionine_salvage_pathway
setSize 10
pANOVA 0.0976
s.dist 0.303
p.adjustANOVA 0.273



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT4G37770 9309
AT1G02500 9264
AT4G34840 7595
AT4G08040 7282
AT4G01850 7169
AT4G38800 4425
AT2G05830 2867
AT5G65800 532
AT4G11280 -4604
AT4G26200 -9870

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT4G37770 9309
AT1G02500 9264
AT4G34840 7595
AT4G08040 7282
AT4G01850 7169
AT4G38800 4425
AT2G05830 2867
AT5G65800 532
AT4G11280 -4604
AT4G26200 -9870


R-ATH-1119430_Chorismate_biosynthesis

R-ATH-1119430_Chorismate_biosynthesis
12
set R-ATH-1119430_Chorismate_biosynthesis
setSize 10
pANOVA 0.102
s.dist 0.299
p.adjustANOVA 0.273



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT4G39980 9284
AT2G21940 8720
AT1G48850 8359
AT1G48860 5874
AT3G06350 4855
AT5G66120 3924
AT4G39540 2918
AT2G45300 2311
AT2G35500 -3717
AT4G33510 -8939

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT4G39980 9284
AT2G21940 8720
AT1G48850 8359
AT1G48860 5874
AT3G06350 4855
AT5G66120 3924
AT4G39540 2918
AT2G45300 2311
AT2G35500 -3717
AT4G33510 -8939


R-ATH-9645850_Activation_of_pre-replication_complex

R-ATH-9645850_Activation_of_pre-replication_complex
43
set R-ATH-9645850_Activation_of_pre-replication_complex
setSize 27
pANOVA 0.0102
s.dist 0.286
p.adjustANOVA 0.088



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT2G20980 10149
AT3G52630 9541
AT2G24490 9116
AT4G02060 7938
AT1G26840 7621
AT5G44635 7323
AT5G61000 6885
AT3G02920 6648
AT5G46280 5904
AT2G29680 5368
AT5G45400 5029
AT1G67320 5018
AT2G37560 4887
AT5G08020 3281
AT3G25100 2990
AT5G16690 2592
AT5G22110 2590
AT1G67630 2309
AT4G29910 1185
AT1G44900 959

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT2G20980 10149
AT3G52630 9541
AT2G24490 9116
AT4G02060 7938
AT1G26840 7621
AT5G44635 7323
AT5G61000 6885
AT3G02920 6648
AT5G46280 5904
AT2G29680 5368
AT5G45400 5029
AT1G67320 5018
AT2G37560 4887
AT5G08020 3281
AT3G25100 2990
AT5G16690 2592
AT5G22110 2590
AT1G67630 2309
AT4G29910 1185
AT1G44900 959
AT2G07690 525
AT2G16440 334
AT5G67100 -1171
AT2G01120 -1445
AT4G18590 -4124
AT1G77320 -5666
AT4G19130 -8981


R-ATH-9618218_Arsenic_uptake_and_detoxification

R-ATH-9618218_Arsenic_uptake_and_detoxification
41
set R-ATH-9618218_Arsenic_uptake_and_detoxification
setSize 19
pANOVA 0.0587
s.dist 0.251
p.adjustANOVA 0.252



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT2G37180 10471
AT3G53420 9231
AT2G34390 8695
AT4G35100 8513
AT2G37170 7609
AT3G54820 7221
AT4G19030 5965
AT1G30420 4333
AT2G21045 3972
AT2G16850 3697
AT4G10380 3614
AT5G66170 2352
AT2G34660 1196
AT1G31885 -492
AT5G60660 -992
AT1G30410 -1674
AT1G30400 -2665
AT2G39010 -6962
AT4G18910 -9974

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT2G37180 10471
AT3G53420 9231
AT2G34390 8695
AT4G35100 8513
AT2G37170 7609
AT3G54820 7221
AT4G19030 5965
AT1G30420 4333
AT2G21045 3972
AT2G16850 3697
AT4G10380 3614
AT5G66170 2352
AT2G34660 1196
AT1G31885 -492
AT5G60660 -992
AT1G30410 -1674
AT1G30400 -2665
AT2G39010 -6962
AT4G18910 -9974


R-ATH-1119486_IAA_biosynthesis_I

R-ATH-1119486_IAA_biosynthesis_I
20
set R-ATH-1119486_IAA_biosynthesis_I
setSize 21
pANOVA 0.0494
s.dist 0.248
p.adjustANOVA 0.236



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT2G22330 10657
AT4G39950 10567
AT1G16400 10486
AT2G20340 10190
AT4G33070 9907
AT5G01330 9832
AT1G31710 9772
AT5G25620 8262
AT1G31690 7495
AT1G70560 6165
AT1G16410 5589
AT4G13260 2298
AT4G28680 1425
AT5G11320 1370
AT3G43600 -2409
AT5G01320 -4980
AT5G22300 -6077
AT2G27150 -6769
AT5G20960 -7256
AT4G24670 -8119

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT2G22330 10657
AT4G39950 10567
AT1G16400 10486
AT2G20340 10190
AT4G33070 9907
AT5G01330 9832
AT1G31710 9772
AT5G25620 8262
AT1G31690 7495
AT1G70560 6165
AT1G16410 5589
AT4G13260 2298
AT4G28680 1425
AT5G11320 1370
AT3G43600 -2409
AT5G01320 -4980
AT5G22300 -6077
AT2G27150 -6769
AT5G20960 -7256
AT4G24670 -8119
AT5G54960 -9217


R-ATH-8879007_Response_to_cold_temperature

R-ATH-8879007_Response_to_cold_temperature
36
set R-ATH-8879007_Response_to_cold_temperature
setSize 20
pANOVA 0.0735
s.dist -0.231
p.adjustANOVA 0.263



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT1G12610 -10186
AT3G50260 -10006
AT1G12860 -9666
AT4G25470 -8401
AT3G26744 -7620
AT5G67190 -7060
AT4G25490 -6322
AT4G04920 -6113
AT4G25480 -5083
AT4G06746 -3424
AT3G49930 -3259
AT5G60570 -2718
AT5G51990 -2290
AT4G36900 426
AT3G19580 1576
AT3G23250 2957
AT1G46768 3784
AT1G63030 8941
AT2G23340 9716
AT2G31180 10321

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT1G12610 -10186
AT3G50260 -10006
AT1G12860 -9666
AT4G25470 -8401
AT3G26744 -7620
AT5G67190 -7060
AT4G25490 -6322
AT4G04920 -6113
AT4G25480 -5083
AT4G06746 -3424
AT3G49930 -3259
AT5G60570 -2718
AT5G51990 -2290
AT4G36900 426
AT3G19580 1576
AT3G23250 2957
AT1G46768 3784
AT1G63030 8941
AT2G23340 9716
AT2G31180 10321


R-ATH-9608575_Reproductive_meristem_phase_change

R-ATH-9608575_Reproductive_meristem_phase_change
38
set R-ATH-9608575_Reproductive_meristem_phase_change
setSize 11
pANOVA 0.223
s.dist 0.212
p.adjustANOVA 0.456



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT5G28640 10256
AT1G12820 5465
AT5G06300 5453
AT2G28550 5388
AT2G35990 5163
AT3G62980 3527
AT4G03190 2206
AT3G26810 1717
AT2G22840 492
AT3G11440 -5959
AT5G06100 -6784

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT5G28640 10256
AT1G12820 5465
AT5G06300 5453
AT2G28550 5388
AT2G35990 5163
AT3G62980 3527
AT4G03190 2206
AT3G26810 1717
AT2G22840 492
AT3G11440 -5959
AT5G06100 -6784


R-ATH-9609573_Tricin_biosynthesis

R-ATH-9609573_Tricin_biosynthesis
39
set R-ATH-9609573_Tricin_biosynthesis
setSize 23
pANOVA 0.0819
s.dist -0.21
p.adjustANOVA 0.265



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT4G15380 -10292
AT3G20130 -9527
AT3G20090 -8983
AT5G42580 -8790
AT3G20960 -8722
AT4G15360 -8653
AT2G14100 -7990
AT1G50520 -6348
AT3G20080 -6203
AT4G15350 -5928
AT3G20120 -3580
AT5G54160 -3072
AT5G06905 -1144
AT3G20940 -787
AT2G42250 -326
AT5G06900 368
AT2G27000 1591
AT3G20100 5200
AT5G07990 5567
AT5G47990 5609

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT4G15380 -10292
AT3G20130 -9527
AT3G20090 -8983
AT5G42580 -8790
AT3G20960 -8722
AT4G15360 -8653
AT2G14100 -7990
AT1G50520 -6348
AT3G20080 -6203
AT4G15350 -5928
AT3G20120 -3580
AT5G54160 -3072
AT5G06905 -1144
AT3G20940 -787
AT2G42250 -326
AT5G06900 368
AT2G27000 1591
AT3G20100 5200
AT5G07990 5567
AT5G47990 5609
AT1G50560 7596
AT4G15330 8314
AT3G20110 10249


R-ATH-1119402_Phospholipid_biosynthesis_I

R-ATH-1119402_Phospholipid_biosynthesis_I
9
set R-ATH-1119402_Phospholipid_biosynthesis_I
setSize 16
pANOVA 0.162
s.dist -0.202
p.adjustANOVA 0.386



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT4G25970 -9434
AT5G60620 -9379
AT1G32200 -8571
AT1G62430 -8232
AT2G41540 -7291
AT3G18850 -5694
AT3G07690 -5383
AT4G26770 -4192
AT4G22340 -2180
AT5G58560 -594
AT4G30580 1790
AT4G16700 3917
AT3G57650 4624
AT5G57190 4798
AT1G51260 6774
AT5G40610 8409

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT4G25970 -9434
AT5G60620 -9379
AT1G32200 -8571
AT1G62430 -8232
AT2G41540 -7291
AT3G18850 -5694
AT3G07690 -5383
AT4G26770 -4192
AT4G22340 -2180
AT5G58560 -594
AT4G30580 1790
AT4G16700 3917
AT3G57650 4624
AT5G57190 4798
AT1G51260 6774
AT5G40610 8409


R-ATH-1119519_Calvin_cycle

R-ATH-1119519_Calvin_cycle
23
set R-ATH-1119519_Calvin_cycle
setSize 28
pANOVA 0.0675
s.dist 0.2
p.adjustANOVA 0.263



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT2G01140 10448
AT3G52930 9219
AT1G79550 8924
AT2G45290 6633
AT5G44520 5772
AT1G67090 5768
AT5G38420 5711
AT2G01290 4954
AT5G38410 4823
AT1G63290 4749
AT3G12780 4173
AT1G56190 3931
AT3G55800 3901
AT1G71100 3276
AT1G18270 3275
AT3G04790 2777
AT3G01850 2638
AT2G21170 2484
AT5G38430 1485
AT3G26650 1162

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT2G01140 10448
AT3G52930 9219
AT1G79550 8924
AT2G45290 6633
AT5G44520 5772
AT1G67090 5768
AT5G38420 5711
AT2G01290 4954
AT5G38410 4823
AT1G63290 4749
AT3G12780 4173
AT1G56190 3931
AT3G55800 3901
AT1G71100 3276
AT1G18270 3275
AT3G04790 2777
AT3G01850 2638
AT2G21170 2484
AT5G38430 1485
AT3G26650 1162
AT5G61410 -399
AT3G54050 -1249
AT5G03690 -1352
AT4G26520 -2075
AT3G60750 -2623
AT5G64380 -6988
AT4G26530 -7282
AT2G36460 -9415


R-ATH-1119620_GDP-L-fucose_biosynthesis_I_(from_GDP-D-mannose)

R-ATH-1119620_GDP-L-fucose_biosynthesis_I_(from_GDP-D-mannose)
27
set R-ATH-1119620_GDP-L-fucose_biosynthesis_I_(from_GDP-D-mannose)
setSize 17
pANOVA 0.183
s.dist 0.187
p.adjustANOVA 0.413



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT4G00110 9884
AT2G45310 9492
AT1G17890 8654
AT3G23820 7346
AT4G33360 6719
AT2G28760 6321
AT4G20460 6281
AT3G51160 5143
AT4G30440 4496
AT5G66280 3397
AT1G73250 1308
AT5G59290 -682
AT3G46440 -4282
AT2G34850 -4616
AT1G30620 -5743
AT4G12250 -6821
AT5G44480 -9902

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT4G00110 9884
AT2G45310 9492
AT1G17890 8654
AT3G23820 7346
AT4G33360 6719
AT2G28760 6321
AT4G20460 6281
AT3G51160 5143
AT4G30440 4496
AT5G66280 3397
AT1G73250 1308
AT5G59290 -682
AT3G46440 -4282
AT2G34850 -4616
AT1G30620 -5743
AT4G12250 -6821
AT5G44480 -9902


R-ATH-5608118_Auxin_signalling

R-ATH-5608118_Auxin_signalling
30
set R-ATH-5608118_Auxin_signalling
setSize 30
pANOVA 0.0863
s.dist 0.181
p.adjustANOVA 0.265



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT3G23050 9451
AT3G04730 9064
AT4G14550 8877
AT3G62100 7851
AT1G04250 7486
AT1G73590 7342
AT1G70940 7224
AT1G51950 7091
AT4G35020 6934
AT5G25890 6653
AT1G12820 5465
AT5G49980 4747
AT2G46990 4617
AT3G62980 3527
AT1G19220 2837
AT4G03190 2206
AT3G16500 1856
AT3G26810 1717
AT2G01420 1064
AT1G75840 378

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT3G23050 9451
AT3G04730 9064
AT4G14550 8877
AT3G62100 7851
AT1G04250 7486
AT1G73590 7342
AT1G70940 7224
AT1G51950 7091
AT4G35020 6934
AT5G25890 6653
AT1G12820 5465
AT5G49980 4747
AT2G46990 4617
AT3G62980 3527
AT1G19220 2837
AT4G03190 2206
AT3G16500 1856
AT3G26810 1717
AT2G01420 1064
AT1G75840 378
AT3G61830 251
AT5G37020 -64
AT2G46530 -2736
AT1G19850 -2818
AT1G20090 -3361
AT4G24390 -5190
AT5G20730 -5810
AT1G30330 -5905
AT2G33860 -8314
AT1G23080 -9003


R-ATH-5679411_Gibberellin_signaling

R-ATH-5679411_Gibberellin_signaling
33
set R-ATH-5679411_Gibberellin_signaling
setSize 20
pANOVA 0.195
s.dist -0.167
p.adjustANOVA 0.42



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT3G63010 -9599
AT3G45260 -9154
AT1G75080 -9058
AT2G02070 -8094
AT5G44160 -7932
AT1G19350 -7430
AT2G02080 -7046
AT3G05120 -6688
AT5G03150 -6133
AT5G27320 -5492
AT1G14580 -4298
AT1G78700 825
AT4G36780 872
AT2G01570 3698
AT1G66350 4515
AT3G59060 4905
AT1G14920 6856
AT3G03450 7871
AT3G50750 9874
AT5G17490 10530

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT3G63010 -9599
AT3G45260 -9154
AT1G75080 -9058
AT2G02070 -8094
AT5G44160 -7932
AT1G19350 -7430
AT2G02080 -7046
AT3G05120 -6688
AT5G03150 -6133
AT5G27320 -5492
AT1G14580 -4298
AT1G78700 825
AT4G36780 872
AT2G01570 3698
AT1G66350 4515
AT3G59060 4905
AT1G14920 6856
AT3G03450 7871
AT3G50750 9874
AT5G17490 10530


R-ATH-1119533_TCA_cycle_(plant)

R-ATH-1119533_TCA_cycle_(plant)
24
set R-ATH-1119533_TCA_cycle_(plant)
setSize 25
pANOVA 0.158
s.dist 0.163
p.adjustANOVA 0.386



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT5G50950 10697
AT1G53240 9792
AT5G55070 8084
AT5G40650 7347
AT5G08300 7149
AT2G47510 6513
AT3G27380 4633
AT5G03290 4408
AT3G09810 4270
AT4G00570 4158
AT2G20420 2891
AT2G17130 2604
AT5G23250 1955
AT2G18450 1877
AT2G44350 1487
AT3G15020 1232
AT4G35260 842
AT4G26910 -194
AT5G66760 -2192
AT3G55410 -2537

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT5G50950 10697
AT1G53240 9792
AT5G55070 8084
AT5G40650 7347
AT5G08300 7149
AT2G47510 6513
AT3G27380 4633
AT5G03290 4408
AT3G09810 4270
AT4G00570 4158
AT2G20420 2891
AT2G17130 2604
AT5G23250 1955
AT2G18450 1877
AT2G44350 1487
AT3G15020 1232
AT4G35260 842
AT4G26910 -194
AT5G66760 -2192
AT3G55410 -2537
AT3G17240 -2571
AT2G13560 -3082
AT5G65750 -5732
AT1G48030 -7140
AT4G35830 -8266


R-ATH-1119540_Leucine_biosynthesis

R-ATH-1119540_Leucine_biosynthesis
25
set R-ATH-1119540_Leucine_biosynthesis
setSize 13
pANOVA 0.336
s.dist 0.154
p.adjustANOVA 0.628



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT3G58990 10065
AT5G23020 8479
AT2G43100 7399
AT5G03290 4408
AT3G09810 4270
AT4G13430 3833
AT2G17130 2604
AT1G74040 2329
AT4G35260 842
AT3G49680 -3057
AT2G43090 -3291
AT5G23010 -5763
AT4G35830 -8266

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT3G58990 10065
AT5G23020 8479
AT2G43100 7399
AT5G03290 4408
AT3G09810 4270
AT4G13430 3833
AT2G17130 2604
AT1G74040 2329
AT4G35260 842
AT3G49680 -3057
AT2G43090 -3291
AT5G23010 -5763
AT4G35830 -8266


R-ATH-1119428_GDP-D-rhamnose_biosynthesis

R-ATH-1119428_GDP-D-rhamnose_biosynthesis
11
set R-ATH-1119428_GDP-D-rhamnose_biosynthesis
setSize 15
pANOVA 0.311
s.dist 0.151
p.adjustANOVA 0.608



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT4G00110 9884
AT2G45310 9492
AT3G23820 7346
AT4G33360 6719
AT2G28760 6321
AT4G20460 6281
AT3G51160 5143
AT4G30440 4496
AT5G66280 3397
AT5G59290 -682
AT3G46440 -4282
AT2G34850 -4616
AT1G30620 -5743
AT4G12250 -6821
AT5G44480 -9902

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT4G00110 9884
AT2G45310 9492
AT3G23820 7346
AT4G33360 6719
AT2G28760 6321
AT4G20460 6281
AT3G51160 5143
AT4G30440 4496
AT5G66280 3397
AT5G59290 -682
AT3G46440 -4282
AT2G34850 -4616
AT1G30620 -5743
AT4G12250 -6821
AT5G44480 -9902


R-ATH-1119325_Sphingolipid_metabolism

R-ATH-1119325_Sphingolipid_metabolism
5
set R-ATH-1119325_Sphingolipid_metabolism
setSize 13
pANOVA 0.359
s.dist -0.147
p.adjustANOVA 0.643



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT1G27980 -9331
AT4G21534 -8915
AT5G19200 -8656
AT3G48780 -8359
AT5G23670 -5982
AT1G69640 -3935
AT4G36480 -1039
AT3G19260 -347
AT3G06060 2715
AT4G21540 4129
AT4G04930 5417
AT3G25540 8452
AT1G14290 8492

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT1G27980 -9331
AT4G21534 -8915
AT5G19200 -8656
AT3G48780 -8359
AT5G23670 -5982
AT1G69640 -3935
AT4G36480 -1039
AT3G19260 -347
AT3G06060 2715
AT4G21540 4129
AT4G04930 5417
AT3G25540 8452
AT1G14290 8492


R-ATH-9640760_G1_phase

R-ATH-9640760_G1_phase
42
set R-ATH-9640760_G1_phase
setSize 10
pANOVA 0.475
s.dist 0.13
p.adjustANOVA 0.732



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT1G73690 7774
AT4G34160 7592
AT5G27620 6164
AT1G66750 3467
AT5G10440 3264
AT3G48750 1801
AT5G65420 -428
AT3G50070 -1973
AT1G70210 -5535
AT2G22490 -6282

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT1G73690 7774
AT4G34160 7592
AT5G27620 6164
AT1G66750 3467
AT5G10440 3264
AT3G48750 1801
AT5G65420 -428
AT3G50070 -1973
AT1G70210 -5535
AT2G22490 -6282


R-ATH-8933811_Circadian_rhythm

R-ATH-8933811_Circadian_rhythm
37
set R-ATH-8933811_Circadian_rhythm
setSize 17
pANOVA 0.384
s.dist -0.122
p.adjustANOVA 0.66



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT1G09570 -8393
AT1G04400 -8265
AT5G61380 -8106
AT4G11110 -7617
AT5G24470 -7364
AT5G08330 -6582
AT4G17640 -3988
AT5G47080 -2498
AT4G08920 -1755
AT2G23070 -1620
AT4G16250 791
AT2G32950 2686
AT2G46830 5561
AT2G18790 6656
AT5G23280 6692
AT2G46340 6846
AT5G11260 8717

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT1G09570 -8393
AT1G04400 -8265
AT5G61380 -8106
AT4G11110 -7617
AT5G24470 -7364
AT5G08330 -6582
AT4G17640 -3988
AT5G47080 -2498
AT4G08920 -1755
AT2G23070 -1620
AT4G16250 791
AT2G32950 2686
AT2G46830 5561
AT2G18790 6656
AT5G23280 6692
AT2G46340 6846
AT5G11260 8717


R-ATH-1119334_Ethylene_biosynthesis_from_methionine

R-ATH-1119334_Ethylene_biosynthesis_from_methionine
7
set R-ATH-1119334_Ethylene_biosynthesis_from_methionine
setSize 10
pANOVA 0.566
s.dist 0.105
p.adjustANOVA 0.737



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT4G37770 9309
AT1G02500 9264
AT1G05010 8364
AT4G08040 7282
AT4G01850 7169
AT5G65800 532
AT4G11280 -4604
AT1G12010 -6131
AT1G62380 -8158
AT4G26200 -9870

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT4G37770 9309
AT1G02500 9264
AT1G05010 8364
AT4G08040 7282
AT4G01850 7169
AT5G65800 532
AT4G11280 -4604
AT1G12010 -6131
AT1G62380 -8158
AT4G26200 -9870


R-ATH-3899351_Abscisic_acid_(ABA)_mediated_signaling

R-ATH-3899351_Abscisic_acid_(ABA)_mediated_signaling
29
set R-ATH-3899351_Abscisic_acid_(ABA)_mediated_signaling
setSize 13
pANOVA 0.52
s.dist 0.103
p.adjustANOVA 0.732



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT2G29380 10743
AT5G59220 10140
AT3G11410 9401
AT5G57050 7957
AT1G72770 6162
AT1G17550 4189
AT5G46240 -883
AT4G33950 -1769
AT4G18290 -2899
AT4G26080 -2966
AT1G12480 -6924
AT5G66880 -7694
AT3G50500 -8595

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT2G29380 10743
AT5G59220 10140
AT3G11410 9401
AT5G57050 7957
AT1G72770 6162
AT1G17550 4189
AT5G46240 -883
AT4G33950 -1769
AT4G18290 -2899
AT4G26080 -2966
AT1G12480 -6924
AT5G66880 -7694
AT3G50500 -8595


R-ATH-1119465_Sucrose_biosynthesis

R-ATH-1119465_Sucrose_biosynthesis
16
set R-ATH-1119465_Sucrose_biosynthesis
setSize 17
pANOVA 0.468
s.dist -0.102
p.adjustANOVA 0.732



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT5G20280 -10056
AT1G70820 -8975
AT5G51820 -7392
AT5G49190 -7114
AT5G37180 -6459
AT5G20830 -5932
AT1G73370 -5324
AT3G54270 -2871
AT5G17530 -2068
AT1G23190 -1626
AT1G70730 539
AT2G35840 3955
AT3G52340 3970
AT4G02280 5588
AT5G11110 8486
AT1G51420 10198
AT3G43190 10475

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT5G20280 -10056
AT1G70820 -8975
AT5G51820 -7392
AT5G49190 -7114
AT5G37180 -6459
AT5G20830 -5932
AT1G73370 -5324
AT3G54270 -2871
AT5G17530 -2068
AT1G23190 -1626
AT1G70730 539
AT2G35840 3955
AT3G52340 3970
AT4G02280 5588
AT5G11110 8486
AT1G51420 10198
AT3G43190 10475


R-ATH-1119452_Galactose_degradation_II

R-ATH-1119452_Galactose_degradation_II
14
set R-ATH-1119452_Galactose_degradation_II
setSize 17
pANOVA 0.525
s.dist 0.089
p.adjustANOVA 0.732



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT3G43190 10475
AT3G29360 8643
AT1G64440 8615
AT5G17310 8449
AT5G39320 8429
AT4G10960 7191
AT5G15490 5710
AT4G02280 5588
AT3G03250 2296
AT1G26570 -1878
AT1G73370 -5324
AT4G23920 -5688
AT5G20830 -5932
AT5G37180 -6459
AT3G06580 -6502
AT1G63180 -6980
AT5G49190 -7114

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT3G43190 10475
AT3G29360 8643
AT1G64440 8615
AT5G17310 8449
AT5G39320 8429
AT4G10960 7191
AT5G15490 5710
AT4G02280 5588
AT3G03250 2296
AT1G26570 -1878
AT1G73370 -5324
AT4G23920 -5688
AT5G20830 -5932
AT5G37180 -6459
AT3G06580 -6502
AT1G63180 -6980
AT5G49190 -7114


R-ATH-1119273_Lysine_biosynthesis_I

R-ATH-1119273_Lysine_biosynthesis_I
1
set R-ATH-1119273_Lysine_biosynthesis_I
setSize 18
pANOVA 0.528
s.dist 0.0859
p.adjustANOVA 0.732



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT3G04120 9241
AT2G45440 7487
AT3G02020 7447
AT3G60880 5960
AT1G16300 5933
AT1G14810 5884
AT1G13440 4219
AT1G31230 1622
AT4G35250 1303
AT5G14060 1242
AT2G19940 -143
AT3G14390 -187
AT3G59890 -1394
AT1G79530 -1913
AT5G11880 -5259
AT4G19710 -6166
AT5G52100 -6191
AT2G44040 -9002

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT3G04120 9241
AT2G45440 7487
AT3G02020 7447
AT3G60880 5960
AT1G16300 5933
AT1G14810 5884
AT1G13440 4219
AT1G31230 1622
AT4G35250 1303
AT5G14060 1242
AT2G19940 -143
AT3G14390 -187
AT3G59890 -1394
AT1G79530 -1913
AT5G11880 -5259
AT4G19710 -6166
AT5G52100 -6191
AT2G44040 -9002


R-ATH-1119283_Lysine_biosynthesis_II

R-ATH-1119283_Lysine_biosynthesis_II
2
set R-ATH-1119283_Lysine_biosynthesis_II
setSize 18
pANOVA 0.528
s.dist 0.0859
p.adjustANOVA 0.732



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT3G04120 9241
AT2G45440 7487
AT3G02020 7447
AT3G60880 5960
AT1G16300 5933
AT1G14810 5884
AT1G13440 4219
AT1G31230 1622
AT4G35250 1303
AT5G14060 1242
AT2G19940 -143
AT3G14390 -187
AT3G59890 -1394
AT1G79530 -1913
AT5G11880 -5259
AT4G19710 -6166
AT5G52100 -6191
AT2G44040 -9002

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT3G04120 9241
AT2G45440 7487
AT3G02020 7447
AT3G60880 5960
AT1G16300 5933
AT1G14810 5884
AT1G13440 4219
AT1G31230 1622
AT4G35250 1303
AT5G14060 1242
AT2G19940 -143
AT3G14390 -187
AT3G59890 -1394
AT1G79530 -1913
AT5G11880 -5259
AT4G19710 -6166
AT5G52100 -6191
AT2G44040 -9002


R-ATH-1119506_Tyrosine_degradation_I

R-ATH-1119506_Tyrosine_degradation_I
22
set R-ATH-1119506_Tyrosine_degradation_I
setSize 10
pANOVA 0.64
s.dist 0.0854
p.adjustANOVA 0.786



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT1G11840 9369
AT3G16700 7395
AT2G22250 6733
AT2G02390 3375
AT5G36160 2704
AT5G53970 1428
AT2G02380 1258
AT5G54080 -6232
AT4G15940 -6624
AT1G12050 -8299

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT1G11840 9369
AT3G16700 7395
AT2G22250 6733
AT2G02390 3375
AT5G36160 2704
AT5G53970 1428
AT2G02380 1258
AT5G54080 -6232
AT4G15940 -6624
AT1G12050 -8299


R-ATH-6788019_Salicylic_acid_signaling

R-ATH-6788019_Salicylic_acid_signaling
35
set R-ATH-6788019_Salicylic_acid_signaling
setSize 17
pANOVA 0.546
s.dist 0.0845
p.adjustANOVA 0.734



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT1G80840 9391
AT3G48090 9322
AT3G12250 6420
AT4G11330 6128
AT4G19660 5492
AT5G20850 5485
AT4G01370 3938
AT4G33925 2815
AT5G06950 2036
AT4G31800 550
AT2G46070 274
AT2G25000 -263
AT5G06960 -2128
AT1G08320 -4426
AT1G64280 -8074
AT3G48080 -8585
AT5G45110 -9664

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT1G80840 9391
AT3G48090 9322
AT3G12250 6420
AT4G11330 6128
AT4G19660 5492
AT5G20850 5485
AT4G01370 3938
AT4G33925 2815
AT5G06950 2036
AT4G31800 550
AT2G46070 274
AT2G25000 -263
AT5G06960 -2128
AT1G08320 -4426
AT1G64280 -8074
AT3G48080 -8585
AT5G45110 -9664


R-ATH-1119419_Lysine_biosynthesis_VI

R-ATH-1119419_Lysine_biosynthesis_VI
10
set R-ATH-1119419_Lysine_biosynthesis_VI
setSize 12
pANOVA 0.682
s.dist -0.0682
p.adjustANOVA 0.815



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT2G44040 -9002
AT5G52100 -6191
AT4G19710 -6166
AT5G11880 -5259
AT4G33680 -1639
AT3G59890 -1394
AT3G14390 -187
AT5G14060 1242
AT1G31230 1622
AT3G60880 5960
AT3G02020 7447
AT2G45440 7487

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT2G44040 -9002
AT5G52100 -6191
AT4G19710 -6166
AT5G11880 -5259
AT4G33680 -1639
AT3G59890 -1394
AT3G14390 -187
AT5G14060 1242
AT1G31230 1622
AT3G60880 5960
AT3G02020 7447
AT2G45440 7487


R-ATH-1119312_Photorespiration

R-ATH-1119312_Photorespiration
4
set R-ATH-1119312_Photorespiration
setSize 25
pANOVA 0.59
s.dist 0.0622
p.adjustANOVA 0.746



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT2G35120 10361
AT5G36790 7147
AT1G67090 5768
AT5G38420 5711
AT4G18360 5590
AT5G38410 4823
AT1G23310 3252
AT2G35370 2870
AT2G26080 2318
AT1G68010 2106
AT1G70580 1985
AT5G36700 1676
AT5G38430 1485
AT1G36370 885
AT1G56500 856
AT3G14420 -10
AT4G33010 -174
AT5G47760 -435
AT3G14415 -2089
AT3G17240 -2571

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT2G35120 10361
AT5G36790 7147
AT1G67090 5768
AT5G38420 5711
AT4G18360 5590
AT5G38410 4823
AT1G23310 3252
AT2G35370 2870
AT2G26080 2318
AT1G68010 2106
AT1G70580 1985
AT5G36700 1676
AT5G38430 1485
AT1G36370 885
AT1G56500 856
AT3G14420 -10
AT4G33010 -174
AT5G47760 -435
AT3G14415 -2089
AT3G17240 -2571
AT1G32470 -4328
AT1G22020 -5385
AT2G13360 -5940
AT1G80380 -7109
AT1G48030 -7140


R-ATH-1119473_Cytokinins-O-glucoside_biosynthesis

R-ATH-1119473_Cytokinins-O-glucoside_biosynthesis
17
set R-ATH-1119473_Cytokinins-O-glucoside_biosynthesis
setSize 25
pANOVA 0.731
s.dist -0.0397
p.adjustANOVA 0.85



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT2G36750 -10209
AT2G36770 -9965
AT2G36780 -9617
AT3G55700 -9506
AT3G46690 -8508
AT3G55710 -8251
AT3G46720 -8239
AT2G36800 -7772
AT3G53160 -7349
AT2G36790 -6293
AT5G05870 -4497
AT3G46670 -977
AT3G11340 1238
AT5G38040 3341
AT5G05890 3356
AT3G53150 3962
AT3G46660 4933
AT5G05860 5414
AT3G46700 7275
AT5G05880 7945

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT2G36750 -10209
AT2G36770 -9965
AT2G36780 -9617
AT3G55700 -9506
AT3G46690 -8508
AT3G55710 -8251
AT3G46720 -8239
AT2G36800 -7772
AT3G53160 -7349
AT2G36790 -6293
AT5G05870 -4497
AT3G46670 -977
AT3G11340 1238
AT5G38040 3341
AT5G05890 3356
AT3G53150 3962
AT3G46660 4933
AT5G05860 5414
AT3G46700 7275
AT5G05880 7945
AT3G46650 8386
AT5G38010 8858
AT5G05900 10012
AT5G59590 10593
AT5G59580 10725


R-ATH-1119479_Valine_degradation

R-ATH-1119479_Valine_degradation
19
set R-ATH-1119479_Valine_degradation
setSize 12
pANOVA 0.869
s.dist 0.0275
p.adjustANOVA 0.974



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT3G19710 9332
AT1G50110 8349
AT1G21400 7759
AT4G16800 3208
AT2G14170 -299
AT1G10070 -1189
AT4G20930 -1985
AT3G13450 -2208
AT3G60510 -3198
AT5G09300 -3339
AT1G55510 -3841
AT3G45300 -6573

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT3G19710 9332
AT1G50110 8349
AT1G21400 7759
AT4G16800 3208
AT2G14170 -299
AT1G10070 -1189
AT4G20930 -1985
AT3G13450 -2208
AT3G60510 -3198
AT5G09300 -3339
AT1G55510 -3841
AT3G45300 -6573


R-ATH-9611432_Recognition_of_fungal_and_bacterial_pathogens_and_immunity_response

R-ATH-9611432_Recognition_of_fungal_and_bacterial_pathogens_and_immunity_response
40
set R-ATH-9611432_Recognition_of_fungal_and_bacterial_pathogens_and_immunity_response
setSize 14
pANOVA 0.912
s.dist -0.017
p.adjustANOVA 0.974



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT2G28830 -9707
AT1G11300 -7581
AT2G28930 -7211
AT1G11350 -4773
AT5G19390 -3305
AT3G46510 -2151
AT3G21630 -1502
AT5G12150 -1252
AT1G11330 2509
AT4G28950 4216
AT1G09090 6604
AT1G07570 7811
AT1G08830 8050
AT1G11303 8744

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT2G28830 -9707
AT1G11300 -7581
AT2G28930 -7211
AT1G11350 -4773
AT5G19390 -3305
AT3G46510 -2151
AT3G21630 -1502
AT5G12150 -1252
AT1G11330 2509
AT4G28950 4216
AT1G09090 6604
AT1G07570 7811
AT1G08830 8050
AT1G11303 8744


R-ATH-5632095_Brassinosteroid_signaling

R-ATH-5632095_Brassinosteroid_signaling
31
set R-ATH-5632095_Brassinosteroid_signaling
setSize 46
pANOVA 0.915
s.dist 0.00913
p.adjustANOVA 0.974



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT3G50750 9874
AT1G10430 9364
AT1G63100 9106
AT5G38480 8763
AT5G65430 7970
AT1G50370 5819
AT5G16050 5775
AT1G22300 5471
AT5G10450 4948
AT3G59060 4905
AT1G15750 4670
AT1G03445 4477
AT3G19980 4149
AT1G34760 3995
AT1G17720 2978
AT3G58500 2601
AT5G27030 2280
AT4G26720 1816
AT5G55260 1305
AT5G44090 1057

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT3G50750 9874
AT1G10430 9364
AT1G63100 9106
AT5G38480 8763
AT5G65430 7970
AT1G50370 5819
AT5G16050 5775
AT1G22300 5471
AT5G10450 4948
AT3G59060 4905
AT1G15750 4670
AT1G03445 4477
AT3G19980 4149
AT1G34760 3995
AT1G17720 2978
AT3G58500 2601
AT5G27030 2280
AT4G26720 1816
AT5G55260 1305
AT5G44090 1057
AT4G36780 872
AT1G78700 825
AT2G42500 139
AT3G02520 -328
AT1G51690 -705
AT1G69960 -789
AT1G54450 -897
AT5G46570 -908
AT1G08420 -1018
AT1G75340 -1207
AT4G03080 -1217
AT1G59830 -2678
AT4G18710 -2702
AT1G13460 -3007
AT3G16830 -3476
AT1G06390 -4042
AT5G28850 -4291
AT2G27210 -4518
AT1G80490 -4935
AT5G28900 -5098
AT3G26020 -6945
AT4G35230 -6972
AT1G03960 -7429
AT1G19350 -7430
AT1G75080 -9058
AT2G30980 -9368


R-ATH-5655101_Xyloglucan_biosynthesis

R-ATH-5655101_Xyloglucan_biosynthesis
32
set R-ATH-5655101_Xyloglucan_biosynthesis
setSize 13
pANOVA 0.965
s.dist -0.00708
p.adjustANOVA 0.974



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT1G14100 -9327
AT2G15350 -8321
AT2G15390 -8168
AT4G37690 -3086
AT5G07720 -1345
AT1G18690 116
AT1G74420 536
AT2G03220 4410
AT2G20370 4773
AT1G14110 5044
AT1G74380 5160
AT2G15370 5846
AT2G22900 6142

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT1G14100 -9327
AT2G15350 -8321
AT2G15390 -8168
AT4G37690 -3086
AT5G07720 -1345
AT1G18690 116
AT1G74420 536
AT2G03220 4410
AT2G20370 4773
AT1G14110 5044
AT1G74380 5160
AT2G15370 5846
AT2G22900 6142


R-ATH-1119460_Isoleucine_biosynthesis_from_threonine

R-ATH-1119460_Isoleucine_biosynthesis_from_threonine
15
set R-ATH-1119460_Isoleucine_biosynthesis_from_threonine
setSize 11
pANOVA 0.969
s.dist -0.00686
p.adjustANOVA 0.974



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT5G54960 -9217
AT3G10050 -9117
AT5G10860 -6060
AT5G01320 -4980
AT3G48560 -3628
AT3G49680 -3057
AT3G58610 3742
AT3G23940 5944
AT5G16290 8166
AT5G01330 9832
AT4G33070 9907

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT5G54960 -9217
AT3G10050 -9117
AT5G10860 -6060
AT5G01320 -4980
AT3G48560 -3628
AT3G49680 -3057
AT3G58610 3742
AT3G23940 5944
AT5G16290 8166
AT5G01330 9832
AT4G33070 9907


R-ATH-1119438_Secologanin_and_strictosidine_biosynthesis

R-ATH-1119438_Secologanin_and_strictosidine_biosynthesis
13
set R-ATH-1119438_Secologanin_and_strictosidine_biosynthesis
setSize 12
pANOVA 0.974
s.dist -0.00538
p.adjustANOVA 0.974



Top enriched genes

Top 20 genes
GeneID Gene Rank
AT1G74010 -10245
AT3G51420 -8506
AT3G51430 -7992
AT3G51440 -7981
AT1G74020 -3388
AT4G28680 1425
AT1G74000 2654
AT5G22020 3558
AT2G41290 5671
AT3G59530 5832
AT2G20340 10190
AT3G51450 10640

Click HERE to show all gene set members

All member genes
GeneID Gene Rank
AT1G74010 -10245
AT3G51420 -8506
AT3G51430 -7992
AT3G51440 -7981
AT1G74020 -3388
AT4G28680 1425
AT1G74000 2654
AT5G22020 3558
AT2G41290 5671
AT3G59530 5832
AT2G20340 10190
AT3G51450 10640


Here is the session info with all the versions of packages used.

sessionInfo()
## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] pkgload_1.1.0               GGally_2.0.0               
##  [3] ggplot2_3.3.2               reshape2_1.4.4             
##  [5] beeswarm_0.2.3              gtools_3.8.2               
##  [7] tibble_3.0.4                dplyr_1.0.2                
##  [9] echarts4r_0.3.3             mitch_1.2.0                
## [11] DESeq2_1.30.0               SummarizedExperiment_1.20.0
## [13] Biobase_2.50.0              MatrixGenerics_1.2.0       
## [15] matrixStats_0.57.0          GenomicRanges_1.42.0       
## [17] GenomeInfoDb_1.26.0         IRanges_2.24.0             
## [19] S4Vectors_0.28.0            BiocGenerics_0.36.0        
## [21] gplots_3.1.0                getDEE2_1.0.0              
## 
## loaded via a namespace (and not attached):
##  [1] bitops_1.0-6           bit64_4.0.5            RColorBrewer_1.1-2    
##  [4] httr_1.4.2             rprojroot_1.3-2        backports_1.2.0       
##  [7] tools_4.0.3            R6_2.5.0               KernSmooth_2.23-18    
## [10] DBI_1.1.0              colorspace_1.4-1       withr_2.3.0           
## [13] htm2txt_2.1.1          tidyselect_1.1.0       gridExtra_2.3         
## [16] bit_4.0.4              compiler_4.0.3         desc_1.2.0            
## [19] DelayedArray_0.16.0    caTools_1.18.0         scales_1.1.1          
## [22] genefilter_1.72.0      stringr_1.4.0          digest_0.6.27         
## [25] rmarkdown_2.5          XVector_0.30.0         pkgconfig_2.0.3       
## [28] htmltools_0.5.0        highr_0.8              fastmap_1.0.1         
## [31] htmlwidgets_1.5.2      rlang_0.4.8            RSQLite_2.2.1         
## [34] shiny_1.5.0            generics_0.1.0         jsonlite_1.7.1        
## [37] BiocParallel_1.24.0    RCurl_1.98-1.2         magrittr_1.5          
## [40] GenomeInfoDbData_1.2.4 Matrix_1.2-18          Rcpp_1.0.5            
## [43] munsell_0.5.0          lifecycle_0.2.0        stringi_1.5.3         
## [46] yaml_2.2.1             MASS_7.3-53            zlibbioc_1.36.0       
## [49] plyr_1.8.6             grid_4.0.3             blob_1.2.1            
## [52] promises_1.1.1         crayon_1.3.4           lattice_0.20-41       
## [55] splines_4.0.3          annotate_1.68.0        locfit_1.5-9.4        
## [58] knitr_1.30             pillar_1.4.6           tcltk_4.0.3           
## [61] geneplotter_1.68.0     XML_3.99-0.5           glue_1.4.2            
## [64] evaluate_0.14          vctrs_0.3.4            httpuv_1.5.4          
## [67] testthat_3.0.0         gtable_0.3.0           purrr_0.3.4           
## [70] assertthat_0.2.1       reshape_0.8.8          xfun_0.19             
## [73] mime_0.9               xtable_1.8-4           later_1.1.0.1         
## [76] survival_3.2-7         pbmcapply_1.5.0        AnnotationDbi_1.52.0  
## [79] memoise_1.1.0          ellipsis_0.3.1

END of report