Table S3. Enrichment of Functional Classes in Clusters 1 and 3

Table S3. Enrichment of functional classes in clusters 1 and 3.

Functional classes were defined using Mapman BINs (Tellström et al., 2007).

Enrichment was defined based on a Fisher's exact test using n>7 genes as a minimal BIN size to be considered (except for "brassinosteroids" in cluster 3 as several small BINs were overlapping) and p<0.05.

Categories discussed in the result section are highlighted in yellow.

Cluster 1
BIN name (functional classes) / pvalue / total gene number in the BIN / number of genes in cluster / MtGI8 ID (TIGR database)
mitochondrial electron transport / ATP synthesis.alternative oxidase / 1,7E-07 / 11 / 7 / TC94674, TC94150, TC94150, TC93979, TC94080, BQ165547, TC94041
transport.ABC transporters and multidrug resistance systems / 4,2E-05 / 63 / 12 / TC94904, TC108537, TC102452, TC108864, TC104271, TC108435, TC107302, TC95110, TC109879, TC110006, TC95112, TC106086
amino acid metabolism.degradation.aspartate family.threonine / 6,7E-05 / 16 / 6 / TC96787, TC107226, TC107599, TC95125, TC103010, TC97222
Biodegradation of Xenobiotics / 2,7E-04 / 20 / 6 / TC96787, TC107226, TC107599, TC95125, TC103010, TC97222
stress.abiotic.unspecified / 5,6E-04 / 60 / 10 / TC106340, TC100563, TC95043, TC101114, TC106492, TC107129, TC95623, TC106660, TC106659, TC95759
redox.ascorbate and glutathione.glutathione / 6,2E-03 / 16 / 4 / TC107373, TC108090, TC94412, TC103582
protein.degradation.aspartate protease / 7,9E-03 / 17 / 4 / TC94330, TC101517, TC96936, TC94330
not assigned.no ontology.glycine rich proteins / 7,9E-03 / 17 / 4 / TC95229, TC95451, TC96915, TC105291
protein.synthesis.chloroplast/mito - plastid ribosomal protein.plastid / 8,2E-03 / 37 / 6 / TC106501, TC95674, TC107820, TC95165, TC107810, TC106680
RNA.regulation of transcription.bZIP transcription factor family / 9,8E-03 / 62 / 8 / TC94788, TC95965, TC108901, TC111494, TC99871, TC101293, TC99971, BM813592
glycolysis.PEPCase / 1,1E-02 / 10 / 3 / TC107077, TC107910, TC94196
hormone metabolism.auxin.induced-regulated-responsive-activated / 1,8E-02 / 69 / 8 / TC94478, TC106906, TC94817, TC95234, TC106481, TC100620, TC102052, TC106471
misc.glutathione S transferases / 2,8E-02 / 48 / 6 / TC106973, TC106973, TC95380, TC102103, TC108817, TC107454
stress.abiotic.heat / 2,8E-02 / 164 / 14 / TC100693, TC96984, TC112416, TC96201, TC106400, TC94382, TC107423, TC107529, TC105037, TC106986, TC100455, TC106400, TC100456, TC100458
signalling.in sugar and nutrient physiology / 2,9E-02 / 36 / 5 / TC102903, TC108931, TC101193, TC94642, TC107209
PS.lightreaction.photosystem I.PSI polypeptide subunits / 4,0E-02 / 16 / 3 / TC95277, TC94216, BF519614
hormone metabolism.cytokinin.signal transduction / 4,6E-02 / 17 / 3 / TC95950, TC103991, TC99919
Cluster 3
BIN name (functional classes) / pvalue / total gene number in the BIN / number of genes in cluster / MtGI8 ID (TIGR database)
DNA.synthesis/chromatin structure.histone / 4,0E-16 / 53 / 20 / TC106936, TC101821, TC109376, TC95372, TC93976, TC94025, TC94030, TC94145, TC94007, TC106934, TC106937, TC106935, TC101236, TC108193, TC95559, TC103694, TC105411, TC107986, TC95721, TC110058
misc.peroxidases / 2,3E-08 / 72 / 15 / TC100885, TC95986, TC97623, TC96044, TC107261, TC109333, TC103024, TC96382, TC96382, TC108472, TC106477, TC106540, TC106484, TC100927, TC100927
stress.abiotic.drought/salt / 1,1E-06 / 72 / 13 / TC107023, TC108162, TC102441, TC107152, TC96441, TC100717, TC95220, TC107152, TC102076, TC97096, TC103642, TC100948, TC100716
misc.gluco-, galacto- and mannosidases / 1,9E-06 / 87 / 14 / TC100947, TC103233, TC102321, TC98880, TC104005, TC102484, TC101834, TC103153, TC109932, TC97248, TC103297, TC106196, TC94655, TC94658
misc.protease inhibitor/seed storage/lipid transfer protein (LTP) family protein / 5,1E-06 / 48 / 10 / TC95002, TC95548, TC108074, TC106576, TC106582, TC101404, TC108008, TC100262, TC100266, TC100736
cell wall.degradation.mannan-xylose-arabinose-fucose / 1,4E-05 / 33 / 8 / TC100947, TC103233, TC98880, TC102484, TC97248, TC103297, TC94655, TC94658
cell wall.cellulose synthesis / 1,8E-05 / 44 / 9 / TC94325, TC95140, TC97867, TC104491, TC95303, TC109241, TC95302, TC107799, TC105482
cell.organisation / 7,2E-05 / 232 / 21 / TC106368, TC106390, TC106936, TC101278, TC100409, TC107640, TC95797, TC101278, TC100118, TC106452, TC106934, TC106937, TC106935, TC95014, TC108193, TC95776, TC109603, TC103694, TC100984, TC95721, TC110058
cell wall.degradation.pectate lyases and polygalacturonases / 7,8E-04 / 44 / 7 / TC95677, TC100683, TC106828, TC95839, TC107808, TC108159, TC105990
secondary metabolism.flavonoids.anthocyanins / 1,0E-03 / 23 / 5 / TC107840, TC107730, TC100521, TC100521, TC104594
hormone metabolism.brassinosteroid.synthesis-degradation.sterols.DWF1 / 1,2E-03 / 2 / 2 / TC107222, TC107222
lipid metabolism.FA synthesis and FA elongation.Acetyl CoA Carboxylation / 2,1E-03 / 8 / 3 / TC94796, TC94594, TC107829
transport.Major Intrinsic Proteins.PIP / 2,1E-03 / 8 / 3 / TC95581, TC100263, TC100283
secondary metabolism.isoprenoids.mevalonate pathway / 2,2E-03 / 27 / 5 / TC100645, TC109608, TC100419, TC103283, TC97250
amino acid metabolism.synthesis.aspartate family.methionine / 4,6E-03 / 20 / 4 / TC106598, TC103188, TC96974, TC99300
lipid metabolism.'exotics' (steroids, squalene etc) / 5,5E-03 / 33 / 5 / TC106871, TC95429, TC95429, TC103300, TC98641
minor CHO metabolism.others / 5,5E-03 / 33 / 5 / TC96181, TC104380, TC109927, TC99333, TC99051
protein.degradation.serine protease / 7,0E-03 / 64 / 7 / TC107480, TC101730, TC102827, TC96461, TC105003, TC105300, TC107481
nucleotide metabolism.deoxynucleotide metabolism / 9,1E-03 / 24 / 4 / TC99896, TC107086, TC95936, TC107089
misc.UDP glucosyl and glucoronyl transferases / 1,4E-02 / 108 / 9 / TC107945, TC102439, TC107945, TC108328, TC109361, TC103607, TC109738, TC108655, TC109255
cell.division / 1,4E-02 / 41 / 5 / TC108015, TC109988, TC103969, TC96111, TC104997
hormone metabolism.brassinosteroid.synthesis-degradation.sterols.other / 1,7E-02 / 6 / 2 / TC106871, TC98641
DNA.repair / 1,7E-02 / 16 / 3 / TC102030, TC101074, TC102237
cell wall.pectin*esterases.PME / 2,0E-02 / 17 / 3 / TC105938, TC100425, TC100424
protein.degradation.aspartate protease / 2,0E-02 / 17 / 3 / TC97053, TC111537, TC101740
PS.photorespiration.serine hydroxymethyltransferase / 2,3E-02 / 7 / 2 / TC106714, TC106715
amino acid metabolism.synthesis.aspartate family.lysine / 2,3E-02 / 7 / 2 / TC104914, TC112181
lipid metabolism.FA synthesis and FA elongation.beta ketoacyl CoA synthase / 3,0E-02 / 8 / 2 / TC95618, TC111025
amino acid metabolism.synthesis.serine-glycine-cysteine group.glycine / 3,0E-02 / 8 / 2 / TC106714, TC106715
lipid metabolism.'exotics' (steroids, squalene etc).sphingolipids / 3,1E-02 / 20 / 3 / TC110634, TC96975, TC110882
misc.beta 1,3 glucan hydrolases / 3,1E-02 / 20 / 3 / TC111160, TC95177, TC108011
hormone metabolism.brassinosteroid.synthesis-degradation.sterols.SMT1 / 3,5E-02 / 1 / 1 / TC95106
hormone metabolism.brassinosteroid.synthesis-degradation.sterols.FACKEL / 3,5E-02 / 1 / 1 / TC99683
hormone metabolism.brassinosteroid.synthesis-degradation.sterols.HYD1 / 3,5E-02 / 1 / 1 / TC95512
N-metabolism.ammonia metabolism.glutamine synthase / 3,8E-02 / 9 / 2 / TC106913, AL385062
hormone metabolism.gibberelin.synthesis-degradation / 4,0E-02 / 22 / 3 / TC99048, TC101533, TC111334
secondary metabolism.wax / 4,6E-02 / 10 / 2 / TC96161, TC109264