Supplementary information: Table S2

Genes coexpressed with different seed genes in GGM solution
At1g19210
ANR1 / MADS-box protein (ANR1)
AOC2 / allene oxide cyclase, putative
At1g10560 / armadillo/beta-catenin repeat family protein
At1g18740 / expressed protein
At1g19210 / member of the DREB subfamily A-5 of ERF/AP2 transcription factor family
At1g23710 / expressed protein
At1g28370 / member of the ERF (ethylene response factor) subfamily B-1 of ERF/AP2 transcription factor family
At1g28480 / glutaredoxin family protein
At1g58420 / expressed protein
At1g61550 / S-locus protein kinase, putative
At1g63720 / expressed protein
At1g69050 / expressed protein
At1g73540 / MutT/nudix family protein
At1g74450 / expressed protein
At1g74930 / member of the DREB subfamily A-5 of ERF/AP2 transcription factor family
At2g05050 / pseudogene, protein phosphatase 2C, putative
At2g17080 / hypothetical protein
At2g25250 / expressed protein
At2g27080 / harpin-induced protein-related / HIN1-related / harpin-responsive protein-related
At2g27310 / F-box family protein
At2g33580 / protein kinase family protein / peptidoglycan-binding LysM domain-containing protein, protein kinase
At2g36220 / expressed protein
At2g41010 / VQ motif-containing protein
At2g44840 / member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family
At2g45680 / TCP family transcription factor, putative
At3g02840 / immediate-early fungal elicitor family protein
At3g10930 / expressed protein
At3g19240 / expressed protein
At3g23250 / myb family transcription factor (MYB15)
At3g28620 / zinc finger (C3HC4-type RING finger) family protein
At3g44260 / CCR4-NOT transcription complex protein, putative
At3g49530 / no apical meristem (NAM) family protein
At3g54810 / zinc finger (GATA type) family protein
At3g62260 / protein phosphatase 2C, putative
At4g13820 / disease resistance family protein / LRR family protein
At4g27652 / expressed protein
At4g27654 / expressed protein
At4g29780 / expressed protein
At4g33985 / expressed protein
At4g34410 / member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family
At4g36550 / U-box domain-containing protein
At5g09980 / expressed protein
At5g17350 / expressed protein
At5g22250 / CCR4-NOT transcription complex protein, putative
At5g43620 / S-locus protein-related
At5g52050 / MATE efflux protein-related
At5g58680 / armadillo/beta-catenin repeat family protein
At5g59510 / expressed protein
At5g59550 / zinc finger (C3HC4-type RING finger) family protein
At5g64900 / expressed protein
AZF2 / zinc finger (C2H2 type) protein 2 (AZF2)
C2H2 / zinc finger (C2H2 type) family protein
CCD7 / dioxygenase-related protein
HKT1 / sodium transporter (HKT1)
RHA3B / zinc finger (C3HC4-type RING finger) family protein
WRKY40 / WRKY family transcription factor
WRKY48 / WRKY family transcription factor
At1g21910
ACS11 / 1-aminocyclopropane-1-carboxylate synthase, putative
AGP18 / arabinogalactan-protein (AGP18)
At1g18400 / basic helix-loop-helix (bHLH) family protein
At1g21910 / member of the DREB subfamily A-5 of ERF/AP2 transcription factor family
At1g23030 / armadillo/beta-catenin repeat family protein
At1g24530 / transducin family protein / WD-40 repeat family protein
At1g25400 / expressed protein
At1g25560 / AP2 domain-containing transcription factor, putative
At1g33760 / member of the DREB subfamily A-4 of ERF/AP2 transcription factor family
At1g35350 / similar to EXS family protein
At1g50040 / expressed protein
At1g66160 / U-box domain-containing protein
At1g66180 / aspartyl protease family protein
At1g68840 / DNA-binding protein RAV2 (RAV2) / AP2 domain-containing protein RAP2.8
At1g72430 / auxin-responsive protein-related
At1g73830 / basic helix-loop-helix (bHLH) family protein
At1g77640 / member of the DREB subfamily A-5 of ERF/AP2 transcription factor family
At2g01300 / expressed protein
At2g17230 / phosphate-responsive 1 family protein
At2g23290 / myb family transcription factor
At2g39360 / protein kinase family protein
At2g44500 / expressed protein
At3g05320 / expressed protein
At3g06070 / expressed protein
At3g19680 / expressed protein
At3g50060 / myb family transcription factor
At3g54810 / zinc finger (GATA type) family protein
At3g59080 / aspartyl protease family protein
At4g08950 / phosphate-responsive protein, putative (EXO)
At4g16563 / aspartyl protease family protein
At4g25620 / hydroxyproline-rich glycoprotein family protein
At5g05440 / expressed protein
At5g11070 / expressed protein
At5g24030 / C4-dicarboxylate transporter/malic acid transport family protein
At5g25190 / member of the ERF (ethylene response factor) subfamily B-6 of ERF/AP2 transcription factor family
At5g25240 / expressed protein
ATEXLA1 / expansin family protein (EXPL1)
CYP707A3 / cytochrome P450 family protein
GAE1 / NAD-dependent epimerase/dehydratase family protein
GT2 / trihelix DNA-binding protein / GT-2 factor (GT2)
IP5PII / inositol polyphosphate 5-phosphatase II (IP5PII)
PHI_1 / phosphate-responsive protein, putative
RALFL33 / rapid alkalinization factor (RALF) family protein
TCH4 / xyloglucan:xyloglucosyl transferase
XTR6 / xyloglucan:xyloglucosyl transferase, putative
At1g22190 = RAP2.4d
RAP2.4d / AP2 domain-containing transcription factor, putative
At1g10560 / armadillo/beta-catenin repeat family protein / U-box domain-containing protein
At1g23710 / expressed protein
At1g31350 / F-box family protein
At1g64470 / ubiquitin family protein
At1g67880 / glycosyl transferase family 17 protein
At2g25690 / senescence-associated protein-related
At2g40000 / expressed protein
At2g47270 / expressed protein
At3g02140 / expressed protein
At3g10930 / expressed protein
At3g48510 / expressed protein
At4g25620 / hydroxyproline-rich glycoprotein family protein
At4g27657 / expressed protein
At4g38060 / expressed protein
At5g16200 / 50S ribosomal protein-related
At5g44060 / expressed protein
At5g60680 / expressed protein
At5g63130 / octicosapeptide/Phox/Bem1p (PB1) domain-containing protein
DREB-74930 / member of the DREB subfamily A-5 of ERF/AP2 transcription factor family
ERF8-53170 / member of the ERF (ethylene response factor) subfamily B-1 of ERF/AP2 transcription factor family (ATERF-8)
NAM-01720 / no apical meristem (NAM) family protein
NAM-63790 / no apical meristem (NAM) family protein
NCED3 / 9-cis-epoxycarotenoid dioxygenase, putative
PI-3,4-K / phosphatidylinositol 3- and 4-kinase family protein
RAP2.4b / member of the DREB subfamily A-6 of ERF/AP2 transcription factor family
SCL11 / scarecrow transcription factor family protein, scarecrow-like 11
SPS / sucrose-phosphate synthase, putative
ZF-37610 / TAZ zinc finger family protein / BTB/POZ domain-containing protein
At1g33760
ACS11 / 1-aminocyclopropane-1-carboxylate synthase, putative
At1g12610 / member of the DREB subfamily A-1 of ERF/AP2 transcription factor family (DDF1)
At1g21910 / member of the DREB subfamily A-5 of ERF/AP2 transcription factor family
At1g24140 / matrixin family protein, similar to matrix metalloproteinase (Cucumis sativus) GI:7159629; contains InterPro accession IPR001818: Matrixin
At1g27820 / CCR4-NOT transcription complex protein, putative
At1g33760 / member of the DREB subfamily A-4 of ERF/AP2 transcription factor family
At1g35210 / expressed protein
At1g56520 / disease resistance protein (TIR-NBS-LRR class), putative
At1g66090 / disease resistance protein (TIR-NBS class), putative
At1g66160 / U-box domain-containing protein
At1g72920 / disease resistance protein (TIR-NBS class), putative
At1g72950 / disease resistance protein (TIR-NBS class), putative
At1g74440 / expressed protein
At1g76650 / calcium-binding EF hand family protein
At1g77640 / member of the DREB subfamily A-5 of ERF/AP2 transcription factor family
At2g19710 / expressed protein
At2g21120 / expressed protein
At2g27080 / harpin-induced protein-related / HIN1-related / harpin-responsive protein-related
At2g34600 / expressed protein
At2g36440 / expressed protein
At2g44500 / expressed protein
At3g02840 / immediate-early fungal elicitor family protein
At3g04640 / glycine-rich protein, predicted
At3g09870 / auxin-responsive family protein
At3g23170 / expressed protein
At3g27540 / glycosyl transferase family 17 protein
At3g44260 / CCR4-NOT transcription complex protein, putative
At3g44350 / no apical meristem (NAM) family protein
At3g54810 / zinc finger (GATA type) family protein
At4g23310 / receptor-like protein kinase, putative
At4g27657 / expressed protein
At4g36030 / armadillo/beta-catenin repeat family protein
At4g38560 / expressed protein
At5g05300 / expressed protein
At5g10750 / expressed protein
At5g11070 / expressed protein
At5g16200 / 50S ribosomal protein-related
At5g52050 / MATE efflux protein-related
At5g58120 / disease resistance protein (TIR-NBS-LRR class)
At5g62570 / calmodulin-binding protein
At5g62620 / galactosyltransferase family protein
At5g64660 / U-box domain-containing protein
ATGLR2.8 / glutamate receptor family protein
ATPAP1 / phosphatidic acid phosphatase family protein / PAP2 family protein
CYP707A3 / cytochrome P450 family protein
NHL2 / harpin-induced family protein
PHI_1 / phosphate-responsive protein, putative
At1g36060
At1g08310 / esterase/lipase/thioesterase family protein
At1g12600 / expressed protein
At1g36060 / member of the DREB subfamily A-6 of ERF/AP2 transcription factor family
At1g50110 / branched-chain amino acid aminotransferase 6 /
At1g52470 / expressed protein
At1g67600 / expressed protein
At1g69526 / UbiE/COQ5 methyltransferase family protein
At1g70080 / terpene synthase/cyclase family protein
At1g72840 / disease resistance protein (TIR-NBS-LRR class), putative
At1g75520 / lateral root primordium (LRP) protein-related
At1g79580 / no apical meristem (NAM) family protein
At2g04460 / expressed protein
At2g37890 / mitochondrial substrate carrier family protein
At2g43140 / basic helix-loop-helix (bHLH) family protein
At2g43880 / polygalacturonase, putative / pectinase, putative
At2g47520 / member of the ERF (ethylene response factor) subfamily B-2 of ERF/AP2 transcription factor family
At3g01070 / plastocyanin-like domain-containing protein
At3g19200 / expressed protein
At3g44520 / esterase/lipase/thioesterase family protein
At4g16540 / heat shock protein-related
At4g23590 / aminotransferase class I and II family protein
At5g05880 / UDP-glucoronosyl/UDP-glucosyl transferase family protein
At5g08565 / expressed protein
At5g12410 / THUMP domain-containing protein
At5g17340 / expressed protein
At5g48175 / expressed protein
ATEXPA14 / expansin, putative (EXP14)
CYP705A27 / cytochrome P450 family protein
MYB94 / myb family transcription factor (MYB94)
NPC4 / phosphoesterase family protein
NRPD1a / DNA-directed RNA polymerase alpha subunit family protein
PLT2 / ovule development protein, putative
WER / myb family transcription factor (MYB66)
At1g43160
AOC2 / allene oxide cyclase, putative
At1g06620 / 2-oxoglutarate-dependent dioxygenase, putative
At1g10585 / similar to basic helix-loop-helix (bHLH) family protein
At1g22400 / UDP-glucoronosyl/UDP-glucosyl transferase family protein
At1g28050 / zinc finger (B-box type) family protein
At1g43160 / member of the ERF (ethylene response factor) subfamily B-4 of ERF/AP2 transcription factor family (RAP2.6)
At1g52890 / no apical meristem (NAM) family protein
At1g69480 / EXS family protein / ERD1/XPR1/SYG1 family protein
At1g70130 / lectin protein kinase, putative
At1g75220 / integral membrane protein, putative
At1g80110 / expressed protein
At2g22760 / basic helix-loop-helix (bHLH) family protein
At2g27830 / expressed protein
At2g36780 / UDP-glucoronosyl/UDP-glucosyl transferase family protein
At2g38240 / oxidoreductase
At2g38250 / DNA-binding protein-related
At2g43820 / UDP-glucoronosyl/UDP-glucosyl transferase family protein
At2g47950 / expressed protein
At3g02750 / protein phosphatase 2C family protein
At3g05390 / expressed protein
At3g06500 / beta-fructofuranosidase, putative
At3g11340 / UDP-glucoronosyl/UDP-glucosyl transferase family protein
At3g16330 / expressed protein
At3g17860 / expressed protein
At3g43250 / cell cycle control protein-related
At3g43270 / pectinesterase family protein
At3g46660 / UDP-glucoronosyl/UDP-glucosyl transferase family protein
At3g46670 / UDP-glucoronosyl/UDP-glucosyl transferase family protein
At3g51450 / strictosidine synthase family protein
At4g21680 / proton-dependent oligopeptide transport (POT) family protein
At4g23060 / similar to calmodulin-binding family protein
At4g27410 / no apical meristem (NAM) family protein (RD26)
At5g01210 / transferase family protein
At5g13220 / expressed protein
At5g52050 / MATE efflux protein-related
At5g65280 / lanthionine synthetase C-like family protein
At5g67480 / TAZ zinc finger family protein / BTB/POZ domain-containing protein
ATEXPA10 / expansin, putative (EXP10)
ATGSTU5 / glutathione S-transferase (103-1A)
ATGSTU6 / glutathione S-transferase, putative
CYP94B1 / cytochrome P450, putative
CYP94B3 / cytochrome P450 family protein
ELI3_2 / mannitol dehydrogenase, putative (ELI3-2)
GGPS6 / geranylgeranyl pyrophosphate synthase (GGPS6)
ILL6 / IAA-amino acid hydrolase 6, putative (ILL6)
MGD1 / 1,2-diacylglycerol 3-beta-galactosyltransferase, putative
WRKY67 / WRKY family transcription factor
At1g79700 = AP2.2
AP2.2 / ovule development protein, putative
ADG / ADP-glucose pyrophosphorylase family protein
AKDH / 2-oxoisovalerate dehydrogenase / 3-methyl-2-oxobutanoate dehydrogenase / branched-chain alpha-keto acid dehydrogenase E1 beta subunit (DIN4)
ALS / acetolactate synthase small subunit, putative
ASN1 / asparagine synthetase 1 (glutamine-hydrolyzing) / glutamine-dependent asparagine synthetase 1
At1g02660 / lipase class 3 family protein
At1g35612 / expressed protein
At1g54740 / expressed protein
At1g56220 / dormancy/auxin associated family protein
At1g70100 / expressed protein
At2g22980 / similar to serine carboxypeptidase S10 family protein
At2g30600 / BTB/POZ domain-containing protein
At3g21870 / cyclin family protein
At4g10910 / expressed protein
At4g14500 / expressed protein
At4g19160 / expressed protein
At4g35770 / senescence-associated protein (SEN1)
At5g14410 / expressed protein
At5g26740 / expressed protein
b-AMY / similar to beta-amylase (CT-BMY)
b-GAL / beta-galactosidase, putative
BZO2H3 / bZIP transcription factor family protein
CA / carbonic anhydrase family protein
GBF1 / G-box binding factor 1 (GBF1)
GRX / glutaredoxin family protein
MCCA / methylcrotonyl-CoA carboxylase alpha chain, mitochondrial / 3-methylcrotonyl-CoA carboxylase 1
PK-01330 / protein kinase family protein
PK-21170 / 5'-AMP-activated protein kinase beta-2 subunit, putative
PK-44610 / protein kinase family protein
PROX / proline oxidase, mitochondrial / osmotic stress-responsive proline dehydrogenase
TPP / glycosyl transferase family 20 protein / trehalose-phosphatase family protein
ZF-22920 / zinc finger (C3HC4-type RING finger) family protein
ABI4 = At2g40220
ABI4 / member of the DREB subfamily A-3 of ERF/AP2 transcription factor family (ABI4)
At1g43780 / serine carboxypeptidase S10 family protein
At1g49600 / RNA-binding protein 47 (RBP47), putative
At1g60160 / potassium transporter family protein
At1g72570 / ovule development protein, putative
At2g20180 / basic helix-loop-helix (bHLH) family protein
At2g24280 / serine carboxypeptidase S28 family protein
At2g26040 / Bet v I allergen family protein
At2g42790 / citrate synthase, glyoxysomal, putative
At3g05190 / aminotransferase class IV family protein
At3g15670 / late embryogenesis abundant protein, putative
At3g48700 / expressed protein
At3g54940 / cysteine proteinase, putative
At3g58060 / cation efflux family protein / metal tolerance protein, putative
At4g12910 / serine carboxypeptidase S10 family protein
At4g16210 / enoyl-CoA hydratase/isomerase family protein
At4g25140 / glycine-rich protein / oleosin
At4g30810 / serine carboxypeptidase S10 family protein
At5g08260 / serine carboxypeptidase S10 family protein
At5g24130 / expressed protein
At5g25020 / expressed protein
At5g44700 / leucine-rich repeat transmembrane protein kinase, putative
At5g54740 / protease inhibitor/seed storage/lipid transfer protein (LTP) family protein
At5g57390 / similar to ovule development protein, putative
At5g66780 / expressed protein
ATEXPA20 / expansin, putative
ATEXPA3 / expansin, putative
AtGRF5 / expressed protein
ATNRT2.7 / transporter, putative
ATOPT6 / oligopeptide transporter OPT family protein
delta_OAT / ornithine aminotransferase, putative
EXGT_A4 / xyloglucan:xyloglucosyl transferase
G_TMT / expressed protein
GA4H / gibberellin 3-beta-dioxygenase
MFP2 / fatty acid multifunctional protein (MFP2)
RGL3 / gibberellin response modulator, putative
SUT4 / sucrose transporter / sucrose-proton symporter
YSL6 / oligopeptide transporter OPT family protein
At3g14230
At1g12200 / flavin-containing monooxygenase family protein
At1g21890 / nodulin MtN21 family protein
At1g24530 / transducin family protein / WD-40 repeat family protein