Table 1 |
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Genes from 22 k Arabidopsis ATH1 array that have the highest correlation across 965 chips with the hub genes. |
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Hub Gene: MCCB, At4g34030, methylcrotonyl-CoA carboxylase, subunit B, leucine catabolism |
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Corr. |
GeneID |
Description |
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0.9 |
At1g03090 |
MCCA, methylcrotonyl-CoA carboxylase, subunit A |
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0.84 |
At3g06850 |
BCE2, E2 subunit of branched chain alpha-ketoacid dehydrogenase |
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0.84 |
At3g13450 |
DIN4, E1 beta subunit of branched-chain alpha-keto acid dehydrogenase |
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0.82 |
At2g43400 |
electron transfer flavoprotein: ubiquinone oxidoreductase family protein |
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0.8 |
At3g45300 |
IVD, isovaleryl-CoA dehydrogenase |
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0.8 |
At4g35770 |
Senescence-associated protein (SEN1) |
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0.79 |
At5g21170 |
AMP-activated protein kinase |
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0.78 |
At1g08630 |
threonine aldolase |
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0.78 |
At1g15040 |
glutamine amidotransferase-related |
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0.77 |
At1g10070 |
BCAT2, branched-chain amino acid transaminase |
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0.74 |
At4g28040 |
nodulin MtN21 family protein |
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0.73 |
At3g47340 |
glutamine-dependent asparagine synthetase 1 (ASN1) |
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0.73 |
At1g21400 |
E1 alpha subunit of branched-chain alpha-keto acid dehydrogenase, BCDH_E1a2 |
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0.72 |
At1g18270 |
ketose-bisphosphate aldolase class-II family protein |
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0.71 |
At5g49450* |
bZIP family transcription factor |
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0.71 |
At1g55510 |
BCDH BETA1, E1 beta subunit of branched-chain alpha-keto acid dehydrogenase |
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0.7 |
At3g49790 |
expressed protein |
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Hub Gene: DE2, At2g40840, disproportionating enzyme, starch metabolism |
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Corr. |
GeneID |
Description |
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0.89 |
At3g46970 |
PHS2, starch phosphorylase |
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0.85 |
At1g10760 |
GWD1, glucan water dikinase |
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0.85 |
At3g52180* |
SEX4, protein tyrosine phosphatase/kinase |
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0.8 |
At1g03310 |
ISA2, isoamylase DB |
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0.79 |
At4g09020 |
ISA3, isoamylase DB |
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0.76 |
At1g06460 |
31.2 kDa small heat shock family protein/hsp20 family protein |
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0.74 |
At5g26570 |
GWD2, glucan water dikinase |
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0.74 |
At3g29320 |
PHS1, starch phosphorylase |
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0.73 |
At5g59130 |
subtilase family protein |
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0.73 |
At2g39920 |
acid phosphatase class B family protein |
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0.72 |
At1g69830 |
AAM3, alpha-amylase |
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0.72 |
At1g67660 |
expressed protein |
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0.71 |
At3g18500 |
similar to endonuclease/exonuclease/phosphatase family protein |
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0.7 |
At2g31040 |
ATP synthase protein I-related |
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0.7 |
At4g33490 |
nucellin-like protein |
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Hub Gene: MOD1, At2g05990, enoyl reductase, fatty acid biosynthesis |
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Corr. |
GeneID |
Description |
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0.86 |
At1g34430 |
PDHC_E2, acetyltransferase subunit of pyruvate dehydrogenase |
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0.86 |
At5g10160 |
HD, 3-hydroxyacyl-[ACP] dehydratase |
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0.84 |
At5g35360 |
CAC2, biotin carboxylase subunit of heteromeric acetyl-CoA carboxylase |
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0.83 |
At5g46290 |
KASI, 3-ketoacyl-[ACP] synthase I |
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0.8 |
At2g30200 |
MAT, malonyl-CoA:ACP transacylase |
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0.8 |
At3g16950 |
LPD1, lipoamide dehydrogenase subunit of pyruvate dehydrogenase |
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0.79 |
At1g62640 |
KAS III, 3-ketoacyl-[ACP] synthase III |
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0.78 |
At1g53520$ |
chalcone-flavanone isomerase-related |
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0.77 |
At3g25860 |
LTA2, acetyltransferase subunit of pyruvate dehydrogenase |
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0.77 |
At5g52920 |
pyruvate kinase |
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0.76 |
At5g16390 |
BCCP1, biotin carboxyl carrier subunit of heteromeric acetyl-CoA carboxylase |
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0.75 |
At5g08415 |
LIP1-like, lipoate synthase |
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0.73 |
At2g22230 |
HD-like, 3-hydroxyacyl-[ACP] dehydratase |
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0.72 |
At1g30120 |
PDHC_E1beta2, E1 beta subunit of plastidic pyruvate dehydrogenase |
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0.72 |
At5g15530 |
BCCP2, biotin carboxyl carrier subunit of heteromeric acetyl-CoA carboxylase |
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0.71 |
At1g01090 |
PDHC_E1alpha, E1 alpha subunit of plastidic pyruvate dehydrogenase |
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0.71 |
At5g50390* |
pentatricopeptide (PPR) repeat-containing protein |
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0.7 |
At4g12700 |
expressed protein |
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Genes used as the hub (at the top of the table) are methylcrotonyl-CoA carboxylase (MCCB), active in leucine degradation in mitochondria; disproportionating enzyme (DE2), from starch metabolism; and enoyl reductase (MOD1), an enzyme from plastidic fatty acid biosynthesis pathway. Genes that code for proteins predicted to be in the same pathway as the hub gene are in bold font. Potential regulatory genes are marked with an asterisk. Pearson coefficients (> 0.7) were calculated by MetaOmGraph. P-values for enrichment of genes from same pathway as hub are 4.35e-36, 2.02e-15, and 3.1e-23, respectively. $ This gene product, although annotated as chalcone isomerase-like, appears to have a direct role in binding and possibly transporting fatty acids (Joe Noel and Florence Pojer, personal communication). |
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Mentzen et al. BMC Plant Biology 2008 8:76 doi:10.1186/1471-2229-8-76 |
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