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Table 4 Regulons (set of genes regulated by a TF) significantly enriched in DEGs (or which TF was DE) and associated with “carbohydrate metabolism”, “generation of precursor metabolites and energy”, or “secondary metabolism” GO terms

From: Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids

TF Regulon GO-EA Regulon size Regulon DE? DE stem DE leaf DE root TF DE? TF description
Misin01G049500 Carb. Met 30 Yes 4 6 2 No TSA1, tryptophan synthase alpha chain
Misin01G452600 Carb. Met 39 Yes 8 6 1 No Homeodomain-leucine zipper transcription factor TaHDZipI-1
Misin02G383200 Carb. Met 21 Yes 4 0 0 No LBD1, LOB domain-containing protein 1
Misin03G207100 Carb. Met 14 Yes 3 0 0 No Beta-1,3-galactosyltransferase 7
Misin03G237200 Sec. met 19 No 0 2 0 Leaf ODORANT1
Misin03G365800 Prec. Met 13 Yes 4 3 1 No Putative MYB DNA-binding
Misin04G236800 Carb. Met & Prec. Met 35 Yes 4 1 0 No TPA: putative HLH DNA-binding
Misin04G243500 Carb. Met 87 No 2 2 0 Leaf Transcription factor bHLH137
Misin04G316000 Sec. met 17 No 0 3 0 Leaf Transcription factor ABORTED MICROSPORES-like
Misin05G004600 Sec. met 18 No 2 0 0 Stem WRKY transcription factor 31
Misin05G170700 Sec. met 23 Yes 4 0 0 No Putative transcription factor bHLH041
Misin06G000800 Carb. Met & Prec. Met 24 Yes 6 8 2 Leaf/Stem/Root TPA: putative HLH DNA-binding
Misin06G026100 Sec. met 22 Yes 6 0 0 No Putative transcription factor bHLH041
Misin06G170200 Sec. met 19 No 3 0 0 Stem Putative transcription factor bHLH041
Misin06G257300 Prec. Met 28 Yes 5 0 0 Stem HSF1, heat stress transcription factor C-1b
Misin07G012200 Sec. met 29 Yes 4 0 0 No Catalase
Misin07G160300 Prec. Met 11 Yes 3 2 1 No RNA polymerase I termination factor isoform X1
Misin07G253100 Prec. Met 69 Yes 7 3 2 No Hydroxymethylglutaryl-CoA synthase
Misin07G375400 Carb. Met & Prec. Met 31 No 3 2 0 Leaf Ethylene-responsive transcription factor
Misin08G219000 Prec. Met 58 Yes 2 5 1 No LAF1
Misin10G025900 Prec. Met 15 Yes 6 3 0 No Light-inducible protein CPRF2
Misin12G063100 Carb. Met & Sec. Met 23 Yes 5 1 0 No Ethylene-responsive transcription factor ERF113
Misin12G092100 Carb. Met 49 No 1 4 0 Leaf Putative 12-oxophytodienoate reductase 11
Misin13G183300 Prec. Met 38 No 2 1 0 Stem bHLH family
Misin15G053900 Sec. met 23 Yes 6 2 0 No GLDP1, glycine dehydrogenase mitochondrial
Misin16G048700 Carb. Met 59 No 1 4 0 Leaf MYB transcription factor
Misin18G114300 Prec. Met 3 No 0 1 0 Leaf ODORANT1
MisinT099300 Sec. met 61 Yes 29 26 22 No Pentatricopeptide repeat-containing
  1. TF, Transcription factor; Regulon GO-EA, GO terms enriched in the target genes; Carb. Met., Carbohydrate metabolism (GO:5976); Sec. met., Secondary metabolism; Prec. Met., Generation of precursor metabolites and energy (GO:6091); Regulon size, Number of target genes in the regulon; Regulon DE? Is the regulon enriched in DE target genes?; DE stem/leaf/root, Number of target genes that are DE in stem/leaf/root, respectively; TF DE? Is the transcription factor DE in any tissue?
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Biotechnology for Biofuels

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