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Table 4 Functional annotations of the TF targets

From: Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors

MIPS Bincodea MIPS Annotation categoryb BHLHc BZIPd HSFe NACf WRKYg AP2 (CBF)h DOFi MYBj MADSk TCP2l AP2 (AtERF)m
01 METABOLISM 10 -2 10-1 10-1 101 101 10-1 10-1 10-1 10-1 10-1 101
01.01.03 Assimilation of ammonia, metabolism of the glutamate group 10 -2 N/A N/A N/A N/A N/A 10-1 10-1 N/A N/A N/A
01.03.04.03 Pyrimidine nucleotide anabolism 10 -2 N/A N/A N/A N/A N/A 10-1 N/A N/A N/A N/A
01.05 C-compound and carbohydrate metabolism 10-1 10 -2 10-1 101 10-1 101 10 -2 10-1 10-1 N/A N/A
01.05.01.03 C-compound, carbohydrate anabolism N/A N/A N/A N/A N/A N/A N/A N/A 10 -2 N/A N/A
01.05.01.03.02 Polysaccharide biosynthesis N/A N/A N/A N/A N/A N/A N/A N/A 10 -2 N/A N/A
01.06 Lipid, fatty acid and isoprenoid metabolism 10-1 101 N/A 10-1 N/A 10-1 10-1 101 N/A 10 -2 N/A
01.06.01.01 Phospholipid biosynthesis N/A 10 -2 N/A 10 -2 N/A 10 -2 101 N/A N/A N/A N/A
01.06.04 Degradation of lipids, fatty acids and isoprenoids 10 -3 N/A N/A 10-1 N/A N/A 10 -2 N/A N/A 10 -2 N/A
01.20.17 Biosynthesis of secondary products derived from primary amino acids 10 -3 N/A 10-1 10-1 N/A N/A 10-1 10 -2 N/A N/A N/A
01.20.17.01 Biosynthesis of nonprotein amino acids 10-1 N/A N/A N/A N/A N/A 10-1 10 -2 N/A N/A N/A
01.20.17.09 Biosynthesis of alkaloids 10-1 N/A N/A 10-1 N/A N/A 10-1 10 -2 N/A N/A N/A
01.20.35 Biosynthesis of secondary products derived from L-phenylalanine and L-tyrosine N/A N/A 10-1 N/A 10-1 10-1 101 N/A N/A N/A 10 -2
01.20.35.01 Biosynthesis of phenylpropanoids N/A N/A 10-1 N/A 10-1 10-1 101 N/A N/A N/A 10 -2
02 ENERGY 10-1 10 -3 10 -2 101 101 10-1 10 -2 10-1 N/A N/A N/A
02.13 Respiration 10-1 10 -2 N/A 10-1 N/A N/A 10-1 10-1 N/A N/A N/A
02.13.03 Aerobic respiration 10-1 10-1 N/A 10-1 N/A N/A 10 -2 N/A N/A N/A N/A
02.19 Metabolism of energy reserves (e.g. glycogen, trehalose) 10-1 10 -4 10 -2 10-1 N/A N/A 10-1 N/A N/A N/A N/A
04 STORAGE PROTEIN N/A N/A N/A N/A N/A N/A 10-1 N/A N/A N/A 10 -2
10.01 DNA processing 10-1 10 -2 101 N/A 10-1 N/A 10-1 N/A N/A N/A N/A
10.03.04.03 Chromosome condensation 10-1 10 -2 N/A N/A N/A N/A N/A N/A N/A N/A N/A
11 TRANSCRIPTION 10-1 10 -2 10 -2 10 -3 10 -4 10-1 10 -4 101 10-1 N/A 10-1
11.02 RNA synthesis 10-1 10 -2 10 -2 10 -4 10 -5 10-1 10 -4 10-1 10-1 N/A 10-1
11.02.01 rRNA synthesis N/A N/A 10 -2 10-1 10-1 10 -2 N/A N/A N/A N/A N/A
11.02.03 mRNA synthesis 10-1 10 -2 10 -2 10 -3 10 -4 10-1 10 -4 10-1 10-1 N/A 10-1
11.02.03.04 Transcriptional control 10-1 10 -2 10-1 10 -3 10 -3 10-1 10 -3 101 10-1 N/A 10-1
11.04 RNA processing 101 10-1 10 -3 10 -2 10 -2 10 -2 10-1 10-1 N/A N/A N/A
11.04.01 rRNA processing N/A N/A 10 -3 10-1 10 -2 10 -3 N/A N/A N/A N/A N/A
11.04.02 tRNA processing N/A 10 -2 N/A N/A N/A N/A 10-1 N/A N/A N/A N/A
11.04.03 mRNA processing (splicing, 5'-, 3'-end processing) 10-1 N/A 10 -2 10 -2 10-1 10-1 10-1 10-1 N/A N/A N/A
11.04.03.01 Splicing 10-1 N/A 10-1 10 -2 10-1 10-1 10-1 10 -2 N/A N/A N/A
12.04.03 Translation termination 10 -2 N/A N/A 10 -2 N/A N/A N/A N/A N/A N/A N/A
16.03.01 DNA binding 10-1 10 -2 N/A N/A N/A N/A N/A N/A N/A N/A N/A
16.13 C-compound binding N/A N/A 10-1 N/A 10 -2 N/A 10-1 N/A N/A N/A N/A
18 PROTEIN ACTIVITY REGULATION N/A 10-1 10-1 10-1 10 -2 10-1 10-1 N/A N/A N/A N/A
18.01.01 Modification N/A N/A 10-1 N/A 10 -2 N/A 10-1 N/A N/A N/A N/A
18.02.05 Regulator of G-protein signalling N/A 10 -2 N/A 10 -2 10 -2 10 -2 10-1 N/A N/A N/A N/A
20 CELLULAR TRANSPORT, TRANSPORT FACILITATION AND TRANSPORT ROUTES 10 -2 101 101 10-1 N/A 101 10-1 10-1 10-1 N/A N/A
20.01 Transported compounds (substrates) 10 -2 101 101 10-1 N/A 10-1 10 -2 10-1 N/A N/A N/A
20.01.01 Ion transport 10-1 N/A 101 101 N/A 10-1 10 -2 10-1 N/A N/A N/A
20.01.03 C-compound and carbohydrate transport 10-1 N/A 10-1 10 -2 N/A 10 -2 N/A 10-1 N/A N/A N/A
20.09.07 Vesicular transport (Golgi network, etc.) 10 -2 10-1 N/A 10-1 N/A N/A 10-1 N/A 10-1 N/A N/A
30.05.01.10 Two-component signal transduction system (sensor kinase component) N/A 10 -2 N/A N/A N/A N/A N/A N/A N/A N/A N/A
32 CELL RESCUE, DEFENSE AND VIRULENCE 10-1 101 10 -2 10 -2 10 -2 10 -4 10 -2 10-1 N/A N/A 10-1
32.01 Stress response 10 -2 101 10 -3 10 -2 101 10 -4 10 -2 10-1 N/A N/A 10-1
32.05 disease, virulence and defense 101 101 101 10-1 10 -2 10-1 10-1 10-1 N/A N/A N/A
32.05.03 defense related proteins N/A 10-1 10-1 10-1 10 -3 10 -3 10-1 10-1 N/A N/A N/A
36.25.16 Immune response N/A N/A 10-1 N/A 10 -2 N/A 10-1 N/A N/A N/A N/A
40 CELL FATE 10 -2 101 N/A 101 N/A 10-1 10-1 101 N/A N/A N/A
40.20 Cell aging 10 -3 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A
41.05.10 Late embryonic development N/A N/A N/A 10 -2 N/A 10 -2 N/A N/A N/A N/A N/A
42.02 Eukaryotic plasma membrane N/A 10 -2 N/A 10-1 10 -2 10-1 N/A N/A N/A N/A N/A
42.10 Nucleus 10-1 10 -2 N/A N/A N/A N/A N/A N/A N/A N/A N/A
42.10.03 Organization of chromosome structure 10-1 10 -2 N/A N/A N/A N/A N/A N/A N/A N/A N/A
70 SUBCELLULAR LOCALIZATION 10 -2 10 -2 10-1 101 10-1 101 10-1 101 101 N/A 10-1
70.01 Cell wall 10-1 N/A N/A 10 -2 10-1 10-1 10-1 N/A N/A N/A N/A
70.08 Golgi 10-1 N/A N/A N/A N/A N/A 10-1 N/A 10 -2 N/A N/A
70.09 Intracellular transport vesicles 10 -2 10-1 N/A 10-1 N/A N/A 10 -2 N/A N/A N/A N/A
70.10 Nucleus 101 10 -3 10-1 101 10 -2 10-1 101 N/A N/A N/A 10-1
70.10.03 Chromosome 10-1 10 -2 N/A N/A N/A N/A N/A N/A N/A N/A N/A
73.03.09 Immune cell N/A N/A 10 -2 N/A 10 -2 N/A 10 -2 N/A N/A N/A N/A
98 CLASSIFICATION NOT YET CLEAR-CUT 10-1 10 -3 10 -3 10 -3 10 -2 10 -3 10 -4 10-1 10-1 10-1 10-1
  1. Significant functional annotations of the cluster of genes putatively regulated by the TF-encoding genes. a and b: annotation categories in the MIPS functional annotation database. c to m: p-values obtained for all the genes putatively regulated by the corresponding TF. The significance of the annotation (p) for the list of all target genes putatively regulated by a TF was calculated using the MIPS online interface. Entries in bold denote significant annotations (p < 0.05).