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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).
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