Co-Expression Analysis of:

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CYP73A5, C4H (At2g30490)

Pathways co-expressed in all four data set

Pathway

Source

Sum of scores

Sum of genes

Find below a list of pathways that are co-expressed with the bait. First a list of pathways is given that are co-expressed in all four data sets. Data for each individual list are shown underneath. To the right of each table a thumbnail of the actual co-expression heatmap is given. Klick on the link to see the heatmap containing all co-expressed genes.

lignin biosynthesis

AraCyc

520

56

lignin biosynthesis

TAIR-GO

480

52

Phenylpropanoid Metabolism

BioPath

400

44

Phenylpropanoid pathway

LitPath

318

35

core phenylpropanoid metabolism

BioPath

260

26

For more information on how these pathway maps were generated please read the description of methods page

phenylpropanoid metabolism

TAIR-GO

250

25

suberin biosynthesis

AraCyc

200

20

Stilbene, coumarine and lignin biosynthesis

KEGG

186

21

phenylpropanoid biosynthesis

TAIR-GO

180

18

phenylpropanoid biosynthesis

AraCyc

170

17

flavonoid biosynthesis

AraCyc

162

17

response to wounding

TAIR-GO

130

13

Phenylalanine metabolism

KEGG

98

13

Flavonoid biosynthesis

KEGG

90

9

Alkaloid biosynthesis I

KEGG

82

9

phenylpropanoid pathway, initial reactions

AraCyc

80

8

biosynthesis of phenylpropanoids

FunCat

80

8

biosynthesis of secondary products derived from L-phenylalanine and L-tyrosine

FunCat

80

8

amino acid metabolism

FunCat

69

7

defense response

TAIR-GO

56

6

Tyrosine metabolism

KEGG

52

6

Fluorene degradation

KEGG

50

5

gamma-Hexachlorocyclohexane degradation

KEGG

50

5

salicylic acid biosynthesis

AraCyc

40

4

metabolism of the cysteine - aromatic group

FunCat

40

4

Alkaloid biosynthesis II

KEGG

40

4

Pathways co-expressed in the Organ and Tissue data set

CYP73A5, C4H (At2g30490)

max. difference between log2-ratios:

4.51

max. difference between log2-ratios excluding lowest and highest 5%:

3.85

Pathway

Source

Scores of Genes

p[Score]

No. of Genes

p[genes]

Link to organ heatmap showing details of all co-expressed genes

Phenylpropanoid pathway

LitPath

80

0.000

8

0.000

Phenylpropanoid Metabolism

BioPath

76

0.000

8

0.000

lignin biosynthesis

AraCyc

70

0.000

7

0.000

core phenylpropanoid metabolism

BioPath

60

0.000

6

0.000

suberin biosynthesis

AraCyc

50

0.000

5

0.000

Stilbene, coumarine and lignin biosynthesis

KEGG

50

0.000

5

0.000

lignin biosynthesis

TAIR-GO

30

0.000

3

0.000

phenylpropanoid biosynthesis

TAIR-GO

30

0.000

3

0.000

response to wounding

TAIR-GO

30

0.000

3

0.000

Phenylalanine metabolism

KEGG

22

0.000

3

0.004

phenylpropanoid biosynthesis

AraCyc

20

0.000

2

0.000

phenylpropanoid pathway, initial reactions

AraCyc

20

0.000

2

0.000

biogenesis of cell wall

FunCat

20

0.000

2

0.000

Phenylalanine, tyrosine and tryptophan biosynthesis

KEGG

18

0.000

3

0.000

Aromatic amino acid (Phe, Tyr, Trp) metabolism

BioPath

16

0.000

2

0.010

aromatic amino acid family biosynthesis

TAIR-GO

16

0.000

2

0.001

aromatic amino acid family biosynthesis, shikimate pathway

TAIR-GO

16

0.000

2

0.000

glyphosate metabolism

TAIR-GO

16

0.000

2

0.000

chorismate biosynthesis

AraCyc

16

0.000

2

0.000

chorismate biosynthesis

LitPath

16

0.000

2

0.001

Shikimate pathway

LitPath

16

0.000

2

0.029

cellulose biosynthesis

AraCyc

14

0.000

2

0.008

Alkaloid biosynthesis I

KEGG

12

0.000

2

0.001

Tyrosine metabolism

KEGG

12

0.000

2

0.003

Pathways co-expressed in the Stress data set

CYP73A5, C4H (At2g30490)

max. difference between log2-ratios:

max. difference between log2-ratios excluding lowest and highest 5%:

Pathway

Source

Scores of Genes

p[Score]

No. of Genes

p[genes]

Link to stress heatmap showing details of all co-expressed genes

Phenylpropanoid Metabolism

BioPath

142

0.000

16

0.000

Phenylpropanoid pathway

LitPath

124

0.000

14

0.000

lignin biosynthesis

AraCyc

110

0.000

11

0.000

core phenylpropanoid metabolism

BioPath

100

0.000

10

0.000

Stilbene, coumarine and lignin biosynthesis

KEGG

64

0.000

8

0.000

suberin biosynthesis

AraCyc

60

0.000

6

0.000

lignin biosynthesis

TAIR-GO

50

0.000

5

0.000

Aromatic amino acid (Phe, Tyr, Trp) metabolism

BioPath

42

0.000

6

0.000

chorismate biosynthesis

LitPath

42

0.000

6

0.000

Shikimate pathway

LitPath

42

0.000

6

0.000

phenylpropanoid biosynthesis

TAIR-GO

40

0.000

4

0.000

response to wounding

TAIR-GO

40

0.000

4

0.000

aromatic amino acid family biosynthesis

TAIR-GO

38

0.000

5

0.000

aromatic amino acid family biosynthesis, shikimate pathway

TAIR-GO

38

0.000

5

0.000

Phenylalanine, tyrosine and tryptophan biosynthesis

KEGG

38

0.000

5

0.000

Intermediary Carbon Metabolism

BioPath

30

0.008

6

0.029

flavonoid biosynthesis

AraCyc

30

0.000

3

0.001

chorismate biosynthesis

AraCyc

26

0.000

4

0.000

Phenylalanine metabolism

KEGG

24

0.000

4

0.016

oxidative branch of the pentose phosphate pathway

AraCyc

22

0.000

4

0.000

biogenesis of cell wall

FunCat

22

0.000

3

0.005

pentose-phosphate pathway

FunCat

22

0.000

4

0.000

Pentose phosphate pathway

KEGG

22

0.000

4

0.001

phenylpropanoid metabolism

TAIR-GO

20

0.000

2

0.000

response to pathogenic fungi

TAIR-GO

20

0.000

2

0.000

response to UV

TAIR-GO

20

0.000

2

0.004

phenylpropanoid biosynthesis

AraCyc

20

0.000

2

0.000

phenylpropanoid pathway, initial reactions

AraCyc

20

0.000

2

0.000

biosynthesis of phenylpropanoids

FunCat

20

0.000

2

0.006

biosynthesis of secondary products derived from L-phenylalanine and L-tyrosine

FunCat

20

0.000

2

0.006

Ascorbate and aldarate metabolism

KEGG

20

0.000

2

0.009

Fluorene degradation

KEGG

20

0.000

2

0.002

gamma-Hexachlorocyclohexane degradation

KEGG

20

0.000

2

0.003

defense response

TAIR-GO

18

0.000

2

0.012

glyphosate metabolism

TAIR-GO

16

0.000

2

0.000

response to light

TAIR-GO

14

0.000

3

0.012

glycerol degradation II

AraCyc

12

0.002

2

0.051

C-compound and carbohydrate utilization

FunCat

12

0.000

2

0.000

Lipid signaling

AcylLipid

12

0.000

2

0.168

Nicotinate and nicotinamide metabolism

KEGG

11

0.034

2

0.166

Pathways co-expressed in the Hormone etc. data set

CYP73A5, C4H (At2g30490)

max. difference between log2-ratios:

max. difference between log2-ratios excluding lowest and highest 5%:

Pathway

Source

Scores of Genes

p[Score]

No. of Genes

p[genes]

Link to hormones etc. heatmap showing details of all co-expressed genes

Phenylpropanoid Metabolism

BioPath

116

0.000

13

0.000

lignin biosynthesis

AraCyc

82

0.000

9

0.000

Phenylpropanoid pathway

LitPath

82

0.000

9

0.000

core phenylpropanoid metabolism

BioPath

70

0.000

7

0.000

suberin biosynthesis

AraCyc

60

0.000

6

0.000

Folding, Sorting and Degradation

KEGG

60

0.000

11

0.000

protein catabolism

TAIR-GO

52

0.000

8

0.000

ubiquitin-dependent protein catabolism

TAIR-GO

52

0.000

8

0.000

flavonoid biosynthesis

AraCyc

52

0.000

6

0.000

Proteasome

KEGG

52

0.000

8

0.000

Stilbene, coumarine and lignin biosynthesis

KEGG

52

0.000

6

0.022

Intermediary Carbon Metabolism

BioPath

44

0.000

8

0.019

response to wounding

TAIR-GO

40

0.000

4

0.001

tricarboxylic-acid pathway (citrate cycle, Krebs cycle, TCA cycle)

FunCat

40

0.000

7

0.002

Flavonoid biosynthesis

KEGG

40

0.000

4

0.000

proteasome core complex (sensu Eukaryota)

TAIR-GO

36

0.000

6

0.000

Oxidative phosphorylation

KEGG

36

0.000

11

0.000

Flavonoid and anthocyanin metabolism

BioPath

32

0.000

4

0.013

Phenylalanine metabolism

KEGG

32

0.000

4

0.101

flavonoid biosynthesis

TAIR-GO

30

0.000

3

0.000

lignin biosynthesis

TAIR-GO

30

0.000

3

0.000

phenylpropanoid biosynthesis

TAIR-GO

30

0.000

3

0.000

response to UV

TAIR-GO

30

0.000

3

0.001

Citrate cycle (TCA cycle)

KEGG

30

0.000

6

0.000

flavonoid, anthocyanin, and proanthocyanidin biosynthesis

LitPath

30

0.000

3

0.000

proanthocyanidin biosynthesis

LitPath

30

0.000

3

0.000

amino acid metabolism

FunCat

29

0.012

3

0.213

transport

FunCat

25

0.000

5

0.000

Carbon fixation

KEGG

24

0.003

3

0.113

Gluconeogenesis from lipids in seeds

BioPath

22

0.003

4

0.030

Glutathione metabolism

BioPath

22

0.008

3

0.103

TCA cycle -- aerobic respiration

AraCyc

22

0.000

4

0.007

TCA cycle variation IV

AraCyc

22

0.000

4

0.006

TCA cycle variation VII

AraCyc

22

0.005

4

0.035

TCA cycle variation VIII

AraCyc

22

0.000

4

0.008

secondary metabolism

FunCat

22

0.000

3

0.048

phenylpropanoid metabolism

TAIR-GO

20

0.000

2

0.001

response to pathogenic fungi

TAIR-GO

20

0.000

2

0.000

aspartate degradation I

AraCyc

20

0.000

2

0.029

aspartate degradation II

AraCyc

20

0.000

2

0.008

phenylpropanoid biosynthesis

AraCyc

20

0.000

2

0.000

phenylpropanoid pathway, initial reactions

AraCyc

20

0.000

2

0.000

biosynthesis of phenylpropanoids

FunCat

20

0.000

2

0.042

biosynthesis of secondary products derived from L-phenylalanine and L-tyrosine

FunCat

20

0.000

2

0.042

Alkaloid biosynthesis I

KEGG

20

0.000

2

0.023

Tyrosine metabolism

KEGG

20

0.000

2

0.104

acetyl-CoA assimilation

AraCyc

18

0.000

3

0.009

aerobic respiration -- electron donors reaction list

AraCyc

18

0.000

5

0.000

mixed acid fermentation

AraCyc

18

0.000

3

0.012

biogenesis of chloroplast

FunCat

18

0.018

2

0.166

Glutamate metabolism

KEGG

18

0.012

2

0.123

electron / hydrogen transport

FunCat

17

0.000

3

0.000

transport facilitation

FunCat

17

0.000

3

0.000

transported compounds (substrates)

FunCat

17

0.000

3

0.000

proteasome regulatory particle, base subcomplex (sensu Eukaryota)

TAIR-GO

16

0.000

2

0.004

Phenylalanine, tyrosine and tryptophan biosynthesis

KEGG

16

0.032

2

0.123

formaldehyde assimilation I (serine pathway)

AraCyc

14

0.001

2

0.053

gluconeogenesis

AraCyc

14

0.020

2

0.111

serine-isocitrate lyase pathway

AraCyc

14

0.025

2

0.111

Glutathione metabolism

KEGG

14

0.041

2

0.116

Chloroplastic protein turnover

BioPath

12

0.000

3

0.000

ClpP protease complex

BioPath

12

0.000

3

0.000

ATP-dependent proteolysis

TAIR-GO

12

0.000

3

0.000

chloroplastic endopeptidase Clp complex

TAIR-GO

12

0.000

3

0.000

Pathways co-expressed in the Mutant data set

CYP73A5, C4H (At2g30490)

max. difference between log2-ratios:

max. difference between log2-ratios excluding lowest and highest 5%:

Pathway

Source

Scores of Genes

p[Score]

No. of Genes

p[genes]

Link to mutants heatmap showing details of all co-expressed genes

Phenylpropanoid Metabolism

BioPath

66

0.000

7

0.000

Ribosome

KEGG

34

0.012

6

0.024

lignin biosynthesis

AraCyc

32

0.000

4

0.000

Phenylpropanoid pathway

LitPath

32

0.000

4

0.008

core phenylpropanoid metabolism

BioPath

30

0.000

3

0.000

Flavonoid and anthocyanin metabolism

BioPath

30

0.000

3

0.000