Displaying PathwaysDisplaying Pathways

Most biologists are familiar with big pathway overviews

• Group biological items together that belong together

• Use a microheatmap, each item is colored according to ist value

• Pathway regulation becomes immedeately visible

Visualizing PathwaysVisualizing Pathways

Turned out to be root isoforms

Visualizing PathwaysVisualizing Pathways

Pathways, ProcessesPathways, Processes

ChromosomesChromosomes

TimecoursesTimecourses

You can only visualize so much data, a pathway(network) is feasible

Different ItemsDifferent Items

Can be depicted using different symbols.Problematic is: we can measure nearly all transcripts, several hundred proteins and about 100-200 known metabolites (routinely)

Case StudyCase Study

noondawn

3 days

6 h after transfer 78 h after transfer

6 h after transfer 78 h after transfer

Temperature (°C)

Pyruvate

0

0.5

1.0

1.5

2.0

Acetyl-CoA

0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

2-Oxoglutarate

0

20406080

100120140160

nmol

.g-1F

Wµ

mol

.g-1F

W (

eq.

gluc

ose)

Glucose-6-P

0

100

200

300

400

500

600

700

Glucose

0

5

10

15

20

25

0

Fructose

5

10

15

Starch

81012141618200

20

40

60

Sucrose

0

2

4

6

Rat

ioR

atio

Rat

io

Rat

ionm

ol.g

-1F

Wnm

ol.g

-1F

W

8101214161820

0

Glutamate

0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

6h treatment 78h treatment

Glutamine

1

2

3

4

Rat

ioR

atio

Serine

0

0.2

0.4

0.6

0.8

1.0

Rat

io

Glycine

0

5

10

15

Protein content

mg.

g-1F

W

0

5

10

15

20

25

Total amino acids

0

10

20

30

40

µm

ol.g

-1F

W

8101214161820

Major metabolitesMajor metabolites

Raffinose metabolismLight reactions

Calvin cycle

Fermentation

Carbonic anhydrase family

Flavonoidmetabolism

At3g22370 AOX1a

Cell wall modification

6h at 12°C6h at 12°C

At1g09350, At2g47180 Galactinol synthases

At5g40390 Raffinose synthase

At1g61800 GPT2

At1g32900 GBS1

At4g39210 APL4

At2g39800At3g55610 P5CSB

At4g33070 PDC

At1g77120 ADH

At5g20830 SuSy5.2

At1g07180 NDA1

SPS3bSPP2

At1g12240, At1g62660 vacuolar invertases

At4g05020 NDA

At4g39800, MIPS1

78h at 8°C78h at 8°C

78 hours, 8°C6 hours, 12°C

RNA and Protein SynthesisRNA and Protein Synthesis