| _________________________________________ |
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| Pathways co-expressed in all 4 data sets (with more than 6 annotation points each) |
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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 data sets. Lists for each individual dataset are shown underneath. Depending on the number of co-expressed pathways only the top scoring pathways are given; all data can be saved as text using the link above. |
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| Pathway |
Source |
Sum of scores |
Sum of genes |
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| lignin biosynthesis |
TAIR-GO |
120 |
12 |
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| lignin biosynthesis |
AraCyc |
120 |
12 |
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| phenylpropanoid biosynthesis |
TAIR-GO |
80 |
8 |
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| Phenylpropanoid Metabolism |
BioPath |
72 |
8 |
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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. |
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| core phenylpropanoid metabolism |
BioPath |
70 |
7 |
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| Phenylpropanoid pathway |
LitPath |
70 |
7 |
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| Stilbene, coumarine and lignin biosynthesis |
KEGG |
62 |
7 |
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For more information on how these pathway maps were generated please read the methods page |
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| Ascorbate and aldarate metabolism |
KEGG |
50 |
5 |
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| Fluorene degradation |
KEGG |
50 |
5 |
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| gamma-Hexachlorocyclohexane degradation |
KEGG |
50 |
5 |
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| biogenesis of cell wall |
FunCat |
42 |
5 |
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| biosynthesis of phenylpropanoids |
FunCat |
40 |
4 |
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| biosynthesis of secondary products derived from L-phenylalanine and L-tyrosine |
FunCat |
40 |
4 |
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| Pathways co-expressed in the Organ and Tissue data set (with more than 6 annotation points) |
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CYP84A1, F5H, FAH1, CA5H (At4g36220) |
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| max. difference between log2-ratios: |
4.5 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
2.8 |
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| Pathway |
Source |
Scores of Genes |
p[Score] |
No. of Genes |
p[genes] |
Link to organ heatmap |
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| core phenylpropanoid metabolism |
BioPath |
10 |
0.000 |
1 |
0.000 |
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| Phenylpropanoid Metabolism |
BioPath |
10 |
0.000 |
1 |
0.004 |
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| lignin biosynthesis |
TAIR-GO |
10 |
0.000 |
1 |
0.000 |
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| phenylpropanoid biosynthesis |
TAIR-GO |
10 |
0.000 |
1 |
0.000 |
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| lignin biosynthesis |
AraCyc |
10 |
0.000 |
1 |
0.000 |
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| biogenesis of cell wall |
FunCat |
10 |
0.000 |
1 |
0.002 |
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| biosynthesis of phenylpropanoids |
FunCat |
10 |
0.000 |
1 |
0.001 |
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| biosynthesis of secondary products derived from L-phenylalanine and L-tyrosine |
FunCat |
10 |
0.000 |
1 |
0.001 |
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| Ascorbate and aldarate metabolism |
KEGG |
10 |
0.000 |
1 |
0.000 |
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| Fluorene degradation |
KEGG |
10 |
0.000 |
1 |
0.000 |
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| gamma-Hexachlorocyclohexane degradation |
KEGG |
10 |
0.000 |
1 |
0.000 |
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| Stilbene, coumarine and lignin biosynthesis |
KEGG |
10 |
0.000 |
1 |
0.004 |
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| Phenylpropanoid pathway |
LitPath |
10 |
0.000 |
1 |
0.000 |
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| Pathways co-expressed in the Stress data set ( with more than 18 annotation points) |
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CYP84A1, F5H, FAH1, CA5H (At4g36220) |
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| max. difference between log2-ratios: |
5.8 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
2.3 |
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| Pathway |
Source |
Scores of Genes |
p[Score] |
No. of Genes |
p[genes] |
Link to stress heatmap |
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| Intermediary Carbon Metabolism |
BioPath |
50 |
0.000 |
8 |
0.000 |
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| core phenylpropanoid metabolism |
BioPath |
40 |
0.000 |
4 |
0.000 |
| Phenylpropanoid Metabolism |
BioPath |
40 |
0.000 |
4 |
0.009 |
| lignin biosynthesis |
AraCyc |
40 |
0.000 |
4 |
0.000 |
| Phenylpropanoid pathway |
LitPath |
40 |
0.000 |
4 |
0.000 |
| C-compound and carbohydrate metabolism |
FunCat |
35 |
0.000 |
6 |
0.004 |
| tricarboxylic-acid pathway (citrate cycle, Krebs cycle, TCA cycle) |
FunCat |
34 |
0.000 |
5 |
0.000 |
| Stilbene, coumarine and lignin biosynthesis |
KEGG |
32 |
0.000 |
4 |
0.002 |
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| lignin biosynthesis |
TAIR-GO |
30 |
0.000 |
3 |
0.000 |
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| phenylpropanoid biosynthesis |
TAIR-GO |
30 |
0.000 |
3 |
0.000 |
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| suberin biosynthesis |
AraCyc |
30 |
0.000 |
3 |
0.000 |
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| TCA cycle -- aerobic respiration |
AraCyc |
28 |
0.000 |
4 |
0.000 |
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| TCA cycle variation VII |
AraCyc |
28 |
0.000 |
4 |
0.003 |
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| TCA cycle variation VIII |
AraCyc |
28 |
0.000 |
4 |
0.001 |
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| Citrate cycle (TCA cycle) |
KEGG |
28 |
0.000 |
4 |
0.000 |
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| acetyl-CoA assimilation |
AraCyc |
24 |
0.000 |
3 |
0.001 |
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| glyoxylate cycle |
AraCyc |
24 |
0.000 |
3 |
0.000 |
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| serine-isocitrate lyase pathway |
AraCyc |
24 |
0.000 |
3 |
0.004 |
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| Glyoxylate and dicarboxylate metabolism |
KEGG |
24 |
0.000 |
3 |
0.000 |
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| Reductive carboxylate cycle (CO2 fixation) |
KEGG |
24 |
0.000 |
3 |
0.000 |
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| phenylpropanoid biosynthesis |
AraCyc |
20 |
0.000 |
2 |
0.000 |
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| Ascorbate and aldarate metabolism |
KEGG |
20 |
0.000 |
2 |
0.001 |
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| Fluorene degradation |
KEGG |
20 |
0.000 |
2 |
0.000 |
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| gamma-Hexachlorocyclohexane degradation |
KEGG |
20 |
0.000 |
2 |
0.000 |
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| Pathways co-expressed in the Hormone etc. data set (with more than 6 annotation points) |
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CYP84A1, F5H, FAH1, CA5H (At4g36220) |
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| max. difference between log2-ratios: |
3.7 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
2.5 |
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| Pathway |
Source |
Scores of Genes |
p[Score] |
No. of Genes |
p[genes] |
Link to hormones etc. heatmap |
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| core phenylpropanoid metabolism |
BioPath |
10 |
0.000 |
1 |
0.000 |
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| Phenylpropanoid Metabolism |
BioPath |
10 |
0.000 |
1 |
0.004 |
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| lignin biosynthesis |
TAIR-GO |
10 |
0.000 |
1 |
0.000 |
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| phenylpropanoid biosynthesis |
TAIR-GO |
10 |
0.000 |
1 |
0.000 |
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| lignin biosynthesis |
AraCyc |
10 |
0.000 |
1 |
0.000 |
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| biogenesis of cell wall |
FunCat |
10 |
0.000 |
1 |
0.001 |
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| biosynthesis of phenylpropanoids |
FunCat |
10 |
0.000 |
1 |
0.000 |
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| biosynthesis of secondary products derived from L-phenylalanine and L-tyrosine |
FunCat |
10 |
0.000 |
1 |
0.000 |
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| Ascorbate and aldarate metabolism |
KEGG |
10 |
0.000 |
1 |
0.000 |
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| Fluorene degradation |
KEGG |
10 |
0.000 |
1 |
0.000 |
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| gamma-Hexachlorocyclohexane degradation |
KEGG |
10 |
0.000 |
1 |
0.000 |
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| Stilbene, coumarine and lignin biosynthesis |
KEGG |
10 |
0.000 |
1 |
0.004 |
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| Phenylpropanoid pathway |
LitPath |
10 |
0.000 |
1 |
0.000 |
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| Pathways co-expressed in the Mutant data set (with more than 6 annotation points) |
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CYP84A1, F5H, FAH1, CA5H (At4g36220) |
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| max. difference between log2-ratios: |
4.5 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
2.7 |
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| Pathway |
Source |
Scores of Genes |
p[Score] |
No. of Genes |
p[genes] |
Link to mutants heatmap |
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| Phenylpropanoid Metabolism |
BioPath |
12 |
0.000 |
2 |
0.005 |
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| Biosynthesis of Amino Acids and Derivatives |
BioPath |
10 |
0.000 |
1 |
0.049 |
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| core phenylpropanoid metabolism |
BioPath |
10 |
0.000 |
1 |
0.004 |
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| Glutathione metabolism |
BioPath |
10 |
0.000 |
1 |
0.009 |
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| development |
TAIR-GO |
10 |
0.000 |
1 |
0.005 |
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| flower development |
TAIR-GO |
10 |
0.000 |
1 |
0.000 |
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| glutathione biosynthesis |
TAIR-GO |
10 |
0.000 |
1 |
0.000 |
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| lignin biosynthesis |
TAIR-GO |
10 |
0.000 |
1 |
0.000 |
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| phenylpropanoid biosynthesis |
TAIR-GO |
10 |
0.000 |
1 |
0.000 |
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| response to cadmium ion |
TAIR-GO |
10 |
0.000 |
1 |
0.000 |
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| glutathione biosynthesis |
AraCyc |
10 |
0.000 |
1 |
0.000 |
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| lignin biosynthesis |
AraCyc |
10 |
0.000 |
1 |
0.001 |
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| biogenesis of cell wall |
FunCat |
10 |
0.000 |
1 |
0.004 |
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| biosynthesis of nonprotein amino acids |
FunCat |
10 |
0.000 |
1 |
0.000 |
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| biosynthesis of phenylpropanoids |
FunCat |
10 |
0.000 |
1 |
0.001 |
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| biosynthesis of secondary products derived from L-phenylalanine and L-tyrosine |
FunCat |
10 |
0.000 |
1 |
0.001 |
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| biosynthesis of secondary products derived from primary amino acids |
FunCat |
10 |
0.000 |
1 |
0.000 |
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| Ascorbate and aldarate metabolism |
KEGG |
10 |
0.000 |
1 |
0.001 |
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| Fluorene degradation |
KEGG |
10 |
0.000 |
1 |
0.000 |
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| gamma-Hexachlorocyclohexane degradation |
KEGG |
10 |
0.000 |
1 |
0.000 |
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| Glutamate metabolism |
KEGG |
10 |
0.000 |
1 |
0.002 |
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| Glutathione metabolism |
KEGG |
10 |
0.000 |
1 |
0.002 |
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| Stilbene, coumarine and lignin biosynthesis |
KEGG |
10 |
0.000 |
1 |
0.012 |
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| Phenylpropanoid pathway |
LitPath |
10 |
0.000 |
1 |
0.000 |
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