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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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| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
620 |
76 |
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| C-compound and carbohydrate metabolism |
FunCat |
411 |
70 |
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| chlorophyll biosynthesis |
AraCyc |
390 |
45 |
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| biogenesis of chloroplast |
FunCat |
367 |
59 |
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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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| photosynthesis |
FunCat |
366 |
54 |
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| chlorophyll biosynthesis |
TAIR-GO |
363 |
40 |
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| chlorophyll biosynthesis |
LitPath |
337 |
37 |
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For more information on how these pathway maps were generated please read the methods page |
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| Chlorophyll biosynthesis and breakdown |
BioPath |
300 |
35 |
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| chlorophyll and phytochromobilin metabolism |
LitPath |
288 |
33 |
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| glycolysis and gluconeogenesis |
FunCat |
277 |
44 |
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| photosynthesis |
TAIR-GO |
268 |
36 |
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| Carbon fixation |
KEGG |
236 |
35 |
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| Porphyrin and chlorophyll metabolism |
KEGG |
218 |
25 |
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| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
196 |
25 |
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| photorespiration |
AraCyc |
196 |
35 |
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| photorespiration |
TAIR-GO |
176 |
28 |
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| Calvin cycle |
AraCyc |
166 |
29 |
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| photosystem I |
TAIR-GO |
152 |
19 |
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| gluconeogenesis |
AraCyc |
139 |
22 |
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| carotenoid biosynthesis |
AraCyc |
134 |
15 |
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| Pentose phosphate pathway |
KEGG |
132 |
18 |
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| chloroplast thylakoid membrane protein import |
TAIR-GO |
114 |
12 |
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| photosystem II |
TAIR-GO |
113 |
14 |
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| Synthesis of membrane lipids in plastids |
AcylLipid |
104 |
11 |
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| Fructose and mannose metabolism |
KEGG |
100 |
15 |
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| MEP (methylerythritol P) pathway, plastids |
LitPath |
94 |
11 |
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| brassinosteroid biosynthesis |
BioPath |
90 |
9 |
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| energy |
FunCat |
88 |
11 |
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| regulation of transcription |
TAIR-GO |
84 |
9 |
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| SRP (signal recognition particle)-dependent pathway for integral membrane proteins |
BioPath |
80 |
8 |
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| isopentenyl diphosphate biosynthesis -- mevalonate-independent |
AraCyc |
64 |
7 |
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| xanthophyll cycle |
AraCyc |
58 |
6 |
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| metabolism of energy reserves (e.g. glycogen, trehalose) |
FunCat |
54 |
7 |
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| xanthophyll cycle |
TAIR-GO |
50 |
5 |
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| pyridoxal 5'-phosphate biosynthesis |
AraCyc |
42 |
5 |
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| thiamine biosynthesis |
AraCyc |
42 |
5 |
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| lipid, fatty acid and isoprenoid metabolism of energy reserves (e.g. glycogen, trehalose) |
FunCat |
40 |
4 |
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| Pathways co-expressed in the Organ and Tissue data set (with more than 70 annotation points) |
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CYP709B3 (At4g27710) |
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| max. difference between log2-ratios: |
4.6 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
3.2 |
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| Pathway |
Source |
Scores of Genes |
p[Score] |
No. of Genes |
p[genes] |
Link to organ heatmap |
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| Photosystems |
BioPath |
460 |
0.000 |
69 |
0.000 |
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| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
322 |
0.000 |
41 |
0.000 |
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| biogenesis of chloroplast |
FunCat |
207 |
0.000 |
32 |
0.000 |
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| C-compound and carbohydrate metabolism |
FunCat |
203 |
0.000 |
35 |
0.039 |
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| additional photosystem II components |
BioPath |
201 |
0.000 |
29 |
0.000 |
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| photosynthesis |
FunCat |
178 |
0.000 |
28 |
0.000 |
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| Photosynthesis |
KEGG |
165 |
0.000 |
29 |
0.000 |
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| Photosystem I |
BioPath |
163 |
0.000 |
26 |
0.000 |
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| glycolysis and gluconeogenesis |
FunCat |
149 |
0.000 |
23 |
0.001 |
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| Chlorophyll biosynthesis and breakdown |
BioPath |
145 |
0.000 |
17 |
0.000 |
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| chlorophyll and phytochromobilin metabolism |
LitPath |
139 |
0.000 |
16 |
0.000 |
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| Chlorophyll a/b binding proteins |
BioPath |
138 |
0.000 |
17 |
0.000 |
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| Carbon fixation |
KEGG |
122 |
0.000 |
18 |
0.000 |
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| photosystem I |
TAIR-GO |
114 |
0.000 |
14 |
0.000 |
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| Porphyrin and chlorophyll metabolism |
KEGG |
113 |
0.000 |
13 |
0.000 |
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| chlorophyll biosynthesis |
AraCyc |
112 |
0.000 |
14 |
0.001 |
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| transport |
FunCat |
98 |
0.000 |
16 |
0.000 |
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| Biosynthesis of steroids |
KEGG |
93 |
0.000 |
11 |
0.000 |
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| Biosynthesis of prenyl diphosphates |
BioPath |
89 |
0.003 |
12 |
0.048 |
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| Photosystem II |
BioPath |
89 |
0.000 |
12 |
0.018 |
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| Calvin cycle |
AraCyc |
86 |
0.000 |
15 |
0.000 |
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| chlorophyll biosynthesis |
TAIR-GO |
85 |
0.000 |
9 |
0.000 |
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| photosynthesis |
TAIR-GO |
80 |
0.000 |
10 |
0.000 |
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| photosystem II |
TAIR-GO |
75 |
0.000 |
9 |
0.000 |
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| Folding, Sorting and Degradation |
KEGG |
74 |
0.009 |
11 |
0.187 |
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| Carotenoid and abscisic acid metabolism |
LitPath |
74 |
0.000 |
10 |
0.000 |
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| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
72 |
0.000 |
9 |
0.000 |
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| Pathways co-expressed in the Stress data set ( with more than 20 annotation points) |
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CYP709B3 (At4g27710) |
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| max. difference between log2-ratios: |
5.5 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
1.9 |
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| Pathway |
Source |
Scores of Genes |
p[Score] |
No. of Genes |
p[genes] |
Link to stress heatmap |
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| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
87 |
0.000 |
10 |
0.001 |
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| Photosystems |
BioPath |
79 |
0.000 |
13 |
0.000 |
| Chlorophyll biosynthesis and breakdown |
BioPath |
63 |
0.000 |
7 |
0.000 |
| chlorophyll and phytochromobilin metabolism |
LitPath |
63 |
0.000 |
7 |
0.000 |
| C-compound and carbohydrate metabolism |
FunCat |
62 |
0.000 |
12 |
0.015 |
| photosynthesis |
FunCat |
61 |
0.000 |
8 |
0.000 |
| Intermediary Carbon Metabolism |
BioPath |
58 |
0.019 |
9 |
0.202 |
| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
58 |
0.000 |
7 |
0.000 |
| Transcription (chloroplast) |
BioPath |
44 |
0.000 |
5 |
0.000 |
| transcription initiation |
TAIR-GO |
44 |
0.000 |
5 |
0.000 |
| photorespiration |
AraCyc |
42 |
0.000 |
8 |
0.000 |
| chlorophyll biosynthesis |
TAIR-GO |
39 |
0.000 |
4 |
0.000 |
| Carbon fixation |
KEGG |
39 |
0.000 |
5 |
0.002 |
| Porphyrin and chlorophyll metabolism |
KEGG |
39 |
0.000 |
4 |
0.000 |
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| chlorophyll biosynthesis |
LitPath |
39 |
0.000 |
4 |
0.000 |
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| additional photosystem II components |
BioPath |
36 |
0.000 |
6 |
0.002 |
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| glycolysis and gluconeogenesis |
FunCat |
36 |
0.000 |
6 |
0.029 |
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| Photosynthesis |
KEGG |
35 |
0.000 |
7 |
0.000 |
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| photorespiration |
TAIR-GO |
34 |
0.000 |
5 |
0.000 |
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| chlorophyll biosynthesis |
AraCyc |
34 |
0.000 |
4 |
0.017 |
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| Folding, Sorting and Degradation |
KEGG |
34 |
0.000 |
4 |
0.074 |
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| Protein export |
KEGG |
34 |
0.000 |
4 |
0.000 |
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| chloroplast thylakoid membrane protein import |
TAIR-GO |
30 |
0.000 |
3 |
0.000 |
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| glycine biosynthesis I |
AraCyc |
26 |
0.000 |
5 |
0.001 |
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| superpathway of serine and glycine biosynthesis II |
AraCyc |
26 |
0.000 |
5 |
0.000 |
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| biogenesis of chloroplast |
FunCat |
26 |
0.000 |
5 |
0.004 |
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| Calvin cycle |
AraCyc |
24 |
0.000 |
3 |
0.023 |
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| Fructose and mannose metabolism |
KEGG |
24 |
0.000 |
4 |
0.003 |
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| Pentose phosphate pathway |
KEGG |
24 |
0.000 |
3 |
0.010 |
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| Glutathione metabolism |
KEGG |
22 |
0.000 |
3 |
0.011 |
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| Pathways co-expressed in the Hormone etc. data set (with more than 10 annotation points) |
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CYP709B3 (At4g27710) |
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| max. difference between log2-ratios: |
3.0 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
1.4 |
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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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| C-compound and carbohydrate metabolism |
FunCat |
76 |
0.000 |
12 |
0.001 |
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| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
67 |
0.000 |
7 |
0.000 |
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| Intermediary Carbon Metabolism |
BioPath |
58 |
0.000 |
9 |
0.001 |
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| biogenesis of chloroplast |
FunCat |
54 |
0.000 |
7 |
0.000 |
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| Biosynthesis of steroids |
KEGG |
38 |
0.000 |
4 |
0.002 |
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| Glycolysis / Gluconeogenesis |
KEGG |
38 |
0.000 |
6 |
0.001 |
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| gluconeogenesis |
AraCyc |
34 |
0.000 |
6 |
0.000 |
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| glycolysis and gluconeogenesis |
FunCat |
34 |
0.000 |
6 |
0.006 |
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| photosynthesis |
FunCat |
34 |
0.000 |
5 |
0.000 |
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| Pyruvate metabolism |
KEGG |
32 |
0.000 |
5 |
0.002 |
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| Carotenoid biosynthesis |
BioPath |
28 |
0.000 |
3 |
0.000 |
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| carotenoid biosynthesis |
AraCyc |
28 |
0.000 |
3 |
0.000 |
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| lipid, fatty acid and isoprenoid metabolism |
FunCat |
28 |
0.000 |
3 |
0.007 |
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| Carbon fixation |
KEGG |
28 |
0.000 |
5 |
0.001 |
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| carotenid biosynthesis |
LitPath |
28 |
0.000 |
3 |
0.000 |
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| Carotenoid and abscisic acid metabolism |
LitPath |
28 |
0.000 |
3 |
0.001 |
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| Pentose phosphate pathway |
KEGG |
26 |
0.000 |
3 |
0.008 |
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| Biosynthesis of prenyl diphosphates |
BioPath |
20 |
0.000 |
2 |
0.054 |
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| Calvin cycle |
AraCyc |
20 |
0.000 |
4 |
0.001 |
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| isopentenyl diphosphate biosynthesis -- mevalonate-independent |
AraCyc |
20 |
0.000 |
2 |
0.000 |
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| tricarboxylic-acid pathway (citrate cycle, Krebs cycle, TCA cycle) |
FunCat |
20 |
0.025 |
3 |
0.122 |
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| Glutathione metabolism |
KEGG |
20 |
0.000 |
2 |
0.046 |
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| IPP (isopentenyl diphosphate) and DMAPP (dimethylallyl diphosphat) biosynthesis |
LitPath |
20 |
0.000 |
2 |
0.006 |
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| MEP (methylerythritol P) pathway, plastids |
LitPath |
20 |
0.000 |
2 |
0.001 |
|
|
|
|
|
|
|
|
|
|
|
| Chlorophyll biosynthesis and breakdown |
BioPath |
19 |
0.000 |
2 |
0.026 |
|
|
|
|
|
|
|
|
|
|
|
| secondary metabolism |
FunCat |
19 |
0.000 |
2 |
0.103 |
|
|
|
|
|
|
|
|
|
|
|
| Porphyrin and chlorophyll metabolism |
KEGG |
19 |
0.000 |
2 |
0.014 |
|
|
|
|
|
|
|
|
|
|
|
| chlorophyll and phytochromobilin metabolism |
LitPath |
19 |
0.000 |
2 |
0.026 |
|
|
|
|
|
|
|
|
|
|
|
| Leaf Glycerolipid Biosynthesis in Plastid |
BioPath |
18 |
0.004 |
2 |
0.099 |
|
|
|
|
|
|
|
|
|
|
|
| glycolysis IV |
AraCyc |
16 |
0.001 |
4 |
0.014 |
|
|
|
|
|
|
|
|
|
|
|
| Citrate cycle (TCA cycle) |
KEGG |
16 |
0.000 |
2 |
0.043 |
|
|
|
|
|
|
|
|
|
|
|
| Glycine, serine and threonine metabolism |
KEGG |
16 |
0.000 |
3 |
0.005 |
|
|
|
|
|
|
|
|
|
|
|
| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
14 |
0.000 |
2 |
0.002 |
|
|
|
|
|
|
|
|
|
|
|
| Nitrogen metabolism |
KEGG |
12 |
0.006 |
2 |
0.023 |
|
|
|
|
|
|
|
|
|
|
|
| Synthesis of fatty acids in plastids |
AcylLipid |
12 |
0.000 |
2 |
0.007 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Pathways co-expressed in the Mutant data set (with more than 24 annotation points) |
|
CYP709B3 (At4g27710) |
|
|
|
|
|
|
|
|
| max. difference between log2-ratios: |
5.0 |
|
|
|
|
|
|
|
|
|
|
|
|
| max. difference between log2-ratios excluding lowest and highest 5%: |
2.1 |
|
|
|
|
|
|
|
|
|
|
|
|
| Pathway |
Source |
Scores of Genes |
p[Score] |
No. of Genes |
p[genes] |
Link to mutants heatmap |
|
|
|
|
|
|
|
| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
144 |
0.000 |
18 |
0.000 |
|
|
|
|
| Photosystems |
BioPath |
91 |
0.000 |
13 |
0.005 |
|
|
|
| photosynthesis |
FunCat |
83 |
0.000 |
12 |
0.000 |
|
|
|
| biogenesis of chloroplast |
FunCat |
80 |
0.000 |
15 |
0.000 |
|
|
|
| Chlorophyll biosynthesis and breakdown |
BioPath |
73 |
0.000 |
9 |
0.000 |
|
|
|
| C-compound and carbohydrate metabolism |
FunCat |
70 |
0.003 |
11 |
0.251 |
|
|
|
| chlorophyll and phytochromobilin metabolism |
LitPath |
67 |
0.000 |
8 |
0.000 |
|
|
|
| glycolysis and gluconeogenesis |
FunCat |
58 |
0.000 |
9 |
0.010 |
|
|
|
| chlorophyll biosynthesis |
TAIR-GO |
55 |
0.000 |
6 |
0.000 |
|
|
|
| chlorophyll biosynthesis |
AraCyc |
54 |
0.000 |
7 |
0.002 |
|
|
|
| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
52 |
0.000 |
7 |
0.000 |
|
|
|
| additional photosystem II components |
BioPath |
50 |
0.000 |
7 |
0.002 |
|
|
|
| Carbon fixation |
KEGG |
47 |
0.000 |
7 |
0.005 |
|
|
|
|
|
|
|
|
|
|
|
| Porphyrin and chlorophyll metabolism |
KEGG |
47 |
0.000 |
6 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Folding, Sorting and Degradation |
KEGG |
43 |
0.000 |
7 |
0.080 |
|
|
|
|
|
|
|
|
|
|
|
| triterpene, sterol, and brassinosteroid metabolism |
LitPath |
42 |
0.018 |
5 |
0.314 |
|
|
|
|
|
|
|
|
|
|
|
| Leaf Glycerolipid Biosynthesis in Plastid |
BioPath |
41 |
0.010 |
5 |
0.143 |
|
|
|
|
|
|
|
|
|
|
|
| amino acid metabolism |
FunCat |
41 |
0.004 |
6 |
0.081 |
|
|
|
|
|
|
|
|
|
|
|
| chlorophyll biosynthesis |
LitPath |
39 |
0.000 |
4 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| chloroplast thylakoid membrane protein import |
TAIR-GO |
37 |
0.000 |
4 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Biosynthesis of steroids |
KEGG |
37 |
0.000 |
4 |
0.042 |
|
|
|
|
|
|
|
|
|
|
|
| Calvin cycle |
AraCyc |
36 |
0.000 |
7 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Protein export |
KEGG |
35 |
0.000 |
5 |
0.001 |
|
|
|
|
|
|
|
|
|
|
|
| sterol biosynthesis |
BioPath |
30 |
0.000 |
3 |
0.075 |
|
|
|
|
|
|
|
|
|
|
|
| sterol biosynthesis |
AraCyc |
30 |
0.000 |
3 |
0.012 |
|
|
|
|
|
|
|
|
|
|
|
| brassinosteroid biosynthesis |
LitPath |
30 |
0.000 |
3 |
0.050 |
|
|
|
|
|
|
|
|
|
|
|
| sterol and brassinosteroid biosynthesis |
LitPath |
30 |
0.000 |
3 |
0.016 |
|
|
|
|
|
|
|
|
|
|
|
| Carotenoid biosynthesis |
BioPath |
28 |
0.000 |
3 |
0.003 |
|
|
|
|
|
|
|
|
|
|
|
| photorespiration |
TAIR-GO |
28 |
0.000 |
4 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| regulation of transcription |
TAIR-GO |
28 |
0.000 |
3 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| acetate fermentation |
AraCyc |
28 |
0.000 |
7 |
0.012 |
|
|
|
|
|
|
|
|
|
|
|
| carotenoid biosynthesis |
AraCyc |
28 |
0.000 |
3 |
0.001 |
|
|
|
|
|
|
|
|
|
|
|
| photorespiration |
AraCyc |
28 |
0.000 |
5 |
0.004 |
|
|
|
|
|
|
|
|
|
|
|
| lipid, fatty acid and isoprenoid metabolism |
FunCat |
28 |
0.000 |
3 |
0.061 |
|
|
|
|
|
|
|
|
|
|
|
| carotenid biosynthesis |
LitPath |
28 |
0.000 |
3 |
0.005 |
|
|
|
|
|
|
|
|
|
|
|
| Carotenoid and abscisic acid metabolism |
LitPath |
28 |
0.000 |
3 |
0.050 |
|
|
|
|
|
|
|
|
|
|
|
| Synthesis of membrane lipids in plastids |
AcylLipid |
27 |
0.000 |
3 |
0.001 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|