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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 |
706 |
92 |
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| biogenesis of chloroplast |
FunCat |
483 |
71 |
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| additional photosystem II components |
BioPath |
370 |
51 |
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| chlorophyll biosynthesis |
AraCyc |
348 |
42 |
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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 |
324 |
50 |
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| transport |
FunCat |
312 |
56 |
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| chlorophyll biosynthesis |
TAIR-GO |
293 |
33 |
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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 |
LitPath |
277 |
31 |
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| photosynthesis |
TAIR-GO |
254 |
35 |
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| photosystem I |
TAIR-GO |
218 |
27 |
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| Biosynthesis of steroids |
KEGG |
216 |
26 |
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| Carotenoid and abscisic acid metabolism |
LitPath |
202 |
24 |
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| carotenoid biosynthesis |
AraCyc |
198 |
22 |
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| Carotenoid biosynthesis |
BioPath |
184 |
21 |
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| carotenid biosynthesis |
LitPath |
184 |
21 |
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| photosystem II |
TAIR-GO |
170 |
21 |
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| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
158 |
20 |
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| photorespiration |
AraCyc |
156 |
27 |
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| photorespiration |
TAIR-GO |
126 |
19 |
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| more common pathways |
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| Pathways co-expressed in the Organ and Tissue data set (with more than 80 annotation points) |
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CYP72A11 (At3g14650) |
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| max. difference between log2-ratios: |
5.6 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
5.3 |
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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 |
512 |
0.000 |
76 |
0.000 |
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| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
330 |
0.000 |
43 |
0.000 |
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| biogenesis of chloroplast |
FunCat |
247 |
0.000 |
37 |
0.000 |
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| C-compound and carbohydrate metabolism |
FunCat |
241 |
0.000 |
42 |
0.038 |
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| additional photosystem II components |
BioPath |
215 |
0.000 |
31 |
0.000 |
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| Photosystem I |
BioPath |
195 |
0.000 |
30 |
0.000 |
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| photosynthesis |
FunCat |
182 |
0.000 |
29 |
0.000 |
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| Chlorophyll biosynthesis and breakdown |
BioPath |
163 |
0.000 |
20 |
0.000 |
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| photosystem I |
TAIR-GO |
161 |
0.000 |
20 |
0.000 |
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| Photosynthesis |
KEGG |
159 |
0.000 |
28 |
0.000 |
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| chlorophyll and phytochromobilin metabolism |
LitPath |
157 |
0.000 |
19 |
0.000 |
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| glycolysis and gluconeogenesis |
FunCat |
155 |
0.000 |
25 |
0.002 |
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| Chlorophyll a/b binding proteins |
BioPath |
146 |
0.000 |
18 |
0.000 |
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| Carbon fixation |
KEGG |
131 |
0.000 |
19 |
0.000 |
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| Porphyrin and chlorophyll metabolism |
KEGG |
131 |
0.000 |
16 |
0.000 |
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| chlorophyll biosynthesis |
AraCyc |
130 |
0.000 |
17 |
0.000 |
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| photosystem II |
TAIR-GO |
128 |
0.000 |
16 |
0.000 |
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| Photosystem II |
BioPath |
121 |
0.000 |
16 |
0.003 |
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| transport |
FunCat |
121 |
0.000 |
21 |
0.000 |
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| photosynthesis |
TAIR-GO |
112 |
0.000 |
14 |
0.000 |
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| Folding, Sorting and Degradation |
KEGG |
87 |
0.016 |
13 |
0.210 |
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| chlorophyll binding |
TAIR-GO |
86 |
0.000 |
10 |
0.000 |
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| Calvin cycle |
AraCyc |
86 |
0.000 |
15 |
0.000 |
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| Biosynthesis of steroids |
KEGG |
83 |
0.000 |
10 |
0.006 |
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| Pathways co-expressed in the Stress data set ( with more than 15 annotation points) |
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CYP72A11 (At3g14650) |
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| max. difference between log2-ratios: |
4.7 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
1.7 |
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| Pathway |
Source |
Scores of Genes |
p[Score] |
No. of Genes |
p[genes] |
Link to stress heatmap |
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| C-compound and carbohydrate metabolism |
FunCat |
41 |
0.000 |
7 |
0.111 |
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| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
34 |
0.000 |
4 |
0.033 |
| Leaf Glycerolipid Biosynthesis in Plastid |
BioPath |
33 |
0.000 |
5 |
0.001 |
| Intermediary Carbon Metabolism |
BioPath |
32 |
0.002 |
4 |
0.257 |
| Carotenoid biosynthesis |
BioPath |
30 |
0.000 |
3 |
0.000 |
| carotenoid biosynthesis |
AraCyc |
30 |
0.000 |
3 |
0.000 |
| Glycolysis / Gluconeogenesis |
KEGG |
30 |
0.000 |
4 |
0.008 |
| carotenid biosynthesis |
LitPath |
30 |
0.000 |
3 |
0.000 |
| Carotenoid and abscisic acid metabolism |
LitPath |
30 |
0.000 |
3 |
0.000 |
| Synthesis of membrane lipids in plastids |
AcylLipid |
29 |
0.000 |
4 |
0.000 |
| Biosynthesis of steroids |
KEGG |
24 |
0.000 |
3 |
0.006 |
| glycolysis and gluconeogenesis |
FunCat |
22 |
0.000 |
3 |
0.172 |
| photosystem I |
TAIR-GO |
21 |
0.000 |
3 |
0.000 |
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| carotene biosynthesis |
TAIR-GO |
20 |
0.000 |
2 |
0.000 |
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| Calvin cycle |
AraCyc |
20 |
0.000 |
4 |
0.001 |
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| Glycine, serine and threonine metabolism |
KEGG |
20 |
0.000 |
4 |
0.000 |
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| Translation (chloroplast) |
BioPath |
18 |
0.000 |
3 |
0.000 |
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| acetate fermentation |
AraCyc |
18 |
0.000 |
3 |
0.039 |
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| fructose degradation (anaerobic) |
AraCyc |
18 |
0.000 |
3 |
0.031 |
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| glycolysis I |
AraCyc |
18 |
0.004 |
3 |
0.226 |
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| glycolysis IV |
AraCyc |
18 |
0.000 |
3 |
0.033 |
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| mannitol degradation |
AraCyc |
18 |
0.000 |
3 |
0.001 |
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| sorbitol degradation |
AraCyc |
18 |
0.000 |
3 |
0.001 |
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| sorbitol fermentation |
AraCyc |
18 |
0.000 |
3 |
0.036 |
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| Gluconeogenesis from lipids in seeds |
BioPath |
16 |
0.010 |
2 |
0.185 |
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| mRNA processing in chloroplast |
BioPath |
16 |
0.000 |
3 |
0.000 |
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| pentose-phosphate pathway |
FunCat |
16 |
0.000 |
2 |
0.006 |
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| Carbon fixation |
KEGG |
16 |
0.000 |
2 |
0.087 |
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| Fructose and mannose metabolism |
KEGG |
16 |
0.000 |
2 |
0.037 |
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| Glycerolipid metabolism |
KEGG |
16 |
0.000 |
3 |
0.002 |
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| Pentose phosphate pathway |
KEGG |
16 |
0.000 |
2 |
0.028 |
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| Pathways co-expressed in the Hormone etc. data set (with more than 20 annotation points) |
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CYP72A11 (At3g14650) |
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| max. difference between log2-ratios: |
3.5 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
0.9 |
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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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| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
130 |
0.000 |
17 |
0.000 |
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| biogenesis of chloroplast |
FunCat |
76 |
0.000 |
9 |
0.000 |
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| Stilbene, coumarine and lignin biosynthesis |
KEGG |
54 |
0.000 |
9 |
0.002 |
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| Carotenoid and abscisic acid metabolism |
LitPath |
50 |
0.000 |
6 |
0.000 |
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| transport |
FunCat |
49 |
0.000 |
10 |
0.000 |
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| Carotenoid biosynthesis |
BioPath |
44 |
0.000 |
5 |
0.000 |
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| carotenoid biosynthesis |
AraCyc |
44 |
0.000 |
5 |
0.000 |
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| carotenid biosynthesis |
LitPath |
44 |
0.000 |
5 |
0.000 |
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| Phenylpropanoid pathway |
LitPath |
44 |
0.014 |
6 |
0.360 |
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| Chlorophyll biosynthesis and breakdown |
BioPath |
40 |
0.000 |
5 |
0.004 |
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| core phenylpropanoid metabolism |
BioPath |
40 |
0.000 |
4 |
0.063 |
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| lignin biosynthesis |
AraCyc |
40 |
0.000 |
4 |
0.006 |
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| additional photosystem II components |
BioPath |
36 |
0.000 |
5 |
0.010 |
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| Biosynthesis of steroids |
KEGG |
34 |
0.000 |
5 |
0.004 |
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| chlorophyll and phytochromobilin metabolism |
LitPath |
34 |
0.005 |
4 |
0.087 |
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| Biosynthesis of prenyl diphosphates |
BioPath |
32 |
0.000 |
5 |
0.018 |
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| chlorophyll biosynthesis |
AraCyc |
30 |
0.000 |
4 |
0.013 |
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| biosynthesis of derivatives of homoisopentenyl pyrophosphate |
FunCat |
28 |
0.000 |
3 |
0.002 |
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| Folding, Sorting and Degradation |
KEGG |
27 |
0.015 |
6 |
0.065 |
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| photosynthesis |
FunCat |
26 |
0.000 |
4 |
0.022 |
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| transport facilitation |
FunCat |
26 |
0.000 |
6 |
0.000 |
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| transport routes |
FunCat |
25 |
0.000 |
4 |
0.000 |
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| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
24 |
0.000 |
3 |
0.003 |
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| biosynthesis of vitamins, cofactors, and prosthetic groups |
FunCat |
22 |
0.000 |
3 |
0.001 |
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| Pathways co-expressed in the Mutant data set (with more than 50 annotation points) |
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CYP72A11 (At3g14650) |
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| max. difference between log2-ratios: |
7.5 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
2.0 |
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| Pathway |
Source |
Scores of Genes |
p[Score] |
No. of Genes |
p[genes] |
Link to mutants heatmap |
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| C-compound and carbohydrate metabolism |
FunCat |
213 |
0.000 |
37 |
0.044 |
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| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
212 |
0.000 |
28 |
0.000 |
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| Photosystems |
BioPath |
186 |
0.000 |
23 |
0.006 |
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| Intermediary Carbon Metabolism |
BioPath |
152 |
0.021 |
25 |
0.157 |
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| biogenesis of chloroplast |
FunCat |
148 |
0.000 |
23 |
0.000 |
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| transport |
FunCat |
127 |
0.000 |
22 |
0.000 |
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| Carbon fixation |
KEGG |
114 |
0.000 |
19 |
0.000 |
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| additional photosystem II components |
BioPath |
104 |
0.000 |
13 |
0.000 |
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| glycolysis and gluconeogenesis |
FunCat |
102 |
0.001 |
18 |
0.052 |
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| Pyruvate metabolism |
KEGG |
102 |
0.000 |
15 |
0.008 |
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| photosynthesis |
FunCat |
92 |
0.000 |
14 |
0.000 |
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| Chlorophyll biosynthesis and breakdown |
BioPath |
85 |
0.000 |
11 |
0.001 |
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| Chlorophyll a/b binding proteins |
BioPath |
80 |
0.000 |
10 |
0.000 |
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| Glycolysis / Gluconeogenesis |
KEGG |
79 |
0.002 |
14 |
0.033 |
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| chlorophyll and phytochromobilin metabolism |
LitPath |
79 |
0.000 |
10 |
0.001 |
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| chlorophyll biosynthesis |
TAIR-GO |
75 |
0.000 |
8 |
0.000 |
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|
| transport facilitation |
FunCat |
75 |
0.000 |
12 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Biosynthesis of steroids |
KEGG |
75 |
0.000 |
8 |
0.085 |
|
|
|
|
|
|
|
|
|
|
|
| Methionin/SAM/ethylene metabolism from cysteine and aspartate |
BioPath |
72 |
0.000 |
8 |
0.015 |
|
|
|
|
|
|
|
|
|
|
|
| Selenoamino acid metabolism |
KEGG |
72 |
0.000 |
9 |
0.002 |
|
|
|
|
|
|
|
|
|
|
|
| triterpene, sterol, and brassinosteroid metabolism |
LitPath |
65 |
0.025 |
9 |
0.307 |
|
|
|
|
|
|
|
|
|
|
|
| Calvin cycle |
AraCyc |
64 |
0.000 |
12 |
0.001 |
|
|
|
|
|
|
|
|
|
|
|
| chlorophyll biosynthesis |
AraCyc |
64 |
0.000 |
8 |
0.219 |
|
|
|
|
|
|
|
|
|
|
|
| Porphyrin and chlorophyll metabolism |
KEGG |
57 |
0.000 |
7 |
0.010 |
|
|
|
|
|
|
|
|
|
|
|
| Citrate cycle (TCA cycle) |
KEGG |
54 |
0.000 |
7 |
0.102 |
|
|
|
|
|
|
|
|
|
|
|
| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
52 |
0.000 |
7 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| TCA cycle variation VIII |
AraCyc |
52 |
0.003 |
8 |
0.171 |
|
|
|
|
|
|
|
|
|
|
|
| Carotenoid and abscisic acid metabolism |
LitPath |
52 |
0.000 |
6 |
0.009 |
|
|
|
|
|
|
|
|
|
|
|
| lipid, fatty acid and isoprenoid metabolism |
FunCat |
51 |
0.000 |
7 |
0.075 |
|
|
|
|
|
|
|
|
|
|
|
| Glycine, serine and threonine metabolism |
KEGG |
51 |
0.000 |
8 |
0.021 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|