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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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| chlorophyll biosynthesis |
TAIR-GO |
533 |
58 |
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| chlorophyll biosynthesis |
AraCyc |
524 |
58 |
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| chlorophyll biosynthesis |
LitPath |
517 |
56 |
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| photosynthesis |
FunCat |
388 |
55 |
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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 |
TAIR-GO |
312 |
44 |
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| photorespiration |
AraCyc |
214 |
40 |
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| photorespiration |
TAIR-GO |
202 |
35 |
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For more information on how these pathway maps were generated please read the methods page |
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| brassinosteroid biosynthesis |
TAIR-GO |
183 |
20 |
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| brassinosteroid biosynthesis |
BioPath |
174 |
19 |
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| carotenoid biosynthesis |
AraCyc |
174 |
19 |
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| carotenoid biosynthesis |
TAIR-GO |
146 |
16 |
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| ascorbic acid biosynthesis |
BioPath |
98 |
14 |
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| glyoxylate cycle |
AraCyc |
89 |
13 |
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| gamma-Hexachlorocyclohexane degradation |
KEGG |
84 |
12 |
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| starch biosynthesis |
AraCyc |
82 |
10 |
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| starch biosynthesis |
TAIR-GO |
81 |
10 |
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| xanthophyll cycle |
AraCyc |
58 |
6 |
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| xanthophyll cycle |
TAIR-GO |
58 |
6 |
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| chlorophyll catabolism |
LitPath |
50 |
5 |
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| chlorophyll catabolism |
TAIR-GO |
50 |
5 |
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| Fluorene degradation |
KEGG |
38 |
6 |
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| Pathways co-expressed in the Organ and Tissue data set (with more than 40 annotation points) |
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CYP90A1, CPD (At5g05690) |
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| max. difference between log2-ratios: |
6.1 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
4.5 |
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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 |
363 |
0.000 |
54 |
0.000 |
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| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
198 |
0.000 |
23 |
0.000 |
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| biogenesis of chloroplast |
FunCat |
157 |
0.000 |
24 |
0.000 |
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| additional photosystem II components |
BioPath |
154 |
0.000 |
22 |
0.000 |
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| Photosynthesis |
KEGG |
143 |
0.000 |
24 |
0.000 |
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| Photosystem I |
BioPath |
133 |
0.000 |
22 |
0.000 |
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| Chlorophyll a/b binding proteins |
BioPath |
124 |
0.000 |
15 |
0.000 |
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| photosynthesis |
FunCat |
112 |
0.000 |
16 |
0.000 |
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| photosystem I |
TAIR-GO |
87 |
0.000 |
11 |
0.000 |
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| transport |
FunCat |
83 |
0.000 |
15 |
0.000 |
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| Chlorophyll biosynthesis and breakdown |
BioPath |
79 |
0.000 |
9 |
0.006 |
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| chlorophyll biosynthesis |
TAIR-GO |
75 |
0.000 |
8 |
0.000 |
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| glycolysis and gluconeogenesis |
FunCat |
75 |
0.001 |
10 |
0.184 |
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| Porphyrin and chlorophyll metabolism |
KEGG |
73 |
0.000 |
9 |
0.000 |
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| chlorophyll and phytochromobilin metabolism |
LitPath |
73 |
0.000 |
8 |
0.000 |
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| Carbon fixation |
KEGG |
72 |
0.000 |
9 |
0.002 |
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| photosystem II |
TAIR-GO |
71 |
0.000 |
9 |
0.000 |
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| Photosystem II |
BioPath |
69 |
0.000 |
9 |
0.020 |
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| Biosynthesis of steroids |
KEGG |
69 |
0.000 |
8 |
0.001 |
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| chlorophyll biosynthesis |
AraCyc |
66 |
0.000 |
8 |
0.015 |
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| chlorophyll biosynthesis |
LitPath |
59 |
0.000 |
6 |
0.000 |
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| chlorophyll binding |
TAIR-GO |
58 |
0.000 |
7 |
0.000 |
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| Fatty acid elongation and wax and cutin metabolism |
AcylLipid |
57 |
0.000 |
9 |
0.001 |
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| Folding, Sorting and Degradation |
KEGG |
52 |
0.002 |
8 |
0.106 |
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| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
48 |
0.000 |
6 |
0.000 |
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| Pentose phosphate pathway |
KEGG |
48 |
0.000 |
7 |
0.001 |
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| Carotenoid biosynthesis |
BioPath |
44 |
0.000 |
5 |
0.001 |
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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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| Carotenoid and abscisic acid metabolism |
LitPath |
44 |
0.000 |
5 |
0.003 |
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| light harvesting complex |
BioPath |
42 |
0.000 |
5 |
0.000 |
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| Pathways co-expressed in the Stress data set ( with more than 38 annotation points) |
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CYP90A1, CPD (At5g05690) |
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| max. difference between log2-ratios: |
4.1 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
1.8 |
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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 |
223 |
0.000 |
25 |
0.000 |
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| Photosystems |
BioPath |
196 |
0.000 |
32 |
0.000 |
| C-compound and carbohydrate metabolism |
FunCat |
141 |
0.000 |
25 |
0.002 |
| Intermediary Carbon Metabolism |
BioPath |
124 |
0.001 |
20 |
0.100 |
| photosynthesis |
FunCat |
112 |
0.000 |
16 |
0.000 |
| biogenesis of chloroplast |
FunCat |
111 |
0.000 |
17 |
0.000 |
| Chlorophyll biosynthesis and breakdown |
BioPath |
99 |
0.000 |
11 |
0.000 |
| Photosynthesis |
KEGG |
93 |
0.000 |
17 |
0.000 |
| chlorophyll and phytochromobilin metabolism |
LitPath |
93 |
0.000 |
10 |
0.000 |
| chlorophyll biosynthesis |
TAIR-GO |
85 |
0.000 |
9 |
0.000 |
| glycolysis and gluconeogenesis |
FunCat |
81 |
0.000 |
12 |
0.012 |
| Porphyrin and chlorophyll metabolism |
KEGG |
79 |
0.000 |
9 |
0.000 |
| chlorophyll biosynthesis |
AraCyc |
76 |
0.000 |
9 |
0.003 |
| Photosystem I |
BioPath |
75 |
0.000 |
13 |
0.001 |
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| Carbon fixation |
KEGG |
72 |
0.000 |
10 |
0.000 |
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| chlorophyll biosynthesis |
LitPath |
69 |
0.000 |
7 |
0.000 |
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| additional photosystem II components |
BioPath |
67 |
0.000 |
11 |
0.000 |
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| photosystem I |
TAIR-GO |
62 |
0.000 |
8 |
0.000 |
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| Glycolysis / Gluconeogenesis |
KEGG |
62 |
0.000 |
9 |
0.003 |
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| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
58 |
0.000 |
7 |
0.000 |
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| Chlorophyll a/b binding proteins |
BioPath |
54 |
0.000 |
7 |
0.000 |
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| Carotenoid and abscisic acid metabolism |
LitPath |
52 |
0.000 |
6 |
0.001 |
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| Carotenoid biosynthesis |
BioPath |
48 |
0.000 |
5 |
0.000 |
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| carotenoid biosynthesis |
AraCyc |
48 |
0.000 |
5 |
0.000 |
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| carotenid biosynthesis |
LitPath |
48 |
0.000 |
5 |
0.000 |
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| Photosystem II |
BioPath |
47 |
0.001 |
7 |
0.036 |
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| photosystem II |
TAIR-GO |
47 |
0.000 |
6 |
0.000 |
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| Calvin cycle |
AraCyc |
46 |
0.000 |
8 |
0.001 |
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| Pentose phosphate pathway |
KEGG |
46 |
0.000 |
7 |
0.001 |
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| Transcription (chloroplast) |
BioPath |
44 |
0.000 |
5 |
0.000 |
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| transcription initiation |
TAIR-GO |
44 |
0.000 |
5 |
0.000 |
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| acetate fermentation |
AraCyc |
44 |
0.000 |
9 |
0.023 |
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| photorespiration |
AraCyc |
44 |
0.000 |
9 |
0.000 |
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| mRNA processing in chloroplast |
BioPath |
42 |
0.000 |
8 |
0.000 |
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| gluconeogenesis |
AraCyc |
42 |
0.000 |
6 |
0.040 |
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| Starch and sucrose metabolism |
KEGG |
42 |
0.000 |
6 |
0.067 |
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| Biosynthesis of steroids |
KEGG |
40 |
0.000 |
4 |
0.068 |
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| Pathways co-expressed in the Hormone etc. data set (with more than 10 annotation points) |
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CYP90A1, CPD (At5g05690) |
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| max. difference between log2-ratios: |
4.2 |
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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 hormones etc. heatmap |
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| steroid biosynthesis |
TAIR-GO |
36 |
0.000 |
4 |
0.000 |
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| brassinosteroid biosynthesis |
LitPath |
36 |
0.000 |
4 |
0.000 |
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| triterpene, sterol, and brassinosteroid metabolism |
LitPath |
36 |
0.000 |
4 |
0.000 |
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| Isoprenoid Biosynthesis in the Cytosol and in Mitochondria |
BioPath |
30 |
0.000 |
3 |
0.000 |
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| growth |
TAIR-GO |
27 |
0.000 |
3 |
0.000 |
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| brassinosteroid biosynthesis |
TAIR-GO |
26 |
0.000 |
3 |
0.000 |
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| brassinosteroid biosynthesis II |
AraCyc |
20 |
0.000 |
2 |
0.000 |
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| brassinosteroid biosynthesis I |
AraCyc |
20 |
0.000 |
2 |
0.000 |
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| Fluorene degradation |
KEGG |
17 |
0.000 |
2 |
0.000 |
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| gamma-Hexachlorocyclohexane degradation |
KEGG |
17 |
0.000 |
2 |
0.000 |
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| Ascorbate and aldarate metabolism |
KEGG |
17 |
0.000 |
2 |
0.000 |
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| Stilbene, coumarine and lignin biosynthesis |
KEGG |
17 |
0.000 |
2 |
0.007 |
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| Glycan Biosynthesis and Metabolism |
KEGG |
11 |
0.000 |
2 |
0.002 |
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| Pathways co-expressed in the Mutant data set (with more than 10 annotation points) |
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CYP90A1, CPD (At5g05690) |
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| max. difference between log2-ratios: |
11.9 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
1.6 |
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| Pathway |
Source |
Scores of Genes |
p[Score] |
No. of Genes |
p[genes] |
Link to mutants heatmap |
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| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
270 |
0.000 |
34 |
0.000 |
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| C-compound and carbohydrate metabolism |
FunCat |
270 |
0.000 |
49 |
0.043 |
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| Intermediary Carbon Metabolism |
BioPath |
210 |
0.000 |
36 |
0.037 |
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| Photosystems |
BioPath |
199 |
0.000 |
25 |
0.048 |
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| biogenesis of chloroplast |
FunCat |
195 |
0.000 |
29 |
0.000 |
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| transport |
FunCat |
155 |
0.000 |
28 |
0.000 |
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| Carbon fixation |
KEGG |
139 |
0.000 |
22 |
0.000 |
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| glycolysis and gluconeogenesis |
FunCat |
137 |
0.000 |
23 |
0.067 |
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| photosynthesis |
FunCat |
128 |
0.000 |
18 |
0.000 |
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| Biosynthesis of steroids |
KEGG |
125 |
0.000 |
13 |
0.016 |
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| Isoprenoid Biosynthesis in the Cytosol and in Mitochondria |
BioPath |
122 |
0.001 |
14 |
0.139 |
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| Glycolysis / Gluconeogenesis |
KEGG |
119 |
0.000 |
20 |
0.014 |
|
|
|
| Chlorophyll biosynthesis and breakdown |
BioPath |
115 |
0.000 |
14 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| chlorophyll and phytochromobilin metabolism |
LitPath |
109 |
0.000 |
13 |
0.001 |
|
|
|
|
|
|
|
|
|
|
|
| additional photosystem II components |
BioPath |
104 |
0.000 |
13 |
0.005 |
|
|
|
|
|
|
|
|
|
|
|
| Pyruvate metabolism |
KEGG |
104 |
0.002 |
16 |
0.088 |
|
|
|
|
|
|
|
|
|
|
|
| transport facilitation |
FunCat |
91 |
0.000 |
15 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Calvin cycle |
AraCyc |
89 |
0.000 |
16 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Biosynthesis of prenyl diphosphates |
BioPath |
85 |
0.005 |
10 |
0.146 |
|
|
|
|
|
|
|
|
|
|
|
| chlorophyll biosynthesis |
TAIR-GO |
85 |
0.000 |
9 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| chlorophyll biosynthesis |
AraCyc |
84 |
0.000 |
10 |
0.301 |
|
|
|
|
|
|
|
|
|
|
|
| Chlorophyll a/b binding proteins |
BioPath |
80 |
0.000 |
10 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| acetate fermentation |
AraCyc |
78 |
0.001 |
16 |
0.077 |
|
|
|
|
|
|
|
|
|
|
|
| Oxidative phosphorylation |
KEGG |
77 |
0.001 |
18 |
0.031 |
|
|
|
|
|
|
|
|
|
|
|
| Porphyrin and chlorophyll metabolism |
KEGG |
77 |
0.000 |
9 |
0.010 |
|
|
|
|
|
|
|
|
|
|
|
| sterol biosynthesis |
BioPath |
76 |
0.000 |
8 |
0.030 |
|
|
|
|
|
|
|
|
|
|
|
| Methionin/SAM/ethylene metabolism from cysteine and aspartate |
BioPath |
72 |
0.000 |
8 |
0.072 |
|
|
|
|
|
|
|
|
|
|
|
| glycolysis IV |
AraCyc |
72 |
0.002 |
14 |
0.143 |
|
|
|
|
|
|
|
|
|
|
|
| Selenoamino acid metabolism |
KEGG |
72 |
0.000 |
9 |
0.021 |
|
|
|
|
|
|
|
|
|
|
|
| Carotenoid and abscisic acid metabolism |
LitPath |
71 |
0.000 |
9 |
0.002 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|