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| Pathways co-expressed in all 4 data sets (with more than 6 annotation points each); shown are only pathways with a total of more than 100 annotation points. |
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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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| Photosystems |
BioPath |
878 |
132 |
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| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
837 |
104 |
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| chlorophyll biosynthesis |
AraCyc |
650 |
74 |
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| chlorophyll biosynthesis |
TAIR-GO |
599 |
66 |
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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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| chlorophyll biosynthesis |
LitPath |
583 |
64 |
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| biogenesis of chloroplast |
FunCat |
554 |
84 |
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| photosynthesis |
FunCat |
527 |
81 |
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For more information on how these pathway maps were generated please read the methods page |
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| photosynthesis |
TAIR-GO |
439 |
65 |
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| Chlorophyll biosynthesis and breakdown |
BioPath |
436 |
50 |
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| chlorophyll and phytochromobilin metabolism |
LitPath |
418 |
47 |
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| additional photosystem II components |
BioPath |
415 |
61 |
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| Porphyrin and chlorophyll metabolism |
KEGG |
370 |
43 |
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| glycolysis and gluconeogenesis |
FunCat |
370 |
61 |
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| Carbon fixation |
KEGG |
334 |
55 |
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| Photosynthesis |
KEGG |
295 |
53 |
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| transport |
FunCat |
278 |
48 |
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| Glycolysis / Gluconeogenesis |
KEGG |
269 |
41 |
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| Calvin cycle |
AraCyc |
220 |
45 |
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| photorespiration |
AraCyc |
212 |
44 |
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| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
206 |
26 |
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| carotenoid biosynthesis |
AraCyc |
205 |
23 |
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| Carotenoid and abscisic acid metabolism |
LitPath |
203 |
25 |
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| Pentose phosphate pathway |
KEGG |
194 |
32 |
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| gluconeogenesis |
AraCyc |
191 |
30 |
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| photosystem I |
TAIR-GO |
188 |
23 |
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| photorespiration |
TAIR-GO |
182 |
36 |
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| acetate fermentation |
AraCyc |
178 |
35 |
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| carotenoid biosynthesis |
TAIR-GO |
177 |
20 |
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| Carotenoid biosynthesis |
BioPath |
174 |
20 |
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| carotenid biosynthesis |
LitPath |
174 |
20 |
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| Synthesis of membrane lipids in plastids |
AcylLipid |
158 |
19 |
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| transport facilitation |
FunCat |
157 |
28 |
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| Glycine, serine and threonine metabolism |
KEGG |
136 |
24 |
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| Protein export |
KEGG |
133 |
18 |
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| photosystem II |
TAIR-GO |
127 |
15 |
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| mRNA processing in chloroplast |
BioPath |
126 |
26 |
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| energy |
FunCat |
116 |
20 |
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| Early light-inducible proteins |
BioPath |
114 |
15 |
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| light harvesting complex |
BioPath |
112 |
14 |
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| regulation of transcription |
TAIR-GO |
111 |
12 |
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| response to light |
TAIR-GO |
102 |
16 |
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| Pathways co-expressed in the Organ and Tissue data set (with more than 60 annotation points) |
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CYP706A5 (At4g12310) |
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| max. difference between log2-ratios: |
7.0 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
6.0 |
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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 |
392 |
0.000 |
61 |
0.000 |
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| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
269 |
0.000 |
35 |
0.000 |
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| biogenesis of chloroplast |
FunCat |
207 |
0.000 |
31 |
0.000 |
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| Photosystem I |
BioPath |
163 |
0.000 |
26 |
0.000 |
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| Photosynthesis |
KEGG |
159 |
0.000 |
28 |
0.000 |
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| photosynthesis |
FunCat |
148 |
0.000 |
24 |
0.000 |
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| Chlorophyll biosynthesis and breakdown |
BioPath |
147 |
0.000 |
17 |
0.000 |
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| chlorophyll and phytochromobilin metabolism |
LitPath |
141 |
0.000 |
16 |
0.000 |
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| additional photosystem II components |
BioPath |
133 |
0.000 |
21 |
0.000 |
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| Porphyrin and chlorophyll metabolism |
KEGG |
127 |
0.000 |
15 |
0.000 |
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| chlorophyll biosynthesis |
AraCyc |
116 |
0.000 |
15 |
0.000 |
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| glycolysis and gluconeogenesis |
FunCat |
109 |
0.000 |
18 |
0.007 |
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| transport |
FunCat |
108 |
0.000 |
18 |
0.000 |
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| photosystem I |
TAIR-GO |
98 |
0.000 |
12 |
0.000 |
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| Carbon fixation |
KEGG |
96 |
0.000 |
15 |
0.000 |
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| Photosystem II |
BioPath |
89 |
0.000 |
12 |
0.005 |
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| Leaf Glycerolipid Biosynthesis in Plastid |
BioPath |
85 |
0.036 |
10 |
0.282 |
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| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
72 |
0.000 |
9 |
0.000 |
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| Chlorophyll a/b binding proteins |
BioPath |
70 |
0.000 |
9 |
0.000 |
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| Glycolysis / Gluconeogenesis |
KEGG |
70 |
0.000 |
11 |
0.008 |
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| transport facilitation |
FunCat |
67 |
0.000 |
11 |
0.000 |
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| biosynthesis of proto- and siroheme |
AraCyc |
66 |
0.000 |
10 |
0.002 |
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| Folding, Sorting and Degradation |
KEGG |
66 |
0.013 |
9 |
0.238 |
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| chlorophyll biosynthesis |
TAIR-GO |
65 |
0.000 |
7 |
0.000 |
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| Synthesis of membrane lipids in plastids |
AcylLipid |
65 |
0.000 |
7 |
0.000 |
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| photorespiration |
AraCyc |
64 |
0.000 |
13 |
0.000 |
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| Calvin cycle |
AraCyc |
62 |
0.000 |
12 |
0.000 |
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| Pathways co-expressed in the Stress data set ( with more than 30 annotation points) |
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CYP706A5 (At4g12310) |
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| max. difference between log2-ratios: |
4.9 |
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| max. difference between log2-ratios excluding lowest and highest 5%: |
2.4 |
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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 |
211 |
0.000 |
25 |
0.000 |
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| C-compound and carbohydrate metabolism |
FunCat |
153 |
0.000 |
27 |
0.000 |
| Chlorophyll biosynthesis and breakdown |
BioPath |
127 |
0.000 |
15 |
0.000 |
| chlorophyll and phytochromobilin metabolism |
LitPath |
121 |
0.000 |
14 |
0.000 |
| Intermediary Carbon Metabolism |
BioPath |
108 |
0.000 |
15 |
0.169 |
| Photosystems |
BioPath |
107 |
0.000 |
18 |
0.000 |
| photosynthesis |
FunCat |
107 |
0.000 |
17 |
0.000 |
| Porphyrin and chlorophyll metabolism |
KEGG |
101 |
0.000 |
11 |
0.000 |
| glycolysis and gluconeogenesis |
FunCat |
93 |
0.000 |
14 |
0.001 |
| chlorophyll biosynthesis |
AraCyc |
92 |
0.000 |
11 |
0.000 |
| biogenesis of chloroplast |
FunCat |
79 |
0.000 |
13 |
0.000 |
| Glycolysis / Gluconeogenesis |
KEGG |
72 |
0.000 |
10 |
0.000 |
| additional photosystem II components |
BioPath |
71 |
0.000 |
12 |
0.000 |
| chlorophyll biosynthesis |
TAIR-GO |
65 |
0.000 |
7 |
0.000 |
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| Carbon fixation |
KEGG |
64 |
0.000 |
10 |
0.000 |
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| Pentose phosphate pathway |
KEGG |
63 |
0.000 |
10 |
0.000 |
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| Calvin cycle |
AraCyc |
61 |
0.000 |
12 |
0.000 |
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| chlorophyll biosynthesis |
LitPath |
59 |
0.000 |
6 |
0.000 |
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| Carotenoid and abscisic acid metabolism |
LitPath |
51 |
0.000 |
6 |
0.002 |
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| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
48 |
0.000 |
6 |
0.000 |
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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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| biosynthesis of proto- and siroheme |
AraCyc |
42 |
0.000 |
6 |
0.004 |
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| Biosynthesis of steroids |
KEGG |
40 |
0.000 |
4 |
0.029 |
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| Carotenoid biosynthesis |
BioPath |
38 |
0.000 |
4 |
0.001 |
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| carotenoid biosynthesis |
AraCyc |
38 |
0.000 |
4 |
0.000 |
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| carotenid biosynthesis |
LitPath |
38 |
0.000 |
4 |
0.002 |
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| mRNA processing in chloroplast |
BioPath |
36 |
0.000 |
8 |
0.000 |
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| acetate fermentation |
AraCyc |
36 |
0.000 |
6 |
0.054 |
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| fructose degradation (anaerobic) |
AraCyc |
36 |
0.000 |
6 |
0.038 |
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| glycolysis I |
AraCyc |
36 |
0.038 |
6 |
0.473 |
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| glycolysis IV |
AraCyc |
36 |
0.000 |
6 |
0.041 |
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| sorbitol fermentation |
AraCyc |
36 |
0.000 |
6 |
0.047 |
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| Fructose and mannose metabolism |
KEGG |
36 |
0.000 |
5 |
0.007 |
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| pentose-phosphate pathway |
FunCat |
33 |
0.000 |
5 |
0.001 |
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| chlorophyll and phyochromobilin biosynthesis |
LitPath |
32 |
0.000 |
5 |
0.001 |
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| Pathways co-expressed in the Hormone etc. data set (with more than 30 annotation points) |
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CYP706A5 (At4g12310) |
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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%: |
1.9 |
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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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| C-compound and carbohydrate metabolism |
FunCat |
119 |
0.000 |
22 |
0.000 |
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| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
103 |
0.000 |
12 |
0.001 |
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| Photosystems |
BioPath |
88 |
0.000 |
14 |
0.001 |
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| Intermediary Carbon Metabolism |
BioPath |
86 |
0.000 |
14 |
0.046 |
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| photosynthesis |
FunCat |
74 |
0.000 |
12 |
0.000 |
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| biogenesis of chloroplast |
FunCat |
73 |
0.000 |
10 |
0.000 |
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| glycolysis and gluconeogenesis |
FunCat |
65 |
0.000 |
12 |
0.001 |
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| Porphyrin and chlorophyll metabolism |
KEGG |
59 |
0.000 |
7 |
0.000 |
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| Carbon fixation |
KEGG |
56 |
0.000 |
11 |
0.000 |
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| additional photosystem II components |
BioPath |
55 |
0.000 |
8 |
0.000 |
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| Chlorophyll biosynthesis and breakdown |
BioPath |
49 |
0.000 |
5 |
0.012 |
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| chlorophyll and phytochromobilin metabolism |
LitPath |
49 |
0.000 |
5 |
0.002 |
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| Glycolysis / Gluconeogenesis |
KEGG |
48 |
0.000 |
7 |
0.004 |
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| gluconeogenesis |
AraCyc |
44 |
0.000 |
7 |
0.010 |
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| Leaf Glycerolipid Biosynthesis in Plastid |
BioPath |
43 |
0.001 |
5 |
0.123 |
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|
| transport |
FunCat |
39 |
0.000 |
7 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| glycosylglyceride desaturation pathway |
AraCyc |
37 |
0.000 |
4 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Synthesis of membrane lipids in plastids |
AcylLipid |
37 |
0.000 |
4 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Carotenoid biosynthesis |
BioPath |
36 |
0.000 |
4 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| carotenoid biosynthesis |
AraCyc |
36 |
0.000 |
4 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| chlorophyll biosynthesis |
AraCyc |
36 |
0.000 |
4 |
0.276 |
|
|
|
|
|
|
|
|
|
|
|
| carotenid biosynthesis |
LitPath |
36 |
0.000 |
4 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Carotenoid and abscisic acid metabolism |
LitPath |
36 |
0.000 |
4 |
0.001 |
|
|
|
|
|
|
|
|
|
|
|
| Calvin cycle |
AraCyc |
35 |
0.000 |
9 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Photosynthesis |
KEGG |
35 |
0.000 |
7 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Pentose phosphate pathway |
KEGG |
33 |
0.000 |
6 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| core phenylpropanoid metabolism |
BioPath |
32 |
0.003 |
4 |
0.129 |
|
|
|
|
|
|
|
|
|
|
|
| Early light-inducible proteins |
BioPath |
32 |
0.000 |
4 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| acetate fermentation |
AraCyc |
32 |
0.002 |
7 |
0.087 |
|
|
|
|
|
|
|
|
|
|
|
| fructose degradation (anaerobic) |
AraCyc |
32 |
0.001 |
7 |
0.061 |
|
|
|
|
|
|
|
|
|
|
|
| glycolysis IV |
AraCyc |
32 |
0.001 |
7 |
0.066 |
|
|
|
|
|
|
|
|
|
|
|
| sorbitol fermentation |
AraCyc |
32 |
0.003 |
7 |
0.076 |
|
|
|
|
|
|
|
|
|
|
|
| Glycine, serine and threonine metabolism |
KEGG |
32 |
0.000 |
6 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Phenylpropanoid pathway |
LitPath |
32 |
0.006 |
4 |
0.263 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Pathways co-expressed in the Mutant data set (with more than 50 annotation points) |
|
CYP706A5 (At4g12310) |
|
|
|
|
|
|
|
|
| max. difference between log2-ratios: |
9.2 |
|
|
|
|
|
|
|
|
|
|
|
|
| max. difference between log2-ratios excluding lowest and highest 5%: |
3.3 |
|
|
|
|
|
|
|
|
|
|
|
|
| Pathway |
Source |
Scores of Genes |
p[Score] |
No. of Genes |
p[genes] |
Link to mutants heatmap |
|
|
|
|
|
|
|
| Photosystems |
BioPath |
291 |
0.000 |
39 |
0.000 |
|
|
|
|
| Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) |
BioPath |
254 |
0.000 |
32 |
0.000 |
|
|
|
| C-compound and carbohydrate metabolism |
FunCat |
232 |
0.000 |
38 |
0.023 |
|
|
|
| biogenesis of chloroplast |
FunCat |
195 |
0.000 |
30 |
0.000 |
|
|
|
| additional photosystem II components |
BioPath |
156 |
0.000 |
20 |
0.000 |
|
|
|
| photosynthesis |
FunCat |
144 |
0.000 |
21 |
0.000 |
|
|
|
| Chlorophyll a/b binding proteins |
BioPath |
118 |
0.000 |
15 |
0.000 |
|
|
|
| Carbon fixation |
KEGG |
118 |
0.000 |
19 |
0.000 |
|
|
|
| Chlorophyll biosynthesis and breakdown |
BioPath |
113 |
0.000 |
13 |
0.000 |
|
|
|
| transport |
FunCat |
112 |
0.000 |
19 |
0.000 |
|
|
|
| chlorophyll and phytochromobilin metabolism |
LitPath |
107 |
0.000 |
12 |
0.000 |
|
|
|
| glycolysis and gluconeogenesis |
FunCat |
103 |
0.000 |
17 |
0.077 |
|
|
|
| Biosynthesis of steroids |
KEGG |
91 |
0.000 |
10 |
0.010 |
|
|
|
|
|
|
|
|
|
|
|
| chlorophyll biosynthesis |
AraCyc |
90 |
0.000 |
11 |
0.016 |
|
|
|
|
|
|
|
|
|
|
|
| Porphyrin and chlorophyll metabolism |
KEGG |
83 |
0.000 |
10 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Glycolysis / Gluconeogenesis |
KEGG |
79 |
0.001 |
13 |
0.040 |
|
|
|
|
|
|
|
|
|
|
|
| chlorophyll biosynthesis |
TAIR-GO |
75 |
0.000 |
8 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Photosynthesis |
KEGG |
71 |
0.000 |
11 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Pyruvate metabolism |
KEGG |
71 |
0.018 |
11 |
0.094 |
|
|
|
|
|
|
|
|
|
|
|
| Stilbene, coumarine and lignin biosynthesis |
KEGG |
68 |
0.001 |
10 |
0.540 |
|
|
|
|
|
|
|
|
|
|
|
| transport facilitation |
FunCat |
64 |
0.000 |
10 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Carotenoid and abscisic acid metabolism |
LitPath |
64 |
0.000 |
8 |
0.001 |
|
|
|
|
|
|
|
|
|
|
|
| Pathway for nuclear-encoded, thylakoid-localized proteins |
BioPath |
62 |
0.000 |
8 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Calvin cycle |
AraCyc |
62 |
0.000 |
12 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| photorespiration |
AraCyc |
62 |
0.000 |
12 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| sterol biosynthesis |
BioPath |
60 |
0.000 |
6 |
0.104 |
|
|
|
|
|
|
|
|
|
|
|
| chlorophyll biosynthesis |
LitPath |
59 |
0.000 |
6 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| gluconeogenesis |
AraCyc |
58 |
0.000 |
10 |
0.014 |
|
|
|
|
|
|
|
|
|
|
|
| Selenoamino acid metabolism |
KEGG |
56 |
0.000 |
6 |
0.041 |
|
|
|
|
|
|
|
|
|
|
|
| Ascorbate and aldarate metabolism |
KEGG |
55 |
0.000 |
7 |
0.004 |
|
|
|
|
|
|
|
|
|
|
|
| Carotenoid biosynthesis |
BioPath |
54 |
0.000 |
6 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| carotenoid biosynthesis |
AraCyc |
54 |
0.000 |
6 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| carotenid biosynthesis |
LitPath |
54 |
0.000 |
6 |
0.000 |
|
|
|
|
|
|
|
|
|
|
|
| Methionin/SAM/ethylene metabolism from cysteine and aspartate |
BioPath |
52 |
0.002 |
6 |
0.185 |
|
|
|
|
|
|
|
|
|
|
|
| acetate fermentation |
AraCyc |
52 |
0.007 |
11 |
0.101 |
|
|
|
|
|
|
|
|
|
|
|
| Cysteine metabolism |
KEGG |
52 |
0.000 |
6 |
0.024 |
|
|
|
|
|
|
|
|
|
|
|
| brassinosteroid biosynthesis |
LitPath |
52 |
0.000 |
6 |
0.017 |
|
|
|
|
|
|
|
|
|
|
|
| sterol and brassinosteroid biosynthesis |
LitPath |
52 |
0.000 |
6 |
0.002 |
|
|
|
|
|
|
|
|
|
|
|
| Sulfur metabolism |
KEGG |
51 |
0.000 |
6 |
0.007 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|