PCL results for AraCyc pathway: carotenoid biosynthesis

KEY: Each row represents a single gene that was identified by PLC (pathway-level co-expression) as being co-expressed with two or more genes in this pathway. Column 2 lists probe sets/genes that are co-expressed with annotated pathway members in column 3. Here, co-expression is defined as a regression p value less than 1e-120. If a gene in the first column is shaded blue, then it is already known to be a member of the pathway.

rank

probe set:gene id

co-expressed with

250531_at : AT5G08650
GO:0005737:cytoplasm
GO:0006415:translational termination
GO:0006414:translational elongation
GO:0016149:translation release factor activity, codon specific
GO:0003924:GTPase activity
GO:0008415:acyltransferase activity
GO:0003743:translation initiation factor activity
GO:0007264:small GTPase mediated signal transduction
GO:0019281:methionine biosynthesis from homoserine via O-succinyl-L-homoserine and cystathione
GO:0001514:selenocysteine incorporation
GO:0003746:translation elongation factor activity
GO:0009507:chloroplast
GO:0006413:translational initiation
GO:0006412:protein biosynthesis
GO:0005524:ATP binding
GO:0005525:GTP binding

probe set,gene	slope	pvalue	rsquared	annotations
250095_at AT5G17230	1	7.36e-208	0.859	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast
245284_at AT4G14210	0.534	1.03e-209	0.861	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.489	4.16e-155	0.767	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
247936_at AT5G57030	0.598	5.2e-146	0.746	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast
264799_at AT1G08550	0.907	1.23e-123	0.685	step: violaxanthin deepoxidase\|\|violaxanthin deepoxidase\|\|violaxanthin deepoxidase GO:0046422:violaxanthin de-epoxidase activity GO:0030095:photosystem II (sensu Viridiplantae) GO:0016122:xanthophyll metabolism GO:0010028:xanthophyll cycle GO:0009543:thylakoid lumen (sensu Viridiplantae)
247025_at AT5G67030	0.878	2.27e-134	0.716	step: zeaxanthin epoxidase\|\|zeaxanthin epoxidase GO:0009688:abscisic acid biosynthesis GO:0016123:xanthophyll biosynthesis GO:0009540:zeaxanthin epoxidase activity GO:0006970:response to osmotic stress GO:0009414:response to water deprivation GO:0010182:sugar mediated signaling GO:0009507:chloroplast
260821_at AT1G06820	0.323	7.93e-130	0.703	step: carotenoid isomerase GO:0016117:carotenoid biosynthesis GO:0009662:etioplast organization and biogenesis GO:0046608:carotenoid isomerase activity GO:0009507:chloroplast

264959_at : AT1G77090
GO:0015979:photosynthesis
GO:0005509:calcium ion binding
GO:0009543:thylakoid lumen (sensu Viridiplantae)

probe set,gene	slope	pvalue	rsquared	annotations
250095_at AT5G17230	1.05	5.24e-205	0.855	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast
245284_at AT4G14210	0.55	3.83e-183	0.821	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.511	3.95e-148	0.751	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
247936_at AT5G57030	0.657	1.01e-175	0.808	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast
247025_at AT5G67030	0.918	3.19e-129	0.702	step: zeaxanthin epoxidase\|\|zeaxanthin epoxidase GO:0009688:abscisic acid biosynthesis GO:0016123:xanthophyll biosynthesis GO:0009540:zeaxanthin epoxidase activity GO:0006970:response to osmotic stress GO:0009414:response to water deprivation GO:0010182:sugar mediated signaling GO:0009507:chloroplast
260821_at AT1G06820	0.336	2.42e-122	0.682	step: carotenoid isomerase GO:0016117:carotenoid biosynthesis GO:0009662:etioplast organization and biogenesis GO:0046608:carotenoid isomerase activity GO:0009507:chloroplast

265182_at : AT1G23740
GO:0006567:threonine catabolism
GO:0006744:ubiquinone biosynthesis
GO:0005351:sugar porter activity
GO:0008425:2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity
GO:0008743:L-threonine 3-dehydrogenase activity
GO:0009401:phosphoenolpyruvate-dependent sugar phosphotransferase system
GO:0008270:zinc ion binding
GO:0009507:chloroplast
GO:0016491:oxidoreductase activity

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.403	1.06e-161	0.781	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.398	1.86e-174	0.806	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
247936_at AT5G57030	0.476	8.36e-148	0.75	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast
250095_at AT5G17230	0.799	1.82e-215	0.869	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast
247025_at AT5G67030	0.7	7.39e-137	0.723	step: zeaxanthin epoxidase\|\|zeaxanthin epoxidase GO:0009688:abscisic acid biosynthesis GO:0016123:xanthophyll biosynthesis GO:0009540:zeaxanthin epoxidase activity GO:0006970:response to osmotic stress GO:0009414:response to water deprivation GO:0010182:sugar mediated signaling GO:0009507:chloroplast

263410_at : AT2G04039
GO:0006952:defense response
GO:0005576:extracellular region
GO:0005554:molecular function unknown
GO:0042742:defense response to bacteria
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.405	2.89e-170	0.798	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.379	3.66e-145	0.744	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
247936_at AT5G57030	0.461	2.2e-134	0.716	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast
250095_at AT5G17230	0.8	2.47e-229	0.885	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast
247025_at AT5G67030	0.686	3.8e-130	0.704	step: zeaxanthin epoxidase\|\|zeaxanthin epoxidase GO:0009688:abscisic acid biosynthesis GO:0016123:xanthophyll biosynthesis GO:0009540:zeaxanthin epoxidase activity GO:0006970:response to osmotic stress GO:0009414:response to water deprivation GO:0010182:sugar mediated signaling GO:0009507:chloroplast

267471_at : AT2G30390
GO:0016852:sirohydrochlorin cobaltochelatase activity
GO:0006783:heme biosynthesis
GO:0016020:membrane
GO:0004325:ferrochelatase activity
GO:0009236:cobalamin biosynthesis
GO:0009341:beta-galactosidase complex
GO:0004565:beta-galactosidase activity
GO:0005975:carbohydrate metabolism
GO:0009765:photosynthesis light harvesting
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.657	4.02e-170	0.798	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
260821_at AT1G06820	0.414	4.22e-130	0.704	step: carotenoid isomerase GO:0016117:carotenoid biosynthesis GO:0009662:etioplast organization and biogenesis GO:0046608:carotenoid isomerase activity GO:0009507:chloroplast
259092_at AT3G04870	0.616	5.73e-145	0.743	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
247936_at AT5G57030	0.793	4.22e-172	0.802	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast
250095_at AT5G17230	1.24	4.33e-176	0.809	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast

256514_at : AT1G66130
GO:0008152:metabolism
GO:0006118:electron transport
GO:0005739:mitochondrion
GO:0016491:oxidoreductase activity

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.562	1.9e-129	0.702	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.568	6.75e-152	0.76	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
247025_at AT5G67030	1.02	4.24e-133	0.712	step: zeaxanthin epoxidase\|\|zeaxanthin epoxidase GO:0009688:abscisic acid biosynthesis GO:0016123:xanthophyll biosynthesis GO:0009540:zeaxanthin epoxidase activity GO:0006970:response to osmotic stress GO:0009414:response to water deprivation GO:0010182:sugar mediated signaling GO:0009507:chloroplast
259140_at AT3G10230	0.601	3.74e-134	0.715	step: lycopene beta cyclase GO:0045436:lycopene beta cyclase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
250095_at AT5G17230	1.1	5.68e-153	0.762	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast

256076_at : AT1G18060
GO:0000004:biological process unknown
GO:0005198:structural molecule activity
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.532	5.89e-150	0.755	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.498	5.01e-129	0.701	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
247936_at AT5G57030	0.638	1.05e-147	0.75	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast
250095_at AT5G17230	1.04	1.02e-176	0.81	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast
247025_at AT5G67030	0.93	1.4e-131	0.708	step: zeaxanthin epoxidase\|\|zeaxanthin epoxidase GO:0009688:abscisic acid biosynthesis GO:0016123:xanthophyll biosynthesis GO:0009540:zeaxanthin epoxidase activity GO:0006970:response to osmotic stress GO:0009414:response to water deprivation GO:0010182:sugar mediated signaling GO:0009507:chloroplast

266207_at : AT2G27680
GO:0005737:cytoplasm
GO:0004033:aldo-keto reductase activity
GO:0006813:potassium ion transport
GO:0005249:voltage-gated potassium channel activity
GO:0009507:chloroplast
GO:0016491:oxidoreductase activity

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.542	2.36e-162	0.782	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.498	2.86e-128	0.699	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
264799_at AT1G08550	1	1.36e-141	0.735	step: violaxanthin deepoxidase\|\|violaxanthin deepoxidase\|\|violaxanthin deepoxidase GO:0046422:violaxanthin de-epoxidase activity GO:0030095:photosystem II (sensu Viridiplantae) GO:0016122:xanthophyll metabolism GO:0010028:xanthophyll cycle GO:0009543:thylakoid lumen (sensu Viridiplantae)
250095_at AT5G17230	1.04	2.67e-183	0.822	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast
247936_at AT5G57030	0.618	1.47e-129	0.703	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast

251885_at : AT3G54050
GO:0042578:phosphoric ester hydrolase activity
GO:0006000:fructose metabolism
GO:0042132:fructose-bisphosphatase activity
GO:0005975:carbohydrate metabolism
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.309	3.66e-173	0.804	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.282	5e-132	0.71	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
264799_at AT1G08550	0.548	7.64e-128	0.698	step: violaxanthin deepoxidase\|\|violaxanthin deepoxidase\|\|violaxanthin deepoxidase GO:0046422:violaxanthin de-epoxidase activity GO:0030095:photosystem II (sensu Viridiplantae) GO:0016122:xanthophyll metabolism GO:0010028:xanthophyll cycle GO:0009543:thylakoid lumen (sensu Viridiplantae)
250095_at AT5G17230	0.606	1.59e-221	0.876	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast
247936_at AT5G57030	0.359	6.71e-147	0.748	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast

250668_at : AT5G07020
GO:0000004:biological process unknown
GO:0005554:molecular function unknown
GO:0008372:cellular component unknown

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.497	8.66e-175	0.807	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.462	1.02e-142	0.738	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
264799_at AT1G08550	0.881	8.19e-128	0.698	step: violaxanthin deepoxidase\|\|violaxanthin deepoxidase\|\|violaxanthin deepoxidase GO:0046422:violaxanthin de-epoxidase activity GO:0030095:photosystem II (sensu Viridiplantae) GO:0016122:xanthophyll metabolism GO:0010028:xanthophyll cycle GO:0009543:thylakoid lumen (sensu Viridiplantae)
250095_at AT5G17230	0.963	7.09e-207	0.857	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast
247936_at AT5G57030	0.566	1.98e-136	0.721	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast

257699_at : AT3G12780
GO:0005737:cytoplasm
GO:0004618:phosphoglycerate kinase activity
GO:0006096:glycolysis
GO:0005739:mitochondrion

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.489	3.42e-166	0.79	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.446	1.16e-127	0.697	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
264799_at AT1G08550	0.887	5.97e-135	0.718	step: violaxanthin deepoxidase\|\|violaxanthin deepoxidase\|\|violaxanthin deepoxidase GO:0046422:violaxanthin de-epoxidase activity GO:0030095:photosystem II (sensu Viridiplantae) GO:0016122:xanthophyll metabolism GO:0010028:xanthophyll cycle GO:0009543:thylakoid lumen (sensu Viridiplantae)
250095_at AT5G17230	0.953	9.75e-203	0.852	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast
247936_at AT5G57030	0.559	7.3e-134	0.715	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast

262612_at : AT1G14150
GO:0030095:photosystem II (sensu Viridiplantae)
GO:0015979:photosynthesis
GO:0005509:calcium ion binding
GO:0009543:thylakoid lumen (sensu Viridiplantae)

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.336	5.71e-159	0.775	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.315	6.25e-136	0.72	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
264799_at AT1G08550	0.605	1.21e-125	0.691	step: violaxanthin deepoxidase\|\|violaxanthin deepoxidase\|\|violaxanthin deepoxidase GO:0046422:violaxanthin de-epoxidase activity GO:0030095:photosystem II (sensu Viridiplantae) GO:0016122:xanthophyll metabolism GO:0010028:xanthophyll cycle GO:0009543:thylakoid lumen (sensu Viridiplantae)
250095_at AT5G17230	0.658	6.06e-196	0.842	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast
247936_at AT5G57030	0.395	4.37e-143	0.739	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast

253283_at : AT4G34090
GO:0000004:biological process unknown
GO:0005554:molecular function unknown
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.452	4.23e-150	0.755	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
260821_at AT1G06820	0.29	1.68e-125	0.691	step: carotenoid isomerase GO:0016117:carotenoid biosynthesis GO:0009662:etioplast organization and biogenesis GO:0046608:carotenoid isomerase activity GO:0009507:chloroplast
259092_at AT3G04870	0.442	4.81e-154	0.764	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
247936_at AT5G57030	0.557	2.18e-166	0.79	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast
250095_at AT5G17230	0.879	3.38e-175	0.807	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast

257172_at : AT3G23700
GO:0003735:structural constituent of ribosome
GO:0003723:RNA binding
GO:0006412:protein biosynthesis
GO:0005840:ribosome
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.482	2.98e-180	0.816	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.437	4.58e-133	0.712	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
264799_at AT1G08550	0.844	4.98e-125	0.69	step: violaxanthin deepoxidase\|\|violaxanthin deepoxidase\|\|violaxanthin deepoxidase GO:0046422:violaxanthin de-epoxidase activity GO:0030095:photosystem II (sensu Viridiplantae) GO:0016122:xanthophyll metabolism GO:0010028:xanthophyll cycle GO:0009543:thylakoid lumen (sensu Viridiplantae)
250095_at AT5G17230	0.909	1.93e-184	0.824	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast
247936_at AT5G57030	0.544	7.23e-135	0.717	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast

259258_at : AT3G07670
GO:0000004:biological process unknown
GO:0005554:molecular function unknown
GO:0005739:mitochondrion

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.605	6.48e-169	0.795	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
260821_at AT1G06820	0.377	3.93e-124	0.687	step: carotenoid isomerase GO:0016117:carotenoid biosynthesis GO:0009662:etioplast organization and biogenesis GO:0046608:carotenoid isomerase activity GO:0009507:chloroplast
259092_at AT3G04870	0.566	2.67e-142	0.737	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
247936_at AT5G57030	0.699	6.1e-141	0.733	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast
250095_at AT5G17230	1.13	1.87e-167	0.793	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast

261788_at : AT1G15980
GO:0016740:transferase activity
GO:0008152:metabolism
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.343	8.49e-171	0.799	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.309	4.23e-124	0.687	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
264799_at AT1G08550	0.607	3.26e-125	0.69	step: violaxanthin deepoxidase\|\|violaxanthin deepoxidase\|\|violaxanthin deepoxidase GO:0046422:violaxanthin de-epoxidase activity GO:0030095:photosystem II (sensu Viridiplantae) GO:0016122:xanthophyll metabolism GO:0010028:xanthophyll cycle GO:0009543:thylakoid lumen (sensu Viridiplantae)
250095_at AT5G17230	0.665	1.03e-202	0.852	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast
247936_at AT5G57030	0.403	6.09e-153	0.762	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast

267430_at : AT2G34860
GO:0031072:heat shock protein binding
GO:0006457:protein folding
GO:0051082:unfolded protein binding
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.495	5.44e-169	0.796	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.456	8.78e-134	0.714	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
264799_at AT1G08550	0.876	5.35e-124	0.687	step: violaxanthin deepoxidase\|\|violaxanthin deepoxidase\|\|violaxanthin deepoxidase GO:0046422:violaxanthin de-epoxidase activity GO:0030095:photosystem II (sensu Viridiplantae) GO:0016122:xanthophyll metabolism GO:0010028:xanthophyll cycle GO:0009543:thylakoid lumen (sensu Viridiplantae)
250095_at AT5G17230	0.959	3.03e-198	0.845	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast
247936_at AT5G57030	0.559	1.51e-128	0.7	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast

252353_at : AT3G48200
GO:0000004:biological process unknown
GO:0005554:molecular function unknown
GO:0012505:endomembrane system

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.521	4.51e-154	0.764	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259092_at AT3G04870	0.509	6.18e-157	0.771	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
247936_at AT5G57030	0.631	7.47e-158	0.773	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast
259140_at AT3G10230	0.522	2.66e-123	0.684	step: lycopene beta cyclase GO:0045436:lycopene beta cyclase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
250095_at AT5G17230	0.997	1.14e-167	0.793	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast

263760_at : AT2G21280
GO:0004043:L-aminoadipate-semialdehyde dehydrogenase activity
GO:0009225:nucleotide-sugar metabolism
GO:0051287:NAD binding
GO:0003824:catalytic activity
GO:0006694:steroid biosynthesis
GO:0003854:3-beta-hydroxy-delta5-steroid dehydrogenase activity
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
245284_at AT4G14210	0.605	1.41e-173	0.804	step: phytoene dehydrogenase GO:0016117:carotenoid biosynthesis GO:0016166:phytoene dehydrogenase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
260821_at AT1G06820	0.374	7.05e-123	0.683	step: carotenoid isomerase GO:0016117:carotenoid biosynthesis GO:0009662:etioplast organization and biogenesis GO:0046608:carotenoid isomerase activity GO:0009507:chloroplast
259092_at AT3G04870	0.557	1.04e-136	0.722	step: carotene 7,8-desaturase GO:0016719:carotene 7,8-desaturase activity GO:0016120:carotene biosynthesis GO:0009507:chloroplast
247936_at AT5G57030	0.718	2.56e-162	0.782	step: lycopene epsilon cyclase GO:0016117:carotenoid biosynthesis GO:0045435:lycopene epsilon cyclase activity GO:0009765:photosynthesis light harvesting GO:0016120:carotene biosynthesis GO:0009507:chloroplast
250095_at AT5G17230	1.13	4.31e-169	0.796	step: geranylgeranyl-diphosphate geranylgeranyltransferase GO:0016117:carotenoid biosynthesis GO:0016021:integral to membrane GO:0016767:geranylgeranyl-diphosphate geranylgeranyltransferase activity GO:0009507:chloroplast

267196_at : AT2G30950
GO:0009535:thylakoid membrane (sensu Viridiplantae)
GO:0004176:ATP-dependent peptidase activity
GO:0010205:photoinhibition
GO:0006510:ATP-dependent proteolysis
GO:0008270:zinc ion binding
GO:0016887:ATPase activity
GO:0010027:thylakoid membrane organization and biogenesis
GO:0008237:metallopeptidase activity
GO:0009507:chloroplast

probe set,gene