PCL results for AraCyc pathway: arginine biosynthesis I

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-80. 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

251599_at : AT3G57610
GO:0004019:adenylosuccinate synthase activity
GO:0006164:purine nucleotide biosynthesis
GO:0005525:GTP binding
GO:0009152:purine ribonucleotide biosynthesis
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
251639_at AT3G57560	0.847	2.22e-93	0.581	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
250403_at AT5G10920	1.01	7.27e-88	0.558	step: adenylosuccinate lyase GO:0004018:adenylosuccinate lyase activity GO:0009152:purine ribonucleotide biosynthesis GO:0004056:argininosuccinate lyase activity GO:0045239:tricarboxylic acid cycle enzyme complex GO:0008797:aspartate ammonia-lyase activity GO:0006526:arginine biosynthesis GO:0003824:catalytic activity GO:0006106:fumarate metabolism GO:0006531:aspartate metabolism GO:0004333:fumarate hydratase activity GO:0009507:chloroplast
261122_at AT1G75330	0.719	7.75e-82	0.532	step: ornithine carbamoyltransferase GO:0006207:'de novo' pyrimidine base biosynthesis GO:0006520:amino acid metabolism GO:0016743:carboxyl- and carbamoyltransferase activity GO:0009348:ornithine carbamoyltransferase complex GO:0009507:chloroplast GO:0016597:amino acid binding GO:0004585:ornithine carbamoyltransferase activity GO:0004070:aspartate carbamoyltransferase activity
265965_at AT2G37500	0.678	1.04e-90	0.57	step: glutamate N-acetyltransferase GO:0006526:arginine biosynthesis GO:0004358:glutamate N-acetyltransferase activity GO:0009507:chloroplast
260286_at AT1G80600	0.855	9.62e-82	0.532	step: acetylornithine transaminase GO:0005737:cytoplasm GO:0030170:pyridoxal phosphate binding GO:0009448:gamma-aminobutyric acid metabolism GO:0009102:biotin biosynthesis GO:0042286:glutamate-1-semialdehyde 2,1-aminomutase activity GO:0004015:adenosylmethionine-8-amino-7-oxononanoate transaminase activity GO:0006526:arginine biosynthesis GO:0004400:histidinol-phosphate transaminase activity GO:0006779:porphyrin biosynthesis GO:0008483:transaminase activity GO:0009058:biosynthesis GO:0006525:arginine metabolism GO:0019555:glutamate catabolism to ornithine GO:0000105:histidine biosynthesis GO:0009507:chloroplast GO:0003867:4-aminobutyrate transaminase activity GO:0003992:acetylornithine transaminase activity
254134_at AT4G24830	1.03	1.02e-87	0.557	step: argininosuccinate synthase GO:0004055:argininosuccinate synthase activity GO:0006526:arginine biosynthesis GO:0005524:ATP binding GO:0009507:chloroplast

256862_at : AT3G23940
GO:0004160:dihydroxy-acid dehydratase activity
GO:0009255:Entner-Doudoroff pathway
GO:0009099:valine biosynthesis
GO:0003824:catalytic activity
GO:0008152:metabolism
GO:0004456:phosphogluconate dehydratase activity
GO:0009097:isoleucine biosynthesis
GO:0009507:chloroplast
GO:0009082:branched chain family amino acid biosynthesis

probe set,gene	slope	pvalue	rsquared	annotations
254134_at AT4G24830	0.683	5.71e-122	0.68	step: argininosuccinate synthase GO:0004055:argininosuccinate synthase activity GO:0006526:arginine biosynthesis GO:0005524:ATP binding GO:0009507:chloroplast
265965_at AT2G37500	0.397	2.21e-84	0.543	step: glutamate N-acetyltransferase GO:0006526:arginine biosynthesis GO:0004358:glutamate N-acetyltransferase activity GO:0009507:chloroplast
251639_at AT3G57560	0.521	1.41e-101	0.612	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
250403_at AT5G10920	0.717	1.09e-164	0.787	step: adenylosuccinate lyase GO:0004018:adenylosuccinate lyase activity GO:0009152:purine ribonucleotide biosynthesis GO:0004056:argininosuccinate lyase activity GO:0045239:tricarboxylic acid cycle enzyme complex GO:0008797:aspartate ammonia-lyase activity GO:0006526:arginine biosynthesis GO:0003824:catalytic activity GO:0006106:fumarate metabolism GO:0006531:aspartate metabolism GO:0004333:fumarate hydratase activity GO:0009507:chloroplast
261122_at AT1G75330	0.472	5.81e-109	0.638	step: ornithine carbamoyltransferase GO:0006207:'de novo' pyrimidine base biosynthesis GO:0006520:amino acid metabolism GO:0016743:carboxyl- and carbamoyltransferase activity GO:0009348:ornithine carbamoyltransferase complex GO:0009507:chloroplast GO:0016597:amino acid binding GO:0004585:ornithine carbamoyltransferase activity GO:0004070:aspartate carbamoyltransferase activity

258243_at : AT3G27740
GO:0005737:cytoplasm
GO:0006207:'de novo' pyrimidine base biosynthesis
GO:0003922:GMP synthase (glutamine-hydrolyzing) activity
GO:0006526:arginine biosynthesis
GO:0004049:anthranilate synthase activity
GO:0003824:catalytic activity
GO:0009058:biosynthesis
GO:0006807:nitrogen compound metabolism
GO:0004086:carbamoyl-phosphate synthase activity
GO:0008152:metabolism
GO:0016763:transferase activity, transferring pentosyl groups
GO:0004088:carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
GO:0006177:GMP biosynthesis
GO:0000105:histidine biosynthesis
GO:0005524:ATP binding
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
254134_at AT4G24830	1.18	4.65e-126	0.693	step: argininosuccinate synthase GO:0004055:argininosuccinate synthase activity GO:0006526:arginine biosynthesis GO:0005524:ATP binding GO:0009507:chloroplast
251639_at AT3G57560	0.888	7.83e-99	0.602	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
250403_at AT5G10920	1.15	7.04e-126	0.692	step: adenylosuccinate lyase GO:0004018:adenylosuccinate lyase activity GO:0009152:purine ribonucleotide biosynthesis GO:0004056:argininosuccinate lyase activity GO:0045239:tricarboxylic acid cycle enzyme complex GO:0008797:aspartate ammonia-lyase activity GO:0006526:arginine biosynthesis GO:0003824:catalytic activity GO:0006106:fumarate metabolism GO:0006531:aspartate metabolism GO:0004333:fumarate hydratase activity GO:0009507:chloroplast
257680_at AT3G20330	0.951	2.08e-126	0.694	step: ornithine carbamoyltransferase GO:0006207:'de novo' pyrimidine base biosynthesis GO:0006520:amino acid metabolism GO:0016743:carboxyl- and carbamoyltransferase activity GO:0009348:ornithine carbamoyltransferase complex GO:0009507:chloroplast GO:0016597:amino acid binding GO:0004585:ornithine carbamoyltransferase activity GO:0004070:aspartate carbamoyltransferase activity

262937_at : AT1G79560
GO:0004176:ATP-dependent peptidase activity
GO:0006310:DNA recombination
GO:0005975:carbohydrate metabolism
GO:0006281:DNA repair
GO:0030163:protein catabolism
GO:0016887:ATPase activity
GO:0006508:proteolysis and peptidolysis
GO:0008237:metallopeptidase activity
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
266704_at AT2G19940	0.462	1.55e-90	0.569	step: dihydrodipicolinate reductase GO:0005737:cytoplasm GO:0008152:metabolism GO:0051287:NAD binding GO:0006520:amino acid metabolism GO:0016620:oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor GO:0006526:arginine biosynthesis GO:0009089:lysine biosynthesis via diaminopimelate GO:0009088:threonine biosynthesis GO:0008839:dihydrodipicolinate reductase activity GO:0003942:N-acetyl-gamma-glutamyl-phosphate reductase activity GO:0009086:methionine biosynthesis GO:0004073:aspartate-semialdehyde dehydrogenase activity GO:0006118:electron transport GO:0016491:oxidoreductase activity
251639_at AT3G57560	0.515	9.04e-93	0.578	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
250403_at AT5G10920	0.619	4.92e-90	0.567	step: adenylosuccinate lyase GO:0004018:adenylosuccinate lyase activity GO:0009152:purine ribonucleotide biosynthesis GO:0004056:argininosuccinate lyase activity GO:0045239:tricarboxylic acid cycle enzyme complex GO:0008797:aspartate ammonia-lyase activity GO:0006526:arginine biosynthesis GO:0003824:catalytic activity GO:0006106:fumarate metabolism GO:0006531:aspartate metabolism GO:0004333:fumarate hydratase activity GO:0009507:chloroplast
265965_at AT2G37500	0.444	8.5e-115	0.658	step: glutamate N-acetyltransferase GO:0006526:arginine biosynthesis GO:0004358:glutamate N-acetyltransferase activity GO:0009507:chloroplast

251083_at : AT5G01590
GO:0009941:chloroplast envelope
GO:0000004:biological process unknown
GO:0005554:molecular function unknown

probe set,gene	slope	pvalue	rsquared	annotations
266704_at AT2G19940	0.416	4.39e-119	0.672	step: dihydrodipicolinate reductase GO:0005737:cytoplasm GO:0008152:metabolism GO:0051287:NAD binding GO:0006520:amino acid metabolism GO:0016620:oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor GO:0006526:arginine biosynthesis GO:0009089:lysine biosynthesis via diaminopimelate GO:0009088:threonine biosynthesis GO:0008839:dihydrodipicolinate reductase activity GO:0003942:N-acetyl-gamma-glutamyl-phosphate reductase activity GO:0009086:methionine biosynthesis GO:0004073:aspartate-semialdehyde dehydrogenase activity GO:0006118:electron transport GO:0016491:oxidoreductase activity
251639_at AT3G57560	0.448	7.54e-109	0.638	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
260286_at AT1G80600	0.476	6.61e-112	0.648	step: acetylornithine transaminase GO:0005737:cytoplasm GO:0030170:pyridoxal phosphate binding GO:0009448:gamma-aminobutyric acid metabolism GO:0009102:biotin biosynthesis GO:0042286:glutamate-1-semialdehyde 2,1-aminomutase activity GO:0004015:adenosylmethionine-8-amino-7-oxononanoate transaminase activity GO:0006526:arginine biosynthesis GO:0004400:histidinol-phosphate transaminase activity GO:0006779:porphyrin biosynthesis GO:0008483:transaminase activity GO:0009058:biosynthesis GO:0006525:arginine metabolism GO:0019555:glutamate catabolism to ornithine GO:0000105:histidine biosynthesis GO:0009507:chloroplast GO:0003867:4-aminobutyrate transaminase activity GO:0003992:acetylornithine transaminase activity
265965_at AT2G37500	0.34	3.69e-89	0.563	step: glutamate N-acetyltransferase GO:0006526:arginine biosynthesis GO:0004358:glutamate N-acetyltransferase activity GO:0009507:chloroplast

255053_at : AT4G09730
GO:0006310:DNA recombination
GO:0009432:SOS response
GO:0008026:ATP-dependent helicase activity
GO:0004003:ATP-dependent DNA helicase activity
GO:0005739:mitochondrion
GO:0004386:helicase activity
GO:0003676:nucleic acid binding
GO:0006259:DNA metabolism
GO:0003774:motor activity
GO:0005524:ATP binding

probe set,gene	slope	pvalue	rsquared	annotations
266704_at AT2G19940	0.48	2.48e-95	0.588	step: dihydrodipicolinate reductase GO:0005737:cytoplasm GO:0008152:metabolism GO:0051287:NAD binding GO:0006520:amino acid metabolism GO:0016620:oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor GO:0006526:arginine biosynthesis GO:0009089:lysine biosynthesis via diaminopimelate GO:0009088:threonine biosynthesis GO:0008839:dihydrodipicolinate reductase activity GO:0003942:N-acetyl-gamma-glutamyl-phosphate reductase activity GO:0009086:methionine biosynthesis GO:0004073:aspartate-semialdehyde dehydrogenase activity GO:0006118:electron transport GO:0016491:oxidoreductase activity
251639_at AT3G57560	0.563	1.01e-116	0.664	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
260286_at AT1G80600	0.545	4.7e-88	0.559	step: acetylornithine transaminase GO:0005737:cytoplasm GO:0030170:pyridoxal phosphate binding GO:0009448:gamma-aminobutyric acid metabolism GO:0009102:biotin biosynthesis GO:0042286:glutamate-1-semialdehyde 2,1-aminomutase activity GO:0004015:adenosylmethionine-8-amino-7-oxononanoate transaminase activity GO:0006526:arginine biosynthesis GO:0004400:histidinol-phosphate transaminase activity GO:0006779:porphyrin biosynthesis GO:0008483:transaminase activity GO:0009058:biosynthesis GO:0006525:arginine metabolism GO:0019555:glutamate catabolism to ornithine GO:0000105:histidine biosynthesis GO:0009507:chloroplast GO:0003867:4-aminobutyrate transaminase activity GO:0003992:acetylornithine transaminase activity
265965_at AT2G37500	0.433	1.14e-98	0.601	step: glutamate N-acetyltransferase GO:0006526:arginine biosynthesis GO:0004358:glutamate N-acetyltransferase activity GO:0009507:chloroplast

259344_at : AT3G03710
GO:0004549:tRNA-specific ribonuclease activity
GO:0000049:tRNA binding
GO:0008033:tRNA processing
GO:0005840:ribosome
GO:0000175:3'-5'-exoribonuclease activity
GO:0003735:structural constituent of ribosome
GO:0003723:RNA binding
GO:0003676:nucleic acid binding
GO:0006412:protein biosynthesis
GO:0006396:RNA processing
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
266704_at AT2G19940	0.438	3.67e-107	0.632	step: dihydrodipicolinate reductase GO:0005737:cytoplasm GO:0008152:metabolism GO:0051287:NAD binding GO:0006520:amino acid metabolism GO:0016620:oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor GO:0006526:arginine biosynthesis GO:0009089:lysine biosynthesis via diaminopimelate GO:0009088:threonine biosynthesis GO:0008839:dihydrodipicolinate reductase activity GO:0003942:N-acetyl-gamma-glutamyl-phosphate reductase activity GO:0009086:methionine biosynthesis GO:0004073:aspartate-semialdehyde dehydrogenase activity GO:0006118:electron transport GO:0016491:oxidoreductase activity
251639_at AT3G57560	0.494	5.89e-115	0.658	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
260286_at AT1G80600	0.478	1.15e-86	0.553	step: acetylornithine transaminase GO:0005737:cytoplasm GO:0030170:pyridoxal phosphate binding GO:0009448:gamma-aminobutyric acid metabolism GO:0009102:biotin biosynthesis GO:0042286:glutamate-1-semialdehyde 2,1-aminomutase activity GO:0004015:adenosylmethionine-8-amino-7-oxononanoate transaminase activity GO:0006526:arginine biosynthesis GO:0004400:histidinol-phosphate transaminase activity GO:0006779:porphyrin biosynthesis GO:0008483:transaminase activity GO:0009058:biosynthesis GO:0006525:arginine metabolism GO:0019555:glutamate catabolism to ornithine GO:0000105:histidine biosynthesis GO:0009507:chloroplast GO:0003867:4-aminobutyrate transaminase activity GO:0003992:acetylornithine transaminase activity
265965_at AT2G37500	0.375	1.34e-93	0.582	step: glutamate N-acetyltransferase GO:0006526:arginine biosynthesis GO:0004358:glutamate N-acetyltransferase activity GO:0009507:chloroplast

267421_at : AT2G35040
GO:0003937:IMP cyclohydrolase activity
GO:0006164:purine nucleotide biosynthesis
GO:0004643:phosphoribosylaminoimidazolecarboxamide formyltransferase activity
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
254134_at AT4G24830	0.779	1.36e-115	0.66	step: argininosuccinate synthase GO:0004055:argininosuccinate synthase activity GO:0006526:arginine biosynthesis GO:0005524:ATP binding GO:0009507:chloroplast
251639_at AT3G57560	0.572	1.09e-85	0.549	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
250403_at AT5G10920	0.797	1.88e-137	0.724	step: adenylosuccinate lyase GO:0004018:adenylosuccinate lyase activity GO:0009152:purine ribonucleotide biosynthesis GO:0004056:argininosuccinate lyase activity GO:0045239:tricarboxylic acid cycle enzyme complex GO:0008797:aspartate ammonia-lyase activity GO:0006526:arginine biosynthesis GO:0003824:catalytic activity GO:0006106:fumarate metabolism GO:0006531:aspartate metabolism GO:0004333:fumarate hydratase activity GO:0009507:chloroplast
261122_at AT1G75330	0.53	1.28e-98	0.601	step: ornithine carbamoyltransferase GO:0006207:'de novo' pyrimidine base biosynthesis GO:0006520:amino acid metabolism GO:0016743:carboxyl- and carbamoyltransferase activity GO:0009348:ornithine carbamoyltransferase complex GO:0009507:chloroplast GO:0016597:amino acid binding GO:0004585:ornithine carbamoyltransferase activity GO:0004070:aspartate carbamoyltransferase activity

257717_at : AT3G18390
GO:0000004:biological process unknown
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
266704_at AT2G19940	0.306	1.13e-110	0.644	step: dihydrodipicolinate reductase GO:0005737:cytoplasm GO:0008152:metabolism GO:0051287:NAD binding GO:0006520:amino acid metabolism GO:0016620:oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor GO:0006526:arginine biosynthesis GO:0009089:lysine biosynthesis via diaminopimelate GO:0009088:threonine biosynthesis GO:0008839:dihydrodipicolinate reductase activity GO:0003942:N-acetyl-gamma-glutamyl-phosphate reductase activity GO:0009086:methionine biosynthesis GO:0004073:aspartate-semialdehyde dehydrogenase activity GO:0006118:electron transport GO:0016491:oxidoreductase activity
251639_at AT3G57560	0.313	3.25e-86	0.551	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
260286_at AT1G80600	0.336	1.15e-90	0.57	step: acetylornithine transaminase GO:0005737:cytoplasm GO:0030170:pyridoxal phosphate binding GO:0009448:gamma-aminobutyric acid metabolism GO:0009102:biotin biosynthesis GO:0042286:glutamate-1-semialdehyde 2,1-aminomutase activity GO:0004015:adenosylmethionine-8-amino-7-oxononanoate transaminase activity GO:0006526:arginine biosynthesis GO:0004400:histidinol-phosphate transaminase activity GO:0006779:porphyrin biosynthesis GO:0008483:transaminase activity GO:0009058:biosynthesis GO:0006525:arginine metabolism GO:0019555:glutamate catabolism to ornithine GO:0000105:histidine biosynthesis GO:0009507:chloroplast GO:0003867:4-aminobutyrate transaminase activity GO:0003992:acetylornithine transaminase activity
265965_at AT2G37500	0.25	1.05e-82	0.536	step: glutamate N-acetyltransferase GO:0006526:arginine biosynthesis GO:0004358:glutamate N-acetyltransferase activity GO:0009507:chloroplast

260292_at : AT1G63680
GO:0005737:cytoplasm
GO:0008766:UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity
GO:0008764:UDP-N-acetylmuramoylalanine-D-glutamate ligase activity
GO:0008763:UDP-N-acetylmuramate-L-alanine ligase activity
GO:0004326:tetrahydrofolylpolyglutamate synthase activity
GO:0016881:acid-amino acid ligase activity
GO:0009058:biosynthesis
GO:0009396:folic acid and derivative biosynthesis
GO:0009089:lysine biosynthesis via diaminopimelate
GO:0007047:cell wall organization and biogenesis
GO:0008839:dihydrodipicolinate reductase activity
GO:0016874:ligase activity
GO:0005524:ATP binding
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
266704_at AT2G19940	0.481	1.85e-90	0.569	step: dihydrodipicolinate reductase GO:0005737:cytoplasm GO:0008152:metabolism GO:0051287:NAD binding GO:0006520:amino acid metabolism GO:0016620:oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor GO:0006526:arginine biosynthesis GO:0009089:lysine biosynthesis via diaminopimelate GO:0009088:threonine biosynthesis GO:0008839:dihydrodipicolinate reductase activity GO:0003942:N-acetyl-gamma-glutamyl-phosphate reductase activity GO:0009086:methionine biosynthesis GO:0004073:aspartate-semialdehyde dehydrogenase activity GO:0006118:electron transport GO:0016491:oxidoreductase activity
251639_at AT3G57560	0.587	1.63e-126	0.694	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
250403_at AT5G10920	0.625	1.55e-82	0.535	step: adenylosuccinate lyase GO:0004018:adenylosuccinate lyase activity GO:0009152:purine ribonucleotide biosynthesis GO:0004056:argininosuccinate lyase activity GO:0045239:tricarboxylic acid cycle enzyme complex GO:0008797:aspartate ammonia-lyase activity GO:0006526:arginine biosynthesis GO:0003824:catalytic activity GO:0006106:fumarate metabolism GO:0006531:aspartate metabolism GO:0004333:fumarate hydratase activity GO:0009507:chloroplast
265965_at AT2G37500	0.43	6.33e-91	0.571	step: glutamate N-acetyltransferase GO:0006526:arginine biosynthesis GO:0004358:glutamate N-acetyltransferase activity GO:0009507:chloroplast

261882_at : AT1G80770
GO:0006400:tRNA modification
GO:0005525:GTP binding
GO:0003924:GTPase activity
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
266704_at AT2G19940	0.512	6.69e-91	0.571	step: dihydrodipicolinate reductase GO:0005737:cytoplasm GO:0008152:metabolism GO:0051287:NAD binding GO:0006520:amino acid metabolism GO:0016620:oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor GO:0006526:arginine biosynthesis GO:0009089:lysine biosynthesis via diaminopimelate GO:0009088:threonine biosynthesis GO:0008839:dihydrodipicolinate reductase activity GO:0003942:N-acetyl-gamma-glutamyl-phosphate reductase activity GO:0009086:methionine biosynthesis GO:0004073:aspartate-semialdehyde dehydrogenase activity GO:0006118:electron transport GO:0016491:oxidoreductase activity
251639_at AT3G57560	0.58	2.05e-98	0.6	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
260286_at AT1G80600	0.579	6.97e-83	0.537	step: acetylornithine transaminase GO:0005737:cytoplasm GO:0030170:pyridoxal phosphate binding GO:0009448:gamma-aminobutyric acid metabolism GO:0009102:biotin biosynthesis GO:0042286:glutamate-1-semialdehyde 2,1-aminomutase activity GO:0004015:adenosylmethionine-8-amino-7-oxononanoate transaminase activity GO:0006526:arginine biosynthesis GO:0004400:histidinol-phosphate transaminase activity GO:0006779:porphyrin biosynthesis GO:0008483:transaminase activity GO:0009058:biosynthesis GO:0006525:arginine metabolism GO:0019555:glutamate catabolism to ornithine GO:0000105:histidine biosynthesis GO:0009507:chloroplast GO:0003867:4-aminobutyrate transaminase activity GO:0003992:acetylornithine transaminase activity
265965_at AT2G37500	0.441	2.09e-81	0.53	step: glutamate N-acetyltransferase GO:0006526:arginine biosynthesis GO:0004358:glutamate N-acetyltransferase activity GO:0009507:chloroplast

253233_at : AT4G34290
GO:0005634:nucleus
GO:0005554:molecular function unknown
GO:0000004:biological process unknown
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
266704_at AT2G19940	0.308	2.04e-98	0.6	step: dihydrodipicolinate reductase GO:0005737:cytoplasm GO:0008152:metabolism GO:0051287:NAD binding GO:0006520:amino acid metabolism GO:0016620:oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor GO:0006526:arginine biosynthesis GO:0009089:lysine biosynthesis via diaminopimelate GO:0009088:threonine biosynthesis GO:0008839:dihydrodipicolinate reductase activity GO:0003942:N-acetyl-gamma-glutamyl-phosphate reductase activity GO:0009086:methionine biosynthesis GO:0004073:aspartate-semialdehyde dehydrogenase activity GO:0006118:electron transport GO:0016491:oxidoreductase activity
251639_at AT3G57560	0.347	2.76e-105	0.625	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
250403_at AT5G10920	0.388	3.08e-81	0.529	step: adenylosuccinate lyase GO:0004018:adenylosuccinate lyase activity GO:0009152:purine ribonucleotide biosynthesis GO:0004056:argininosuccinate lyase activity GO:0045239:tricarboxylic acid cycle enzyme complex GO:0008797:aspartate ammonia-lyase activity GO:0006526:arginine biosynthesis GO:0003824:catalytic activity GO:0006106:fumarate metabolism GO:0006531:aspartate metabolism GO:0004333:fumarate hydratase activity GO:0009507:chloroplast
265965_at AT2G37500	0.26	7.97e-83	0.536	step: glutamate N-acetyltransferase GO:0006526:arginine biosynthesis GO:0004358:glutamate N-acetyltransferase activity GO:0009507:chloroplast

252492_at : AT3G46740
GO:0009658:chloroplast organization and biogenesis
GO:0010006:toc complex
GO:0015450:protein translocase activity
GO:0004478:methionine adenosyltransferase activity
GO:0005524:ATP binding

probe set,gene	slope	pvalue	rsquared	annotations
254134_at AT4G24830	0.696	5.36e-81	0.528	step: argininosuccinate synthase GO:0004055:argininosuccinate synthase activity GO:0006526:arginine biosynthesis GO:0005524:ATP binding GO:0009507:chloroplast
265965_at AT2G37500	0.459	5.81e-84	0.541	step: glutamate N-acetyltransferase GO:0006526:arginine biosynthesis GO:0004358:glutamate N-acetyltransferase activity GO:0009507:chloroplast
251639_at AT3G57560	0.637	1.56e-122	0.682	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
250403_at AT5G10920	0.744	3.44e-107	0.632	step: adenylosuccinate lyase GO:0004018:adenylosuccinate lyase activity GO:0009152:purine ribonucleotide biosynthesis GO:0004056:argininosuccinate lyase activity GO:0045239:tricarboxylic acid cycle enzyme complex GO:0008797:aspartate ammonia-lyase activity GO:0006526:arginine biosynthesis GO:0003824:catalytic activity GO:0006106:fumarate metabolism GO:0006531:aspartate metabolism GO:0004333:fumarate hydratase activity GO:0009507:chloroplast

245150_at : AT2G47590
GO:0003913:DNA photolyase activity
GO:0008372:cellular component unknown
GO:0006281:DNA repair

probe set,gene	slope	pvalue	rsquared	annotations
266704_at AT2G19940	0.441	5.92e-115	0.658	step: dihydrodipicolinate reductase GO:0005737:cytoplasm GO:0008152:metabolism GO:0051287:NAD binding GO:0006520:amino acid metabolism GO:0016620:oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor GO:0006526:arginine biosynthesis GO:0009089:lysine biosynthesis via diaminopimelate GO:0009088:threonine biosynthesis GO:0008839:dihydrodipicolinate reductase activity GO:0003942:N-acetyl-gamma-glutamyl-phosphate reductase activity GO:0009086:methionine biosynthesis GO:0004073:aspartate-semialdehyde dehydrogenase activity GO:0006118:electron transport GO:0016491:oxidoreductase activity
251639_at AT3G57560	0.436	5.47e-81	0.528	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
260286_at AT1G80600	0.46	6.67e-81	0.528	step: acetylornithine transaminase GO:0005737:cytoplasm GO:0030170:pyridoxal phosphate binding GO:0009448:gamma-aminobutyric acid metabolism GO:0009102:biotin biosynthesis GO:0042286:glutamate-1-semialdehyde 2,1-aminomutase activity GO:0004015:adenosylmethionine-8-amino-7-oxononanoate transaminase activity GO:0006526:arginine biosynthesis GO:0004400:histidinol-phosphate transaminase activity GO:0006779:porphyrin biosynthesis GO:0008483:transaminase activity GO:0009058:biosynthesis GO:0006525:arginine metabolism GO:0019555:glutamate catabolism to ornithine GO:0000105:histidine biosynthesis GO:0009507:chloroplast GO:0003867:4-aminobutyrate transaminase activity GO:0003992:acetylornithine transaminase activity
265965_at AT2G37500	0.363	1.4e-88	0.561	step: glutamate N-acetyltransferase GO:0006526:arginine biosynthesis GO:0004358:glutamate N-acetyltransferase activity GO:0009507:chloroplast

253921_at : AT4G26900
GO:0000107:imidazoleglycerol phosphate synthase activity
GO:0000105:histidine biosynthesis
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
254134_at AT4G24830	0.881	3.37e-114	0.656	step: argininosuccinate synthase GO:0004055:argininosuccinate synthase activity GO:0006526:arginine biosynthesis GO:0005524:ATP binding GO:0009507:chloroplast
250403_at AT5G10920	0.911	1.53e-141	0.735	step: adenylosuccinate lyase GO:0004018:adenylosuccinate lyase activity GO:0009152:purine ribonucleotide biosynthesis GO:0004056:argininosuccinate lyase activity GO:0045239:tricarboxylic acid cycle enzyme complex GO:0008797:aspartate ammonia-lyase activity GO:0006526:arginine biosynthesis GO:0003824:catalytic activity GO:0006106:fumarate metabolism GO:0006531:aspartate metabolism GO:0004333:fumarate hydratase activity GO:0009507:chloroplast
261122_at AT1G75330	0.604	9.82e-100	0.605	step: ornithine carbamoyltransferase GO:0006207:'de novo' pyrimidine base biosynthesis GO:0006520:amino acid metabolism GO:0016743:carboxyl- and carbamoyltransferase activity GO:0009348:ornithine carbamoyltransferase complex GO:0009507:chloroplast GO:0016597:amino acid binding GO:0004585:ornithine carbamoyltransferase activity GO:0004070:aspartate carbamoyltransferase activity

251958_at : AT3G53560
GO:0000004:biological process unknown
GO:0005554:molecular function unknown
GO:0009543:thylakoid lumen (sensu Viridiplantae)

probe set,gene	slope	pvalue	rsquared	annotations
266704_at AT2G19940	0.396	4.79e-104	0.621	step: dihydrodipicolinate reductase GO:0005737:cytoplasm GO:0008152:metabolism GO:0051287:NAD binding GO:0006520:amino acid metabolism GO:0016620:oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor GO:0006526:arginine biosynthesis GO:0009089:lysine biosynthesis via diaminopimelate GO:0009088:threonine biosynthesis GO:0008839:dihydrodipicolinate reductase activity GO:0003942:N-acetyl-gamma-glutamyl-phosphate reductase activity GO:0009086:methionine biosynthesis GO:0004073:aspartate-semialdehyde dehydrogenase activity GO:0006118:electron transport GO:0016491:oxidoreductase activity
251639_at AT3G57560	0.426	1.8e-95	0.589	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
260286_at AT1G80600	0.453	1.33e-97	0.597	step: acetylornithine transaminase GO:0005737:cytoplasm GO:0030170:pyridoxal phosphate binding GO:0009448:gamma-aminobutyric acid metabolism GO:0009102:biotin biosynthesis GO:0042286:glutamate-1-semialdehyde 2,1-aminomutase activity GO:0004015:adenosylmethionine-8-amino-7-oxononanoate transaminase activity GO:0006526:arginine biosynthesis GO:0004400:histidinol-phosphate transaminase activity GO:0006779:porphyrin biosynthesis GO:0008483:transaminase activity GO:0009058:biosynthesis GO:0006525:arginine metabolism GO:0019555:glutamate catabolism to ornithine GO:0000105:histidine biosynthesis GO:0009507:chloroplast GO:0003867:4-aminobutyrate transaminase activity GO:0003992:acetylornithine transaminase activity

250061_at : AT5G17710
GO:0000774:adenyl-nucleotide exchange factor activity
GO:0042803:protein homodimerization activity
GO:0006457:protein folding
GO:0051087:chaperone binding
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
266704_at AT2G19940	0.442	3.74e-103	0.618	step: dihydrodipicolinate reductase GO:0005737:cytoplasm GO:0008152:metabolism GO:0051287:NAD binding GO:0006520:amino acid metabolism GO:0016620:oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor GO:0006526:arginine biosynthesis GO:0009089:lysine biosynthesis via diaminopimelate GO:0009088:threonine biosynthesis GO:0008839:dihydrodipicolinate reductase activity GO:0003942:N-acetyl-gamma-glutamyl-phosphate reductase activity GO:0009086:methionine biosynthesis GO:0004073:aspartate-semialdehyde dehydrogenase activity GO:0006118:electron transport GO:0016491:oxidoreductase activity
251639_at AT3G57560	0.476	7.28e-95	0.586	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
260286_at AT1G80600	0.504	6.51e-96	0.591	step: acetylornithine transaminase GO:0005737:cytoplasm GO:0030170:pyridoxal phosphate binding GO:0009448:gamma-aminobutyric acid metabolism GO:0009102:biotin biosynthesis GO:0042286:glutamate-1-semialdehyde 2,1-aminomutase activity GO:0004015:adenosylmethionine-8-amino-7-oxononanoate transaminase activity GO:0006526:arginine biosynthesis GO:0004400:histidinol-phosphate transaminase activity GO:0006779:porphyrin biosynthesis GO:0008483:transaminase activity GO:0009058:biosynthesis GO:0006525:arginine metabolism GO:0019555:glutamate catabolism to ornithine GO:0000105:histidine biosynthesis GO:0009507:chloroplast GO:0003867:4-aminobutyrate transaminase activity GO:0003992:acetylornithine transaminase activity

245914_at : AT5G19620
GO:0009941:chloroplast envelope
GO:0006886:intracellular protein transport
GO:0015450:protein translocase activity

probe set,gene	slope	pvalue	rsquared	annotations
265965_at AT2G37500	0.885	3.34e-93	0.58	step: glutamate N-acetyltransferase GO:0006526:arginine biosynthesis GO:0004358:glutamate N-acetyltransferase activity GO:0009507:chloroplast
251639_at AT3G57560	1.14	2.54e-105	0.626	step: acetylglutamate kinase GO:0005737:cytoplasm GO:0008652:amino acid biosynthesis GO:0008804:carbamate kinase activity GO:0004042:amino-acid N-acetyltransferase activity GO:0006561:proline biosynthesis GO:0006526:arginine biosynthesis GO:0006525:arginine metabolism GO:0004349:glutamate 5-kinase activity GO:0003991:acetylglutamate kinase activity GO:0009507:chloroplast
250403_at AT5G10920	1.38	8.19e-106	0.627	step: adenylosuccinate lyase GO:0004018:adenylosuccinate lyase activity GO:0009152:purine ribonucleotide biosynthesis GO:0004056:argininosuccinate lyase activity GO:0045239:tricarboxylic acid cycle enzyme complex GO:0008797:aspartate ammonia-lyase activity GO:0006526:arginine biosynthesis GO:0003824:catalytic activity GO:0006106:fumarate metabolism GO:0006531:aspartate metabolism GO:0004333:fumarate hydratase activity GO:0009507:chloroplast

262086_at : AT1G56050