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-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

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
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

263882_at : AT2G21790
GO:0005971:ribonucleoside-diphosphate reductase complex
GO:0004748:ribonucleoside-diphosphate reductase activity
GO:0006260:DNA replication

probe set,gene	slope	pvalue	rsquared	annotations
254134_at AT4G24830	0.551	6.1e-132	0.709	step: argininosuccinate synthase GO:0004055:argininosuccinate synthase activity GO:0006526:arginine biosynthesis GO:0005524:ATP binding GO:0009507:chloroplast
250403_at AT5G10920	0.549	9.93e-143	0.738	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

251830_at : AT3G55010
GO:0005737:cytoplasm
GO:0009113:purine base biosynthesis
GO:0009228:thiamin biosynthesis
GO:0009030:thiamin phosphate kinase activity
GO:0004641:phosphoribosylformylglycinamidine cyclo-ligase activity
GO:0004860:protein kinase inhibitor activity
GO:0003824:catalytic activity
GO:0005576:extracellular region
GO:0006189:'de novo' IMP biosynthesis
GO:0009405:pathogenesis
GO:0009507:chloroplast

probe set,gene	slope	pvalue	rsquared	annotations
254134_at AT4G24830	0.788	5.49e-148	0.75	step: argininosuccinate synthase GO:0004055:argininosuccinate synthase activity GO:0006526:arginine biosynthesis GO:0005524:ATP binding GO:0009507:chloroplast
250403_at AT5G10920	0.743	2.37e-128	0.699	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

262880_at : AT1G64880
GO:0015935:small ribosomal subunit
GO:0016020:membrane
GO:0005622:intracellular
GO:0003735:structural constituent of ribosome
GO:0006412:protein biosynthesis
GO:0005840:ribosome

probe set,gene	slope	pvalue	rsquared	annotations
254134_at AT4G24830	0.702	4.22e-127	0.696	step: argininosuccinate synthase GO:0004055:argininosuccinate synthase activity GO:0006526:arginine biosynthesis GO:0005524:ATP binding GO:0009507:chloroplast
250403_at AT5G10920	0.683	2.27e-125	0.691	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

252442_at : AT3G46940
GO:0046080:dUTP metabolism
GO:0016787:hydrolase activity
GO:0004170:dUTP diphosphatase activity
GO:0008372:cellular component unknown
GO:0009394:2'-deoxyribonucleotide metabolism

probe set,gene	slope	pvalue	rsquared	annotations
254134_at AT4G24830	0.538	6.77e-125	0.689	step: argininosuccinate synthase GO:0004055:argininosuccinate synthase activity GO:0006526:arginine biosynthesis GO:0005524:ATP binding GO:0009507:chloroplast
250403_at AT5G10920	0.528	8.4e-127	0.695	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

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
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

247606_at : AT5G61000
GO:0005634:nucleus
GO:0006260:DNA replication
GO:0003676:nucleic acid binding
GO:0003677:DNA binding

probe set,gene	slope	pvalue	rsquared	annotations
254134_at AT4G24830	0.781	4.39e-128	0.698	step: argininosuccinate synthase GO:0004055:argininosuccinate synthase activity GO:0006526:arginine biosynthesis GO:0005524:ATP binding GO:0009507:chloroplast
250403_at AT5G10920	0.751	5.55e-121	0.677	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