Co-expression analysis

Gene ID At3g49680
Gene name BCAT3 (BRANCHED-CHAIN AMINOTRANSFERASE 3)
Module size 24 genes
NF 0.43
%ile 61.3



Co-expression network

pink confeito: Transcription factor, green bicone: Binding protein, red cone: Enzyme protein, blue sphere: Other protein
large node: VF over 0.50, middle node: over 0.25, small node: below 0.25



Co-expressed genes

Click gene/probe ID to show a list of genes that are co-expressed with the gene.

VF %ile CC Gene ID Repr. ID Gene name Func. O.I. H.G. S.X. Other DB
0.6680.11.00At3g49680824130BCAT3 (BRANCHED-CHAIN AMINOTRANSFERASE 3)Encodes a chloroplast branched-chain amino acid aminotransferase. Complements the yeast leu/iso-leu/val auxotrophy mutant.O.I.H.G.S.X.
0.6781.60.93At2g19940816513N-acetyl-gamma-glutamyl-phosphate reductase/ NAD or NADH binding / binding / catalytic/ oxidoreductase, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / protein dimerizationF:in 6 functions;P:amino acid metabolic process, response to cadmium ion;C:nucleolus, chloroplast stroma, chloroplast, membrane;BOAFPO.I.H.G.S.X.
0.5873.80.92At5g04710830349aspartyl aminopeptidase, putativeF:aminopeptidase activity, zinc ion binding;P:proteolysis;C:chloroplast, vacuole;BOFMPAO.I.H.G.S.X.
0.5873.80.93At3g57560824923aspartate/glutamate/uridylate kinase family proteinencodes a N-acetylglutamate kinase, involved in arginine biosynthesisO.I.H.G.S.X.
0.5673.00.93At3g20320821576TGD2 (TRIGALACTOSYLDIACYLGLYCEROL2)Encodes a permease-like component of an ABC transporter involved in lipid transfer from ER to chloroplast. A phosphatidic acid-binding protein with a predicted mycobacterial cell entry domain. It is tethered to the inner chloroplast envelope membrane facing the outer envelope membrane. Presumed bacterial orthologs of TGD1 and TGD2 in Gram-negative bacteria are typically organized in transcriptional units, suggesting their involvement in a common biological process.O.I.H.G.S.X.
0.5673.00.93At4g33680829510AGD2 (ABERRANT GROWTH AND DEATH 2)Involved in disease resistance against Pseudomonas syringae. mutants have elevated SA levels, a low level of spontaneous cell death, callose deposition, and enlarged cells in leaves. genetically maps on chr 4 between L23H3 and nga1139.O.I.H.G.S.X.
0.5570.60.92At1g80600844399WIN1 (HOPW1-1-INTERACTING 1)Encodes HopW1-1-Interacting protein 1 (WIN1). Interacts with the P. syringae effector HopW1-1. WIN1 is a putative acetylornithine transaminase. Modulates plant defenses against bacteria. Three WIN proteins are identified so far (WIN1: AT1G80600; WIN2: AT4G31750; WIN3: AT5G13320).O.I.H.G.S.X.
0.5570.60.92At3g13490820551OVA5 (OVULE ABORTION 5)Encodes a dual targeted lysyl-tRNA ligase that is found both in the mitochondrion and the chloroplast. Plants mutated in this gene exhibit an ovule abortion phenotype.O.I.H.G.S.X.
0.5368.60.93At1g19800838568TGD1 (TRIGALACTOSYLDIACYLGLYCEROL 1)Encodes a permease-Like protein involved in lipid transfer from the ER to the chloroplast, more specifically, transfer of phosphatidate across the chloroplast inner membrane. Mutant leaves accumulate trigalactosyldiacylglycerol, triacylglycerol and phosphatidate. Chloroplast lipids are altered in their fatty acid composition and as a consequence the development of chloroplasts in the mutants are impacted. The mutant seeds has a higher abortion rate.O.I.H.G.S.X.
0.5267.40.92At3g51140824278-F:unknown;P:biological_process unknown;C:chloroplast, chloroplast inner membrane, chloroplast envelope;BPOO.I.H.G.S.X.
0.5166.30.92At4g33350829471chloroplast inner membrane import protein Tic22, putativeF:unknown;P:unknown;C:mitochondrion, chloroplast, plastid, chloroplast inner membrane, chloroplast envelope;BPOO.I.H.G.S.X.
0.4862.50.93At3g49560824118mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23 family proteinF:protein transporter activity, P-P-bond-hydrolysis-driven protein transmembrane transporter activity;P:protein transport;C:in 6 components;PMOO.I.H.G.S.X.
0.4761.20.92At5g63890836509ATHDH (HISTIDINOL DEHYDROGENASE)Encodes histidinol dehydrogenase. Up-regulated in response to UV-B.O.I.H.G.S.X.
0.4558.30.92At2g42070818807ATNUDX23 (ARABIDOPSIS THALIANA NUDIX HYDROLASE HOMOLOG 23)F:hydrolase activity, FAD diphosphatase activity;P:unknown;C:chloroplast;BOMAPFO.I.H.G.S.X.
0.3948.40.92At5g19370832057rhodanese-like domain-containing protein / PPIC-type PPIASE domain-containing proteinF:isomerase activity;P:biological_process unknown;C:chloroplast;BOMFPAO.I.H.G.S.X.
0.3948.40.92At1g11870837734SRS (SERYL-TRNA SYNTHETASE)Seryl-tRNA synthetase targeted to chloroplasts and mitochondria. Its inactivation causes developmental arrest of chloroplasts and mitochondria in Nicotiana benthamiana.O.I.H.G.S.X.
0.3846.70.92At1g08640837386unknown proteinF:unknown;P:unknown;C:chloroplast, chloroplast envelope;PBOO.I.H.G.S.X.
0.3643.60.93At4g20960827843cytidine/deoxycytidylate deaminase family proteinencodes diaminohydroxyphosphoribosylaminopyrimidine deaminase catalyzing the second step in the riboflavin biosynthesisO.I.H.G.S.X.
0.3643.60.92At5g20720832195CPN20 (CHAPERONIN 20)Encodes a chloroplast co-chaperonin with similarity to CPN21 from spinach, E.coli GroES.O.I.H.G.S.X.
0.3541.60.94At5g13120831151peptidyl-prolyl cis-trans isomerase cyclophilin-type family proteinF:peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;OBMFPAVO.I.H.G.S.X.
0.3439.80.92At3g02660821282emb2768 (EMBRYO DEFECTIVE 2768)F:RNA binding, tyrosine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:embryonic development ending in seed dormancy, tRNA aminoacylation for protein translation;C:mitochondrion, chloroplast;OBFMPAO.I.H.G.S.X.
0.2930.30.93At3g10670820236ATNAP7Plastidic SufC-like ATP-binding cassette/ATPase essential for Arabidopsis embryogenesis. Involved in the biogenesis and/or repair of oxidatively damaged FeS clusters. Expressed in embryos and meristems.O.I.H.G.S.X.
0.2930.30.91At5g52520835328OVA6 (OVULE ABORTION 6)F:proline-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:regulation of photosynthesis, seed development, embryo sac development, ovule development, tRNA aminoacylation for protein translation;C:mitochondrion, chloroplast, chloroplast stroma;BOAMFPO.I.H.G.S.X.
0.2522.60.92At4g32915829428-F:molecular_function unknown;P:regulation of translational fidelity;C:chloroplast;BOAPO.I.H.G.S.X.

Click More genes

Link to AtGenExpress Visualization Tool



Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
82.799.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
66.199.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
65.399.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
61.899.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
61.199.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
60.799.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
56.899.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
56.399.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
55.299.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
54.599.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
53.399.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
53.299.8GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
52.499.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.899.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
50.999.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.999.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.199.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.199.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.999.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.299.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.199.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
30.899.7GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
30.699.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
26.099.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.899.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
19.799.6GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
18.799.5GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
15.599.5E-MEXP-546-raw-cel-863289424
15.199.4E-MEXP-546-raw-cel-863289532
14.099.4E-MEXP-509-raw-cel-829148703
13.799.4GSM311294Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
13.699.4GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
11.099.2GSM133029BC482-1GSE5684AtGenExpress: Pathogen Series: Response to Botrytis cinerea infectionLink to GEO
10.199.2GSM133030BC482-2GSE5684AtGenExpress: Pathogen Series: Response to Botrytis cinerea infectionLink to GEO
9.199.1GSM311293Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
8.799.0GSM133304RIKEN-NAKABAYASHI1BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
8.799.0GSM176879AWP_Control_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1153GO:0048481The process whose specific outcome is the progression of the ovule over time, from its formation to the mature structure. The ovule is the structure in seed plants enclosing the female gametophyte, and is composed of the nucellus, one or two integuments, and the funiculus; it develops into the seed.Link to AmiGO
0.0913GO:0006418The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.Link to AmiGO
0.0801GO:0006450Any process that modulates the ability of the translational apparatus to interpret the genetic code.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.113400970Aminoacyl-tRNA biosynthesisLink to KEGG PATHWAY
0.081300330Arginine and proline metabolismLink to KEGG PATHWAY
0.063100740Riboflavin metabolismLink to KEGG PATHWAY

Inter-species module comparison

Select a plant to compare co-expressed genes between species.
Glycine_max
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays



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