Co-expression analysis

Gene ID At1g17650
Gene name GLYR2 (GLYOXYLATE REDUCTASE 2)
Module size 63 genes
NF 0.52
%ile 73.1



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
1.00100.01.00At1g17650838342GLYR2 (GLYOXYLATE REDUCTASE 2)Glyoxylate reductase located in chloroplasts.O.I.H.G.S.X.
0.7486.10.93At4g24750828577-F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PBOAO.I.H.G.S.X.
0.7184.20.93At3g48730824034GSA2 (glutamate-1-semialdehyde 2,1-aminomutase 2)F:glutamate-1-semialdehyde 2,1-aminomutase activity, pyridoxal phosphate binding, transaminase activity, catalytic activity;P:porphyrin biosynthetic process;C:chloroplast stroma, chloroplast, chloroplast envelope;BOFMAPVO.I.H.G.S.X.
0.7083.50.93At5g63310836451NDPK2 (NUCLEOSIDE DIPHOSPHATE KINASE 2)Maintains intracellular dNTP levels except ATP. Plays a role in response to oxidative stress and UV. Involved in phytochrome-mediated light signaling. Participates in auxin-regulated processes, partly through the modulation of auxin transport. H-bonding with His-197 inside the nucleotide-binding pocket is critical for NDPK2 functioning.O.I.H.G.S.X.
0.7083.50.92At4g38160829972pde191 (pigment defective 191)F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.6982.90.92At3g14110820628FLU (FLUORESCENT IN BLUE LIGHT)Encodes a novel coiled-coil, TPR domain containing protein that is localized to the chloroplast membrane and is involved in chlorophyll biosynthesis. Mutants accumulate protochlorophyllide, an intermediate in the chlorophyll biosynthesis pathway, in dark and release singlet oxygen in plastids in a controlled and non-invasive manner upon a dark/light shift.O.I.H.G.S.X.
0.6882.20.91At3g44890823623RPL9 (RIBOSOMAL PROTEIN L9)Plastid ribosomal protein CL9O.I.H.G.S.X.
0.6579.60.92At5g58250835937unknown proteinF:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast;OBPO.I.H.G.S.X.
0.6478.90.92At3g25660822154glutamyl-tRNA(Gln) amidotransferase, putativeF:glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity, carbon-nitrogen ligase activity, with glutamine as amido-N-donor;P:translation;C:chloroplast, chloroplast stroma;OBFMPAO.I.H.G.S.X.
0.6478.90.93At4g17560827471ribosomal protein L19 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, chloroplast stroma, chloroplast, membrane, chloroplast envelope;BOPMFO.I.H.G.S.X.
0.6378.10.92At2g37660818343binding / catalytic/ coenzyme bindingF:coenzyme binding, binding, catalytic activity;P:defense response to bacterium;C:thylakoid, apoplast, chloroplast stroma, chloroplast;BOPFAMO.I.H.G.S.X.
0.6378.10.92At2g47590819372PHR2 (photolyase/blue-light receptor 2)photolyase/blue light photoreceptor PHR2 (PHR2) mRNA,O.I.H.G.S.X.
0.6378.10.91At4g39040830059RNA bindingF:RNA binding;P:biological_process unknown;C:chloroplast;MOBFPVAO.I.H.G.S.X.
0.6277.30.92At2g25840817126OVA4 (ovule abortion 4)F:nucleotide binding, aminoacyl-tRNA ligase activity, tryptophan-tRNA ligase activity, ATP binding;P:N-terminal protein myristoylation, ovule development, tRNA aminoacylation for protein translation;C:mitochondrion, chloroplast;OBMFAPO.I.H.G.S.X.
0.6277.30.92At3g08740820021elongation factor P (EF-P) family proteinF:translation elongation factor activity;P:translational elongation;C:chloroplast, chloroplast stroma;BOPAO.I.H.G.S.X.
0.6075.70.91At3g18680821399aspartate/glutamate/uridylate kinase family proteinF:uridylate kinase activity, UMP kinase activity;P:amino acid biosynthetic process, 'de novo' pyrimidine base biosynthetic process, pyrimidine nucleotide biosynthetic process;C:chloroplast;BOAPFO.I.H.G.S.X.
0.6075.70.91At5g08280830724HEMC (HYDROXYMETHYLBILANE SYNTHASE)Encodes a protein with porphobilinogen deaminase activity. This protein is targeted to the chloroplast.O.I.H.G.S.X.
0.5974.70.92At1g02150839577pentatricopeptide (PPR) repeat-containing proteinF:binding;P:unknown;C:chloroplast;POFMBO.I.H.G.S.X.
0.5974.70.92At3g12930820478-F:unknown;P:biological_process unknown;C:chloroplast;BOPMO.I.H.G.S.X.
0.5773.80.91At2g24060816940translation initiation factor 3 (IF-3) family proteinF:translation initiation factor activity;P:translational initiation;C:chloroplast;OBMPFVAO.I.H.G.S.X.
0.5773.80.91At2g47940819406DEGP2Encodes DegP2 protease (DEGP2); nuclear gene for chloroplast product.O.I.H.G.S.X.
0.5773.80.91At3g52380824403CP33chloroplast RNA-binding proteinO.I.H.G.S.X.
0.5570.60.91At3g28460822476unknown proteinF:unknown;P:biological_process unknown;C:chloroplast;BOPAO.I.H.G.S.X.
0.5570.60.92At3g63490825524ribosomal protein L1 family proteinF:structural constituent of ribosome, RNA binding;P:translation, RNA processing;C:in 6 components;OBAFMPO.I.H.G.S.X.
0.5570.60.93At1g32990840194PRPL11 (PLASTID RIBOSOMAL PROTEIN L11)mutant has Decreased effective quantum yield of photosystem II; Pale green plants; Reduced growth rate; Plastid Ribosomal Protein L11O.I.H.G.S.X.
0.5570.60.92At5g22340832294unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;POO.I.H.G.S.X.
0.5469.50.91At3g63190825494RRF (RIBOSOME RECYCLING FACTOR, CHLOROPLAST PRECURSOR)F:molecular_function unknown;P:defense response to bacterium, translation;C:thylakoid, chloroplast stroma, chloroplast;BOMPFO.I.H.G.S.X.
0.5469.50.91At5g55220835615trigger factor type chaperone family proteinF:peptidyl-prolyl cis-trans isomerase activity;P:protein folding, protein transport;C:chloroplast, chloroplast stroma, chloroplast envelope;BOMPFVO.I.H.G.S.X.
0.5368.60.92At1g0108083946333 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein cp33, putativeF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:chloroplast stroma, nucleus, chloroplast, chloroplast envelope;MPOFBAO.I.H.G.S.X.
0.5267.40.91At4g01310827947ribosomal protein L5 family proteinF:structural constituent of ribosome;P:translation;C:in 6 components;BOPAFMO.I.H.G.S.X.
0.5267.40.92At5g47190834765ribosomal protein L19 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, chloroplast stroma, chloroplast, membrane, chloroplast envelope;BOPMFO.I.H.G.S.X.
0.5267.40.91At1g48350841255ribosomal protein L18 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, chloroplast, chloroplast envelope;BOPMO.I.H.G.S.X.
0.5166.30.92At5g51100835183FSD2 (FE SUPEROXIDE DISMUTASE 2)Fe superoxide dismutase whose mRNA levels are increased in response to exposure to UV-B.O.I.H.G.S.X.
0.5065.30.91At4g39460830101SAMC1 (S-ADENOSYLMETHIONINE CARRIER 1)Encodes a plastid metabolite transporter required for the import of S-Adenosylmethionine from the cytosol. Impaired function of SAMT1 led to decreased accumulation of prenyllipids and mainly affected the chlorophyll pathway.O.I.H.G.S.X.
0.4963.50.92At3g1312082050030S ribosomal protein S10, chloroplast, putativeF:structural constituent of ribosome, RNA binding;P:translation;C:small ribosomal subunit, chloroplast;BOMAPFO.I.H.G.S.X.
0.4963.50.91At3g25480822132rhodanese-like domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast thylakoid membrane, chloroplast;PO.I.H.G.S.X.
0.4963.50.91At1g11870837734SRS (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.
0.4963.50.91At3g52150824379RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast stroma, chloroplast, chloroplast envelope;MPOFBAO.I.H.G.S.X.
0.4862.50.91At5g11450831016oxygen-evolving complex-relatedF:calcium ion binding;P:photosynthesis;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;PBO.I.H.G.S.X.
0.4862.50.91At5g40160834014EMB506 (embryo defective 506)Encodes ankyrin repeat protein EMB506.O.I.H.G.S.X.
0.4862.50.91At1g07320837243RPL4encodes a plastid ribosomal protein L4O.I.H.G.S.X.
0.4761.20.91At1g60600842354ABC4 (ABERRANT CHLOROPLAST DEVELOPMENT 4)Encodes a protein similar to 1,4-dihydroxy-2-naphthoic acid phytyltransferase involved in phylloquinone and plastoquinone biosynthesis. Mutants are pale green and heterotrophic with defects in photosynthetic electron transport.O.I.H.G.S.X.
0.4659.80.92At1g78630844199emb1473 (embryo defective 1473)F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation;C:thylakoid, ribosome, chloroplast, chloroplast stroma;BOMFAPO.I.H.G.S.X.
0.4659.80.91At5g13510831195ribosomal protein L10 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic ribosome, ribosome, chloroplast, chloroplast stroma;BOAPMFO.I.H.G.S.X.
0.4558.30.91At5g14910831343heavy-metal-associated domain-containing proteinF:metal ion binding;P:metal ion transport;C:thylakoid, chloroplast thylakoid membrane, chloroplast stroma, chloroplast;PO.I.H.G.S.X.
0.4457.20.92At3g51140824278-F:unknown;P:biological_process unknown;C:chloroplast, chloroplast inner membrane, chloroplast envelope;BPOO.I.H.G.S.X.
0.4457.20.91At1g05190839273emb2394 (embryo defective 2394)F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation;C:chloroplast stroma, chloroplast, large ribosomal subunit, membrane, chloroplast envelope;BOAFPMO.I.H.G.S.X.
0.4457.20.91At3g15520820791peptidyl-prolyl cis-trans isomerase TLP38, chloroplast / thylakoid lumen PPIase of 38 kDa / cyclophilin / rotamaseF:peptidyl-prolyl cis-trans isomerase activity;P:unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;BOPAO.I.H.G.S.X.
0.4457.20.91At2g3345081791050S ribosomal protein L28, chloroplast (CL28)F:structural constituent of ribosome;P:translation;C:ribosome, chloroplast, membrane;BOPFO.I.H.G.S.X.
0.4457.20.91At1g29070839781ribosomal protein L34 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, intracellular, chloroplast;BPOFO.I.H.G.S.X.
0.4355.30.92At1g32200840112ATS1Encodes a chloroplast glycerol-3-phosphate acyltransferase.Involved in the biosynthesis of chloroplast phosphatidylglycerol.O.I.H.G.S.X.
0.4355.30.91At1g64510842759ribosomal protein S6 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:thylakoid, chloroplast thylakoid membrane, ribosome, chloroplast;BOPO.I.H.G.S.X.
0.4355.30.92At5g42765834286-F:unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast;PO.I.H.G.S.X.
0.4253.90.92At1g11750837719CLPP6One of several nuclear-encoded ClpPs (caseinolytic protease). Contains a highly conserved catalytic triad of Ser-type proteases (Ser-His-Asp). The name reflects nomenclature described in Adam et. al (2001).O.I.H.G.S.X.
0.4253.90.92At5g1432083128230S ribosomal protein S13, chloroplast (CS13)F:structural constituent of ribosome, RNA binding, nucleic acid binding;P:translation;C:small ribosomal subunit, chloroplast, chloroplast envelope;BOPMFAO.I.H.G.S.X.
0.4253.90.91At4g24770828579RBP31 (31-KDA RNA BINDING PROTEIN)Encodes a chloroplast RNA-binding protein. A substrate of the type III effector HopU1 (mono-ADP-ribosyltransferase).O.I.H.G.S.X.
0.4253.90.91At5g63570836476GSA1 (GLUTAMATE-1-SEMIALDEHYDE-2,1-AMINOMUTASE)Encodes a protein with homology to glutamate-1-semialdehyde 2,1-aminomutase catalyzing the conversion of glutamate-1-semialdehyde (GSA) into 5-amino levulinate. The expression of this gene was demonstrated to be light-induced.O.I.H.G.S.X.
0.4152.40.91At1g48520841273GATB (GLU-ADT SUBUNIT B)Encodes Glu-tRNA(Gln) amidotransferase subunit B (from Genbank record AF239836).O.I.H.G.S.X.
0.4152.40.91At4g36390829791radical SAM domain-containing protein / TRAM domain-containing proteinF:iron-sulfur cluster binding, catalytic activity;P:biological_process unknown;C:chloroplast;OBMAPO.I.H.G.S.X.
0.3948.40.91At1g3568084047250S ribosomal protein L21, chloroplast / CL21 (RPL21)F:structural constituent of ribosome, RNA binding;P:response to cold, translation;C:ribosome, chloroplast stroma, nucleus, chloroplast, chloroplast envelope;BOPMFO.I.H.G.S.X.
0.3846.70.91At1g08640837386unknown proteinF:unknown;P:unknown;C:chloroplast, chloroplast envelope;PBOO.I.H.G.S.X.
0.3846.70.91At5g52520835328OVA6 (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.
0.3745.00.91At3g58140824983phenylalanyl-tRNA synthetase class IIc family proteinF:in 6 functions;P:tRNA processing, phenylalanyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:mitochondrion, chloroplast, membrane;BOMFAPO.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
56.699.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
54.899.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
47.499.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.999.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
46.799.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
42.799.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
42.199.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.699.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.299.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.999.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.699.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.199.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.399.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.699.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.799.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.399.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.899.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.499.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.299.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.399.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.199.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.199.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.499.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.599.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.099.6GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.399.6GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
20.799.6E-MEXP-807-raw-cel-1173273252
16.999.5E-MEXP-807-raw-cel-1173273144
16.399.5GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
15.899.5GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
15.099.4GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.399.4GSM266667Arabidopsis, root cells, columella root cap, -Fe, replicate 2GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
13.399.4GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
12.299.3GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
12.199.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
9.999.1E-MEXP-1443-raw-cel-1581869745
8.699.0GSM266668Arabidopsis, root cells, columella root cap, -Fe, replicate 3GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0948GO:0042254The process of the formation of the constituents of the ribosome subunits, their assembly, and their transport to the sites of protein synthesis.Link to AmiGO
0.0763GO:0006779The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.Link to AmiGO
0.0663GO: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

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.091500970Aminoacyl-tRNA biosynthesisLink to KEGG PATHWAY
0.067300860Porphyrin and chlorophyll metabolismLink to KEGG PATHWAY
0.047703010RibosomeLink 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



Back to the CoP portal site

Back to the KAGIANA project homepage