Co-expression analysis

Gene ID At4g34350
Gene name HDR (4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE)
Module size 5 genes
NF 0.41
%ile 56.5



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
0.4253.91.00At4g34350829585HDR (4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE)Arabidopsis ISPH is involved in the plastid nonmevalonate pathway of isoprenoid biosynthesis. It was shown to complement the lethal phenotype of E. coli ispH mutant and is therefore most likely encodes a protein with 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity involved in the last step of mevalonate-independent isopentenyl biosynthesis. Mutant has Albino seedling.O.I.H.G.S.X.
0.6781.60.92At5g64840836607ATGCN5 (A. THALIANA GENERAL CONTROL NON-REPRESSIBLE 5)member of GCN subfamilyO.I.H.G.S.X.
0.4761.20.92At5g58870836004ftsh9 (FtsH protease 9)encodes an FtsH protease that is localized to the chloroplastO.I.H.G.S.X.
0.3846.70.92At1g16720838243HCF173 (high chlorophyll fluorescence phenotype 173)Encodes HCF173, a protein with weak similarities to the superfamily of the short-chain dehydrogenases/reductases. HCF173 is involved in the initiation of translation of the psbA mRNA. Mutants shows a high chlorophyll fluorescence phenotype (hcf) and are severely affected in the accumulation of PSII subunits. The protein HCF173 is localized in the chloroplast, where it is mainly associated with the membrane system and is part of a higher molecular weight complex with psbA mRNA as a component of this complex.O.I.H.G.S.X.
0.2217.50.92At1g79600844298ABC1 family proteinF:protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:chloroplast, plastoglobule;OBMPFAVO.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
116.799.9GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
75.699.9GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
75.299.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
61.599.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
60.299.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
58.199.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
56.299.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
54.399.8GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
51.499.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.799.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.199.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
46.699.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
42.599.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.499.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.999.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
38.099.8GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
36.899.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.699.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.499.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.099.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.499.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.699.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.199.7E-MEXP-509-raw-cel-829148561
28.399.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.299.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.799.7GSM10448WT Cotyledon Stage Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
27.299.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
24.999.6GSM311278Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
24.899.6GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
23.599.6GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
21.699.6GSM311289Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
21.699.6GSM10449WT Cotyledon Stage Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
20.599.6E-MEXP-509-raw-cel-829148456
20.299.6GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.199.6GSM311277Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
19.199.6GSM131695ATGE_79_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
17.199.5GSM131696ATGE_79_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
17.099.5GSM131693ATGE_78_FGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
16.899.5E-MEXP-509-raw-cel-829148525
16.699.5E-MEXP-509-raw-cel-829148492
15.999.5GSM131694ATGE_79_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
15.799.5GSM131691ATGE_78_DGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
15.799.5GSM133304RIKEN-NAKABAYASHI1BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
15.099.4GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.999.4GSM131692ATGE_78_EGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
14.899.4GSM131689ATGE_77_EGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
14.399.4E-MEXP-509-raw-cel-829148597
14.099.4GSM131690ATGE_77_FGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
13.999.4E-ATMX-1-raw-cel-1112746154
13.499.4E-MEXP-509-raw-cel-829148240
13.399.4GSM133303RIKEN-NAKABAYASHI1AGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
13.199.4E-MEXP-509-raw-cel-829148090
12.399.3E-MEXP-1451-raw-cel-1585200330
12.299.3GSM311290Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
12.199.3E-MEXP-509-raw-cel-829148348
11.599.3E-MEXP-1451-raw-cel-1585200298
11.199.2GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
11.099.2E-MEXP-509-raw-cel-829148129
10.299.2GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
9.899.1GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.799.1E-MEXP-509-raw-cel-829148420
9.699.1GSM10479lec1-1 Cotyledon Stage Seed 1GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
9.199.1GSM131688ATGE_77_DGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.099.1GSM131697ATGE_81_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
8.999.0E-MEXP-509-raw-cel-829148165
8.999.0E-MEXP-509-raw-cel-829148877
8.899.0GSM131698ATGE_81_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
8.699.0E-MEXP-509-raw-cel-829148385

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.2501GO:0046677A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.Link to AmiGO
0.1671GO:0019288The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.Link to AmiGO
0.0631GO:0030163The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.043100900Terpenoid backbone biosynthesisLink to KEGG PATHWAY
0.013101066Biosynthesis of alkaloids derived from terpenoid and polyketideLink to KEGG PATHWAY
0.010101062Biosynthesis of terpenoids and steroidsLink 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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