Co-expression analysis

Gene ID At5g67360
Gene name ARA12
Module size 5 genes
NF 0.02
%ile 0.9



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
1.00100.01.00At5g67360836871ARA12Encodes a subtilisin-like serine protease essential for mucilage release from seed coats.O.I.H.G.S.X.
0.124.90.85At3g02050821063KUP3 (K+ UPTAKE TRANSPORTER 3)potassium transporter KUP3p (KUP3)O.I.H.G.S.X.
0.030.60.84At4g38130829969HD1 (HISTONE DEACETYLASE 1)Encodes a histone deacetylase that enhances AtERF7-mediated transcriptional repression. Binds SIM3 and ERF7. Expressed in the nucleus in most tissues examined and throughout the life of the plant. Involved in jasmonic acid and ethylene dependent pathogen resistance. The sequence in GenBank has 17 AG dinucleotide repeats missing, which is also missing in Ler shotgun sequence from Cereon. Although it is annotated to be in Columbia, the GB sequence is probably not of Columbia origin. Plays a role in embryogenesis as mutants grown at higher temperatures display abnormalities in the organization of the root and shoot. Plant lines expressing an RNAi construct targeted against HDA19 shows some resistance to agrobacterium-mediated root transformation.O.I.H.G.S.X.
0.010.20.85At3g14860820715NHL repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BOPAMO.I.H.G.S.X.
0.010.20.85At1g09620837489ATP binding / aminoacyl-tRNA ligase/ leucine-tRNA ligase/ nucleotide bindingF:nucleotide binding, aminoacyl-tRNA ligase activity, leucine-tRNA ligase activity, ATP binding;P:leucyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:chloroplast;BOMAFPO.I.H.G.S.X.

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Link to AtGenExpress Visualization Tool



Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
86.499.9GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
82.199.9GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
49.799.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.199.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
40.099.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.999.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.299.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.799.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.999.7GSM133755Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
36.099.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.799.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.099.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.499.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.999.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.399.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.299.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.899.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.199.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.999.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.799.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.399.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.299.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.299.7GSM311279Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
23.199.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
22.999.6GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
19.399.6GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
19.299.6GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
19.099.5GSM311292Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
18.399.5GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.499.5GSM131699ATGE_81_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
16.199.5GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.199.5GSM133760Lindsey_1-12_heart-stage-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
15.699.5GSM131695ATGE_79_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
14.299.4GSM10453WT Mature Green Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
14.299.4GSM131694ATGE_79_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
12.799.3GSM133756Lindsey_1-10_heart-stage-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.399.3GSM131696ATGE_79_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
11.599.3GSM311291Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
11.599.3GSM131698ATGE_81_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
11.399.3GSM133769Lindsey_1-21_torpedo-basal_Rep6_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.999.1GSM131697ATGE_81_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.799.1GSM10451WT Mature Green Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
9.599.1GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.099.1GSM176879AWP_Control_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
8.799.0GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.3331GO:0006429The process of coupling leucine to leucyl-tRNA, catalyzed by leucyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.Link to AmiGO
0.3331GO:0048359The chemical reactions and pathways involving mucilage that occur during seed coat development; mucilage is normally synthesized during seed coat development.Link to AmiGO
0.3331GO:0080001The process by which seed mucilage expands through hydration and breaks the outer cell wall that encapsulates the whole seed upon imbibition. Mucilage, mainly composed of pectins, is formed during seed development and deposited into the apoplast underneath the outer wall of the seed coat.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.056100290Valine, leucine and isoleucine biosynthesisLink to KEGG PATHWAY
0.038100970Aminoacyl-tRNA biosynthesisLink 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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