Co-expression analysis

Gene ID At5g23570
Module size 26 genes
NF 0.54
%ile 75.8

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
0.5570.61.00At5g23570832422SGS3 (SUPPRESSOR OF GENE SILENCING 3)Required for posttranscriptional gene silencing and natural virus resistance.SGS3 is a member of an 'unknown' protein family. Members of this family have predicted coiled coiled domains suggesting oligomerization and a potential zinc finger domain. Involved in the production of trans-acting siRNAs, through direct or indirect stabilization of cleavage fragments of the primary ta-siRNA transcript. Acts before RDR6 in this pathway.O.I.H.G.S.X.
0.7385.50.79At5g16950831558unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7184.20.81At2g40650818660pre-mRNA splicing factor PRP38 family proteinF:binding;P:RNA processing;C:cellular_component unknown;MBOFPVAO.I.H.G.S.X.
0.6982.90.79At3g50690824233leucine-rich repeat family proteinF:protein binding;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.6680.10.77At1g74250843765DNAJ heat shock N-terminal domain-containing proteinF:heat shock protein binding, zinc ion binding, nucleic acid binding;P:protein folding;C:intracellular;MOBFPVAO.I.H.G.S.X.
0.6680.10.81At3g02760820930ATP binding / aminoacyl-tRNA ligase/ histidine-tRNA ligase/ nucleotide bindingF:histidine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:histidyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:chloroplast, cytoplasm;OBMFAPO.I.H.G.S.X.
0.6478.90.79At1g53720841810CYP59 (CYCLOPHILIN 59)Encodes a cyclophilin, member of a family modular proteins consisting of a peptidyl-prolyl cis– trans isomerase (PPIase) domain, followed by an RNA recognition motif (RRM), and a C-terminal domain enriched in charged amino acids. Interacts with with SCL33/SR33 and with a majority of Arabidopsis SR proteins and the largest subunit of RNA polymerase II. Localizes to the nucleus, but it does not significantly colocalize with SR proteins in nuclear speckles.O.I.H.G.S.X.
0.6176.70.76At3g07780819969OBE1 (OBERON1)Encodes a nuclear PHD finger protein that is functionally redundant with OBE2 and plays an important role in the maintenance and/or establishment of the root and shoot apical meristems.O.I.H.G.S.X.
0.6176.70.82At5g23890832454-F:unknown;P:unknown;C:mitochondrion, chloroplast thylakoid membrane, chloroplast, plastid, chloroplast envelope;MOBFPAVO.I.H.G.S.X.
0.6075.70.81At4g29940829117PRHA (PATHOGENESIS RELATED HOMEODOMAIN PROTEIN A)Homeodomain protein (PRHA). Expression of the gene differs in various vegetative and floral plant tissues and is positively influenced by the phytohormone auxin. It is often associated with regions of developing vascular tissue. The prha promoter is highly responsive to the synthetic auxin, naphthalene acetic acid, in transient assays using tobacco protoplasts. The PRHA protein has the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding.O.I.H.G.S.X.
0.5873.80.83At3g24490822039transcription factorF:transcription factor activity;P:regulation of transcription;C:cellular_component unknown;MOPFBVO.I.H.G.S.X.
0.5773.80.80At1g15200838086protein-protein interaction regulator family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.5469.50.76At5g19900832112PRLI-interacting factor, putativeF:molecular_function unknown;P:biological_process unknown;C:chloroplast;OMFPBVAO.I.H.G.S.X.
0.5469.50.76At1g28420839740HB-1 (homeobox-1)F:transcription factor activity;P:regulation of transcription, DNA-dependent, regulation of transcription;C:nucleus;MOFBPVAO.I.H.G.S.X.
0.5469.50.76At5g61310836252cytochrome c oxidase subunit Vc, putative / COX5C, putativeF:cytochrome-c oxidase activity;P:unknown;C:mitochondrial respiratory chain, endomembrane system;PO.I.H.G.S.X.
0.5267.40.85At1g18950838476aminoacyl-tRNA synthetase familyF:aminoacyl-tRNA ligase activity;P:biological_process unknown;C:unknown;MOFBPVAO.I.H.G.S.X.
0.5166.30.76At1g65440842855GTB1Related to yeast Spt6 protein, which functions as part of a protein complex in transcription initiation and also plays a role in chromatin structure / assembly.O.I.H.G.S.X.
0.4963.50.83At2g06210815177ELF8 (EARLY FLOWERING 8)Encodes a yeast CTR9 homolog that is involved in the control of flowering time by elevating FLC expression to a level that creates the vernalization-responsive, winter-annual habit. Yeast CTR9 is a component of a five-member PAF1 complex that associates with RNA pol II and is thought to regulate gene expression by recruiting SET1 (a histone 3 Lys 4 [H3-K4] methyl transferase) to the initially transcribed [5'] regions of target chromatin. Mutants display reduced H3-K4 methylation in both FLC and FLM chromatin.O.I.H.G.S.X.
0.4963.50.77At2g39260818511RNA binding / binding / protein bindingF:protein binding, RNA binding, binding;P:translation, RNA metabolic process;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.4761.20.80At1g03830839398guanylate-binding family proteinF:GTP binding, GTPase activity;P:immune response;C:cellular_component unknown;MOBFPAVO.I.H.G.S.X.
0.4761.20.75At3g51270824290ATP binding / catalytic/ protein serine/threonine kinaseF:protein serine/threonine kinase activity, catalytic activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.4761.20.75At3g18100821335MYB4R1 (myb domain protein 4R1)Member of the R2R3 transcription factor gene family.O.I.H.G.S.X.
0.4659.80.86At1g68790843210LINC3 (LITTLE NUCLEI3)F:unknown;P:biological_process unknown;C:nucleolus;MOBFPAVO.I.H.G.S.X.
0.4152.40.81At3g29310822589calmodulin-binding protein-relatedF:molecular_function unknown;P:biological_process unknown;C:plasma membrane;MOFPBVO.I.H.G.S.X.
0.4050.80.74At5g05210830403nucleolar matrix protein-relatedF:unknown;P:unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.3846.70.76At5g55670835661RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MBOFPVAO.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
41.799.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.299.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.799.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.699.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.799.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.399.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.999.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.899.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.699.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.499.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.099.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.699.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.499.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.899.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.599.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.299.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.399.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.399.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
21.799.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.899.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.299.6GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
19.099.5GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
17.099.5GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.799.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.499.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.199.4GSM311289Laser 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
12.699.3GSM311290Laser 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

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0691GO:0006427The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-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
0.0691GO:0010071The specification of a meristem which will give rise to a primary or lateral root.Link to AmiGO
0.0671GO:0006955Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.027100970Aminoacyl-tRNA biosynthesisLink to KEGG PATHWAY

Inter-species module comparison

Select a plant to compare co-expressed genes between species.

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