Co-expression analysis

Gene ID At3g42670
Module size 14 genes
NF 0.18
%ile 15.3

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
1.00100.01.00At3g42670823287CHR38 (CHROMATIN REMODELING 38)Encodes a nuclear localized SNF domain containing protein involved in RNA silencing. Mutants were identified in a screen for defects in the spread of RNA silencing. CLSY1 may affect production of dsRNA from the locus to be silenced.O.I.H.G.S.X.
0.2217.50.81At5g12080831081MSL10 (MECHANOSENSITIVE CHANNEL OF SMALL CONDUCTANCE-LIKE 10)F:mechanically-gated ion channel activity;P:detection of mechanical stimulus;C:plasma membrane, membrane;BOFAPO.I.H.G.S.X.
0.2115.80.81At4g00990827933transcription factor jumonji (jmjC) domain-containing proteinF:protein binding, transcription factor activity, zinc ion binding;P:unknown;C:unknown;MPOFBO.I.H.G.S.X.
0.1912.70.80At1g27680839660APL2 (ADPGLC-PPASE LARGE SUBUNIT)ADP-glucose pyrophosphorylase catalyzes the first, rate limiting step in starch biosynthesis. The large subunit plays a regulatory role whereas the small subunit (ApS) is the catalytic isoform. Four isoforms of the large subunit (ApL1-4) have been described.Mutational analysis of APS1 suggests that APL1 and APL2 can compensate for loss of APS1 catalytic activity,suggesting both have catalytic as well as regulatory functions.O.I.H.G.S.X.
0.1811.40.80At1g10180837556unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMO.I.H.G.S.X.
0.1710.20.81At3g22780821849TSO1 (CHINESE FOR 'UGLY')putative DNA binding protein (tso1) mRNA, tso1-3 allele,O.I.H.G.S.X.
0.1710.20.81At5g37890833768seven in absentia (SINA) protein, putativeF:ubiquitin-protein ligase activity, protein binding, zinc ion binding;P:multicellular organismal development, protein ubiquitination, ubiquitin-dependent protein catabolic process;C:nucleus, intracellular;MPOFO.I.H.G.S.X. cis-trans isomerase cyclophilin-type family proteinF:peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:unknown;MOBFPVAO.I.H.G.S.X., putative / tRNA adenylyltransferase, putativeF:tRNA adenylyltransferase activity, RNA binding, nucleotidyltransferase activity;P:tRNA processing, RNA processing;C:mitochondrion;BOFMPVAO.I.H.G.S.X. (SU(VAR)3-9 HOMOLOG 3)Encodes a SU(VAR)3-9 homolog, a SET domain protein. Known SET domain proteins are involved in epigenetic control of gene expression and act as histone methyltransferases. There are 10 SUVH genes in Arabidopsis and members of this subfamily of the SET proteins have an additional conserved SRA domain.O.I.H.G.S.X. (RNA-DEPENDENT RNA POLYMERASE 2)Encodes RNA-dependent RNA polymerase that is required for endogenous siRNA (but not miRNA) formation. Nomenclature according to Xie, et al. (2004).O.I.H.G.S.X. (MUTS HOMOLOG 2)Encodes a DNA mismatch repair homolog of human MutS gene, MSH6. MSH2 is involved in maintaining genome stability and repressing recombination of mismatched heteroduplexes.There are four MutS genes in Arabidopsis, MSH2, MSH3, MSH6, and MSH7, which all act as heterodimers and bind to 51-mer duplexes. MSH2 has different binding specificity to different mismatches in combination with MSH3, MSH6, or MSH7.O.I.H.G.S.X. (MRNA ADENOSINE METHYLASE)F:S-adenosylmethionine-dependent methyltransferase activity, methyltransferase activity;P:embryonic development ending in seed dormancy, mRNA methylation;C:nuclear speck, chloroplast;MOBPFAVO.I.H.G.S.X. proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOO.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
93.899.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
61.399.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
55.899.8GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
48.199.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.799.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.299.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.799.8GSM311291Laser 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
42.699.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.899.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.799.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.699.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.599.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.099.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.199.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.799.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.499.7GSM131453AtGen_6-9321_Heatstress-Roots-3.0h_Rep1GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
33.199.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.699.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.999.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.399.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.899.7GSM131454AtGen_6-9322_Heatstress-Roots-3.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
30.299.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.499.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.699.6GSM290758root - 01% oxygen - 48h - AGSE11558transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plantsLink to GEO
23.499.6GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.999.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.999.5GSM131452AtGen_6-9312_Heatstress-Shoots-3.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
16.299.5GSM131451AtGen_6-9311_Heatstress-Shoots-3.0h_Rep1GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
15.199.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.399.4GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.799.2GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.299.2GSM13783Dexamethasone plus cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
10.199.2GSM131448AtGen_6-9212_Heatstress-Shoots-1.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
10.199.2GSM13780CycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
10.099.2GSM131449AtGen_6-9221_Heatstress-Roots-1.0h_Rep1GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
9.299.1GSM13784Cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
8.999.0GSM13779Dexamethasone plus cycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
8.999.0GSM133760Lindsey_1-12_heart-stage-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1331GO:0045128Any process that decreases the frequency, rate or extent of recombination during meiosis. Reciprocal meiotic recombination is the cell cycle process whereby double strand breaks are formed and repaired through a double Holliday junction intermediate.Link to AmiGO
0.1331GO:0080009The posttranscriptional addition of methyl groups to specific residues in an mRNA molecule.Link to AmiGO
0.1251GO:0050982The series of events by which a mechanical stimulus is received by a cell and converted into a molecular signal.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.050103430Mismatch repairLink to KEGG PATHWAY
0.023100520Amino sugar and nucleotide sugar metabolismLink to KEGG PATHWAY
0.020100500Starch and sucrose metabolismLink to KEGG PATHWAY

Inter-species module comparison

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

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