Co-expression analysis

Gene ID At5g45710
Gene name RHA1 (ROOT HANDEDNESS 1)
Module size 22 genes
NF 0.55
%ile 76.6



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
0.6277.31.00At5g45710834610RHA1 (ROOT HANDEDNESS 1)member of Heat Stress Transcription Factor (Hsf) familyO.I.H.G.S.X.
0.6982.90.87At1g15880838158GOS11 (golgi snare 11)Golgi SNARE 11 protein (GOS11)O.I.H.G.S.X.
0.6882.20.90At5g54310835519AGD5 (ARF-GAP domain 5)A member of ARF GAP domain (AGD), A thaliana has 15 members, grouped into four classes.O.I.H.G.S.X.
0.6781.60.87At1g06890837199transporter-relatedF:unknown;P:unknown;C:Golgi apparatus, membrane;PMFOBAO.I.H.G.S.X.
0.6781.60.86At4g35790829733ATPLDDELTAEncodes a protein with phospholipase D activity. Involved in phospolipase metabolism. Mutants are affected in hydrogen peroxide mediated cell death.O.I.H.G.S.X.
0.6378.10.87At1g19110838494inter-alpha-trypsin inhibitor heavy chain-relatedF:molecular_function unknown;P:biological_process unknown;C:plasma membrane, membrane;MBOPFAO.I.H.G.S.X.
0.6378.10.88At5g06560830544unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOBFVAO.I.H.G.S.X.
0.6277.30.86At5g01800831924saposin B domain-containing proteinF:molecular_function unknown;P:N-terminal protein myristoylation, lipid metabolic process;C:endomembrane system;MOPO.I.H.G.S.X.
0.5773.80.88At5g23670832432LCB2Encodes the LCB2 subunit of serine palmitoyltransferase, an enzyme involved in sphingosine biosynthesis. The protein is localized to the endoplasmic reticulum.O.I.H.G.S.X.
0.5673.00.87At1g28960839773ATNUDX15 (ARABIDOPSIS THALIANA NUDIX HYDROLASE HOMOLOG 15)F:hydrolase activity, CoA pyrophosphatase activity (sent to SF);P:biological_process unknown;C:mitochondrion;BOMFPAO.I.H.G.S.X.
0.5673.00.89At1g71410843482protein kinase family proteinF:binding, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:membrane;MOFPBVAO.I.H.G.S.X.
0.5673.00.87At4g00720828023ATSK32 (SHAGGY-LIKE PROTEIN KINASE 32)F:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cytosol;MOPFBVAO.I.H.G.S.X.
0.5570.60.88At5g22000832260RHF2A (RING-H2 GROUP F2A)encodes a RING-type E3 ubiquitin ligase implicated in gametogenesis. Double mutant analyses with RHF1a suggests that RHF2a may be involved in targetting ICK4KRP6 for degradation following meiosis in order to allow the mitoses associated with megagametogenesis and microgametogenesis to occur. RHF2a is expressed in all four floral whorls and is present at ~8-fold higher levels than RHF1a in inflorescences by RT-PCR analyses.O.I.H.G.S.X.
0.5570.60.87At2g31350817693GLX2-5 (GLYOXALASE 2-5)Encodes a mitochondrial glyoxalase 2 that can accommodate a number of different metal centers and with the predominant metal center being Fe(III)Zn(II).O.I.H.G.S.X.
0.5065.30.86At4g26650828772RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:unknown;MPOFBVAO.I.H.G.S.X.
0.4963.50.87At4g38260829983unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BOMFPAVO.I.H.G.S.X.
0.4862.50.87At4g01960828190unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.4862.50.87At4g19110827649protein kinase, putativeF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MOPFBVAO.I.H.G.S.X.
0.4457.20.87At5g64920836616CIP8 (COP1-INTERACTING PROTEIN 8)Encodes a RING-H2 protein that interacts with the RING finger domain of COP1. CIP8 exhibits a strong interaction with the E2 ubiquitin conjugating enzyme AtUBC8 through its N-terminal domain and promotes ubiquitination in an E2-dependent fashion in vitro. It is possible that the AtUBC8-CIP8 module might interact with COP1 in vivo, thereby participating in proteasome-mediated degradation of HY5.O.I.H.G.S.X.
0.4355.30.85At1g61770842474DNAJ heat shock N-terminal domain-containing proteinJ domain protein.O.I.H.G.S.X.
0.4355.30.88At1g65430842854zinc finger protein-relatedF:ubiquitin-protein ligase activity;P:unknown;C:intracellular;MOPFVO.I.H.G.S.X.
0.3948.40.86At1g13900837949calcineurin-like phosphoesterase family proteinF:hydrolase activity, protein serine/threonine phosphatase activity, metal ion binding, acid phosphatase activity;P:biological_process unknown;C:chloroplast;PBMOFO.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
82.299.9GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
57.999.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
52.699.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.699.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
50.899.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.999.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.999.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.099.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.299.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.499.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.799.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.599.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.399.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
41.199.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.199.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.299.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.899.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.899.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.199.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.499.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
30.599.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.799.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
28.999.7GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.299.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
24.899.6GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
24.699.6GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
24.399.6GSM154508Arabidopsis growing pollen tubes rep2GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
22.199.6GSM158702HY213-ESTRADIOL-REP1GSE6954Identification of AGL24 downstream genes by using XVE inducible systemLink to GEO
20.499.6GSM106913opr3_JA_8 hrs_Rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
17.699.5GSM133304RIKEN-NAKABAYASHI1BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
16.699.5GSM106914opr3_JA_8 hrs_Rep3GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
16.399.5GSM106912opr3_JA 8hrs_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
14.899.4GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.199.4GSM133117RIKEN-YAMAUCHI1AGSE5687AtGenExpress: Different temperature treatment of seedsLink to GEO
14.099.4GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.599.4GSM154507Arabidopsis growing pollen tubes rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
12.699.3GSM106910opr3_JA_2 hrs_rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
12.299.3GSM133303RIKEN-NAKABAYASHI1AGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
11.999.3GSM106911opr2_JA_2 hrs_Rep3GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
10.599.2GSM106915opr3_JA_22 hrs_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
10.199.2GSM106909opr3-JA_2 hrs_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
9.599.1E-MEXP-807-raw-cel-1173273116
9.299.1GSM131593ATGE_36_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.099.1GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
8.999.0E-MEXP-1443-raw-cel-1581869515
8.899.0GSM131591ATGE_36_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
8.699.0GSM106973ws_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0871GO:0032857Any process that initiates the activity of the inactive enzyme ARF GTPase through the replacement of GDP by GTP.Link to AmiGO
0.0871GO:0046473The chemical reactions and pathways involving phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.Link to AmiGO
0.0871GO:0046512The chemical reactions and pathways resulting in the formation of sphingosine (sphing-4-enine), trans-D-erytho-2-amino-octadec-4-ene-1,3-diol, a long chain amino diol sphingoid base that occurs in most sphingolipids in animal tissues.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.063100600Sphingolipid metabolismLink to KEGG PATHWAY
0.029104130SNARE interactions in vesicular transportLink to KEGG PATHWAY
0.023104144EndocytosisLink 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