Co-expression analysis

Gene ID At5g36670
Gene name PHD finger family protein
Module size 39 genes
NF 0.43
%ile 61.0



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
0.7687.41.00At5g36670833632PHD finger family proteinF:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:nucleus;MOPFBVO.I.H.G.S.X.
0.8089.80.80At1g34460840348CYCB1B1 type cyclinO.I.H.G.S.X.
0.7184.20.77At2g36200818192kinesin motor protein-relatedF:microtubule motor activity, ATP binding;P:microtubule-based movement;C:microtubule associated complex;MOFBPAVO.I.H.G.S.X.
0.6982.90.76At4g02060828153PRL (PROLIFERA)Member of the minichromosome maintenance complex, involved in DNA replication initiation. Abundant in proliferating and endocycling tissues. Localized in the nucleus during G1, S and G2 phases of the cell cycle, and are released into the cytoplasmic compartment during mitosis. Binds chromatin.O.I.H.G.S.X.
0.6781.60.79At2g29890817539VLN1 (VILLIN-LIKE 1)Encodes a ubiquitously expressed villin-like protein, whose mRNA may be alternatively processed. Villin belongs to a superfamily of actin binding proteins called the villin/gelsolin family. Animal villins are involved in actin binding. VLN1 protein co-localizes with actin filaments in several assays. VLN1 binds and bundles F-actin in a calcium-independent manner. It does not nucleate, cap or sever actin filaments and it stabilizes actin filaments, protecting them from ADF-mediated depolymerization.O.I.H.G.S.X.
0.6781.60.79At5g66750836808CHR1 (CHROMATIN REMODELING 1)Protein is similar to SWI2/SNF2 chromatin remodeling proteins. DDM1 is appears to act as a chromatin-remodeling ATPase involved in cytosine methylation in CG and non-CG contexts. Involved in gene silencing and maintenance of DNA methylation and histone methylation. Hypomethylation of many genomic regions occurs in ddm1 mutants, and can cause several phenotypic abnormalities, but some loci, such as BONSAI (At1g73177) can be hypermethylated in ddm1 mutants after several generations, leading to different phenotypes. DDM1 might be involved in establishing a heterochromain boundary. A line expressing an RNAi targeted against DDM1 shows some resistance to agrobacterium-mediated root transformation.O.I.H.G.S.X.
0.6176.70.79At3g49660824128transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:G-protein coupled receptor protein signaling pathway;C:chloroplast, heterotrimeric G-protein complex;MFOPBAVO.I.H.G.S.X.
0.6176.70.80At1g16330838202CYCB3core cell cycle genesO.I.H.G.S.X.
0.5974.70.78At2g31270817684CDT1A (ARABIDOPSIS HOMOLOG OF YEAST CDT1 A)Encodes a cyclin-dependent protein kinase. Involved in nuclear DNA replication and plastid division. Located in nucleus and chloroplast.O.I.H.G.S.X.
0.5773.80.81At2g35160818083SUVH5 (SU(VAR)3-9 HOMOLOG 5)Encodes SU(var)3-9 homologue 5 (SUVH5). SUVH5 has histone methyltransferase (MTase) activity in vitro and contributes to the maintenance of H3 mK9 (methylation of histone H3 at Lys-9) and CMT3-mediated non-CG methylation in vivo. This is a member of a subfamily of SET proteins that shares a conserved SRA domain.O.I.H.G.S.X.
0.5673.00.75At1g20930838687CDKB2Cyclin-dependent kinase, expressed in flowers and suspension cell culture, expression peaks during M phase in synchronized cultures. Required for proper organization of the shoot apical meristem and for hormone signaling. Expressed in the shoot apical meristem. Involved in regulation of the G2/M transition of the mitotic cell cycle.O.I.H.G.S.X.
0.5570.60.80At3g59550825124SYN3Encodes an alpha-kleisin protein that is localized primarily in the nucleolus and is essential for megagametogenesis and plays an important role in pollen development. alpha-kleisins are core components of meiotic and mitotic cohesin complexes.O.I.H.G.S.X.
0.4963.50.76At5g41880834193POLA3F:DNA primase activity;P:DNA replication, synthesis of RNA primer, DNA replication;C:unknown;MFOAPO.I.H.G.S.X.
0.4862.50.79At2g45490819157AtAUR3 (ATAURORA3)Encodes a member of a family of Ser/Thr kinases whose activities peak during cell division. Transcripts are abundant in tissues rich in dividing cells like roots and flowers but are low or absent in fully expanded leaves and stems. In interphase cells, the protein is predominantly nuclear. During mitosis, the protein associates with plant-specific cytoskeletal structures (preprophase band, phragmoplast, nascent cell plate) that are necessary for cytokinesis as well as with the microtubule spindle. The protein is concentrated in nuclear dots arranged around the nucleolus and the nuclear periphery in early prophase cells.O.I.H.G.S.X.
0.4862.50.76At1g77720844108protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:chloroplast;MOPFBVAO.I.H.G.S.X.
0.4761.20.78At3g450908236442-phosphoglycerate kinase-relatedF:unknown;P:unknown;C:unknown;BOMFPVAO.I.H.G.S.X.
0.4659.80.79At3g16650820917PP1/PP2A phosphatases pleiotropic regulator 2 (PRL2)F:nucleotide binding;P:response to salt stress;C:CUL4 RING ubiquitin ligase complex;MFOBPAO.I.H.G.S.X.
0.4659.80.78At5g46280834670DNA replication licensing factor, putativeF:nucleoside-triphosphatase activity, DNA-dependent ATPase activity, DNA binding, nucleotide binding, ATP binding;P:DNA replication initiation, DNA replication;C:nucleus;MOFPABVO.I.H.G.S.X.
0.4457.20.76At3g12530820432PSF2F:molecular_function unknown;P:DNA replication;C:nucleus;MFOPO.I.H.G.S.X.
0.4355.30.75At2g02350814766SKIP3 (SKP1 INTERACTING PARTNER 3)encodes a protein containing an F-box domain and physically interacts with SCF subunit SKP1/ASK1. The protein also exhibits similarity in sequence to phloem protein 2 (PP2) from cucumber.O.I.H.G.S.X.
0.4253.90.76At2g31650817721ATX1 (ARABIDOPSIS HOMOLOGUE OF TRITHORAX)Encodes a homolog of trithorax, a histone-lysine N-methyltransferase. Involved in trimethylating histone H3-lysine 4. Involved in the formation, placement, and identity of flower organs. Role in regulation of homeotic genes. Functions as a receptor of phosphatidylinositol 5-phosphate. Localizes to cytoplasm, plasma membrane and nuclei, shifting to nuclei in the presence of PI5P.O.I.H.G.S.X.
0.4253.90.75At3g03970819552bindingF:binding;P:spliceosome assembly, nuclear mRNA splicing, via spliceosome;C:cellular_component unknown;PO.I.H.G.S.X.
0.4152.40.82At5g22750832338RAD5DNA repair gene. gamma-radiation hypersensitive (RAD5) involved in stable transformation and T-DNA transferO.I.H.G.S.X.
0.4050.80.77At3g58800825049unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PVOO.I.H.G.S.X.
0.3948.40.75At1g47570841166zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MOFPVO.I.H.G.S.X.
0.3948.40.75At1g17040838274SHA (SH2 DOMAIN PROTEIN A)Encodes a protein that contains an SH2 domain. It can pull down a 120-kD tyrosine-phosphorylated protein in vitro. It is predicted to act as a transcription factor.O.I.H.G.S.X.
0.3745.00.79At1g35530840448DEAD/DEAH box helicase, putativeF:in 6 functions;P:unknown;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.3643.60.75At2g26470817188unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OBMFAPVO.I.H.G.S.X.
0.3643.60.80At3g10180820180kinesin motor protein-relatedF:microtubule motor activity, ATP binding;P:microtubule-based movement;C:microtubule associated complex;MOBFPAVO.I.H.G.S.X.
0.3643.60.75At1g67630843086POLA2 (DNA POLYMERASE ALPHA 2)F:DNA binding, DNA-directed DNA polymerase activity;P:DNA replication;C:mitochondrion;MFOPO.I.H.G.S.X.
0.3541.60.80At5g16690831530ORC3 (ORIGIN RECOGNITION COMPLEX SUBUNIT 3)Origin Recognition Complex subunit 3. Involved in the initiation of DNA replication. Regulated transcriptionally during cell cycle, peaking at G1/S-phase. Target of E2F/DF family of transcription factors. Interacts with all ORC subunits except ORC1b.O.I.H.G.S.X.
0.3338.10.74At5g25380832610CYCA2core cell cycle genesO.I.H.G.S.X.
0.3338.10.80At2g46040819212ARID/BRIGHT DNA-binding domain-containing protein / ELM2 domain-containing proteinF:DNA binding;P:biological_process unknown;C:intracellular;PMOFO.I.H.G.S.X.
0.3338.10.74At3g03110821074XPO1BEncodes a member of the exportin family (XPO1B)which function as receptors for nuclear transport.Along with XPO1A involved in the development of male and female gametophytes.O.I.H.G.S.X.
0.3032.10.75At5g07810830674SNF2 domain-containing protein / helicase domain-containing protein / HNH endonuclease domain-containing proteinF:helicase activity, DNA binding, ATP binding, nucleic acid binding, endonuclease activity;P:unknown;C:unknown;MBOFPVAO.I.H.G.S.X.
0.3032.10.74At3g20040821543ATHXK4F:hexokinase activity, fructokinase activity, glucokinase activity, ATP binding;P:glucose catabolic process to butanediol, glucose catabolic process to lactate and acetate, glycolysis, anaerobic glycolysis, glucose catabolic process to D-lactate and ethanol;C:mitochondrion;MFPOBO.I.H.G.S.X.
0.3032.10.76At3g48440824003zinc finger (CCCH-type) family proteinF:zinc ion binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;PMFOO.I.H.G.S.X.
0.2830.30.76At1g48360841256hydrolase, acting on acid anhydrides, in phosphorus-containing anhydrides / nucleic acid binding / zinc ion bindingF:hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, zinc ion binding, nucleic acid binding;P:biological_process unknown;C:mitochondrion;BFMOPO.I.H.G.S.X.
0.2726.20.76At1g05120839319SNF2 domain-containing protein / helicase domain-containing protein / RING finger domain-containing proteinF:in 6 functions;P:unknown;C:unknown;MFBOPVAO.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
76.199.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
70.999.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
69.799.9GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
69.299.9GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
66.199.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
65.099.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
64.999.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
64.599.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
60.999.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
60.599.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
57.999.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
57.199.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
56.399.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
55.099.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
54.599.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
54.599.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
53.499.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
53.499.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
53.299.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.499.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
49.699.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.299.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
45.299.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.099.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
33.399.7GSM67087Arabidopsis_Stigma03GSE3056Arabidopsis Pollination StudyLink to GEO
33.199.7GSM311289Laser 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
31.999.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
26.599.7GSM67086Arabidopsis_Stigma02GSE3056Arabidopsis Pollination StudyLink to GEO
17.299.5GSM184477Lateral Root Cap root cells 2hr KCl control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.899.4GSM311290Laser 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
12.699.3GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.799.2E-ATMX-31-raw-cel-1516947882
10.599.2GSM184483Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.599.2GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
10.499.2GSM184480Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.599.1GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.399.1GSM134206Murray_3-3_D5-GROWTH_Rep1_ATH1GSE5750Growth of suspension-cultured cellsLink to GEO
8.799.0GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1145GO:0006260The process whereby new strands of DNA are synthesized. The template for replication can either be an existing DNA molecule or RNA.Link to AmiGO
0.0822GO:0006268The process by which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.Link to AmiGO
0.0802GO:0006270The process by which DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.105403030DNA replicationLink to KEGG PATHWAY
0.036200240Pyrimidine metabolismLink to KEGG PATHWAY
0.027200230Purine metabolismLink 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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