Co-expression analysis

Gene ID At1g49910
Gene name WD-40 repeat family protein / mitotic checkpoint protein, putative
Module size 48 genes
NF 0.45
%ile 63.8



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
0.7586.91.00At1g49910841414WD-40 repeat family protein / mitotic checkpoint protein, putativeF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MBFOPAO.I.H.G.S.X.
0.6882.20.84At1g67630843086POLA2 (DNA POLYMERASE ALPHA 2)F:DNA binding, DNA-directed DNA polymerase activity;P:DNA replication;C:mitochondrion;MFOPO.I.H.G.S.X.
0.6478.90.81At3g12530820432PSF2F:molecular_function unknown;P:DNA replication;C:nucleus;MFOPO.I.H.G.S.X.
0.6277.30.78At1g20220838610nucleic acid bindingF:nucleic acid binding;P:biological_process unknown;C:plant-type cell wall;MBOPFVAO.I.H.G.S.X.
0.6277.30.83At5g16690831530ORC3 (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.
0.6075.70.82At1g63160842620replication factor C 40 kDa, putativeF:in 6 functions;P:DNA replication;C:DNA replication factor C complex;BOMFAPVO.I.H.G.S.X.
0.6075.70.82At3g03110821074XPO1BEncodes 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.
0.5974.70.82At4g31400829267DNA-directed DNA polymerase/ damaged DNA bindingF:damaged DNA binding, DNA-directed DNA polymerase activity;P:DNA repair;C:unknown;MFPOBO.I.H.G.S.X.
0.5974.70.83At1g03110839572transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:cellular_component unknown;MBFOPAO.I.H.G.S.X.
0.5469.50.79At3g53320824500unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVO.I.H.G.S.X.
0.5368.60.80At1g20930838687CDKB2Cyclin-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.
0.5267.40.82At1g48360841256hydrolase, 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.
0.5267.40.81At5g41880834193POLA3F:DNA primase activity;P:DNA replication, synthesis of RNA primer, DNA replication;C:unknown;MFOAPO.I.H.G.S.X.
0.5166.30.79At1g47570841166zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MOFPVO.I.H.G.S.X.
0.5166.30.81At5g49220834982unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.5166.30.81At1g32730840167unknown proteinF:unknown;P:unknown;C:chloroplast;MPOBFO.I.H.G.S.X.
0.5166.30.79At2g30320817582tRNA pseudouridine synthase family proteinF:pseudouridine synthase activity;P:tRNA processing, pseudouridine synthesis;C:unknown;OBMFPAO.I.H.G.S.X.
0.5166.30.80At5g65000836624nucleotide-sugar transporter family proteinF:nucleotide-sugar transmembrane transporter activity, sugar:hydrogen symporter activity;P:carbohydrate transport, nucleotide-sugar transport;C:integral to membrane, Golgi membrane;MPOFABO.I.H.G.S.X.
0.5065.30.81At1g55915842042zinc ion bindingF:zinc ion binding;P:biological_process unknown;C:intracellular;FMOPO.I.H.G.S.X.
0.5065.30.78At5g46280834670DNA 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.
0.4963.50.78At1g0721083723230S ribosomal protein S18 familyF:structural constituent of ribosome;P:translation;C:ribosome, intracellular;BOPMFO.I.H.G.S.X.
0.4963.50.81At5g63630836483DEAD box RNA helicase, putativeF:helicase activity, ATP binding, ATP-dependent helicase activity, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.4862.50.83At2g29680817518CDC6 (CELL DIVISION CONTROL 6)Encodes cell division control protein 6 (CDC6).O.I.H.G.S.X.
0.4659.80.80At1g71350843476eukaryotic translation initiation factor SUI1 family proteinF:RNA binding, translation initiation factor activity;P:translational initiation;C:unknown;MFOPAO.I.H.G.S.X.
0.4558.30.81At1g05120839319SNF2 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.
0.4457.20.80At1g04790839412zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVO.I.H.G.S.X.
0.4457.20.80At2g39760818561BPM3F:protein binding;P:biological_process unknown;C:unknown;MPOFVO.I.H.G.S.X.
0.4457.20.81At5g53150835396heat shock protein binding / unfolded protein bindingF:unfolded protein binding, heat shock protein binding;P:protein folding;C:cellular_component unknown;BOMPFAVO.I.H.G.S.X.
0.4355.30.81At5g49610835023F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.4355.30.85At5g49010834960SLD5 (SYNTHETIC LETHALITY WITH DPB11-1 5)Similar to the SLD5 component of GINS complex, which in other organism was shown to be involved in the initiation of DNA replication.O.I.H.G.S.X.
0.4253.90.79At2g16370816134THY-1 (THYMIDYLATE SYNTHASE 1)Encodes a bifunctional dihydrofolate reductase - thymidylate synthase gene. This is unique in Arabidopsis and protozoa. Other organisms have independent genes for this function.O.I.H.G.S.X.
0.4152.40.81At1g04230839575unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPBVO.I.H.G.S.X.
0.3846.70.81At1g71800843510cleavage stimulation factor, putativeF:protein binding, RNA binding;P:biological_process unknown;C:cellular_component unknown;MPFOBAO.I.H.G.S.X.
0.3846.70.84At4g11560826760bromo-adjacent homology (BAH) domain-containing proteinF:DNA binding;P:transcription;C:cellular_component unknown;MOFPVBAO.I.H.G.S.X.
0.3745.00.85At1g78650844201POLD3Similar to DNA polymerase delta (POLD3), which in other organism was shown to be involved in the elongation of DNA replication.O.I.H.G.S.X.
0.3745.00.80At3g61740825347SDG14 (SET DOMAIN PROTEIN 14)F:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:unknown;MOPFBAO.I.H.G.S.X.
0.3643.60.80At5g18420831960unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPO.I.H.G.S.X.
0.3643.60.81At4g17060827414unknown proteinEncodes one of the FRI interacting proteins: FRIGIDA INTERACTING PROTEIN 1 (FIP1)/At2g06005, FIP2/ At4g17060. FRI (At4G00650) is a major determinant of natural variation in Arabidopsis flowering time.O.I.H.G.S.X.
0.3541.60.80At4g02070828147MSH6 (MUTS HOMOLOG 6)encodes a DNA mismatch repair homolog of human MutS gene, MSH6. There are four MutS genes in Arabidopsis, MSH2, MSH3, MSH6, and MSH7, which all act as heterodimers and bind to 51-mer duplexes. MSH2*MSH6 bound the (+T) substrate strongly, (T/G) well, and (+AAG) no better than it did a (T/A) homoduplex.O.I.H.G.S.X.
0.3541.60.79At5g66010836731RNA binding / nucleic acid binding / nucleotide bindingF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MOPFO.I.H.G.S.X.
0.3235.70.80At5g04110830289DNA topoisomerase II family proteinF:DNA topoisomerase (ATP-hydrolyzing) activity, DNA binding, ATP binding;P:DNA topological change, DNA metabolic process;C:chromosome;BOPMAFVO.I.H.G.S.X.
0.3133.80.79At2g31650817721ATX1 (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.
0.3032.10.79At4g35050829657MSI3 (MULTICOPY SUPPRESSOR OF IRA1 3)Encodes a WD-40 repeat protein similar to yeast MSI1. The predicted protein has a DWD motif. It can bind to DDB1a in Y2H assays, and DDB1b in co-IP assays, and may be involved in the formation of a CUL4-based E3 ubiquitin ligaseO.I.H.G.S.X.
0.3032.10.81At4g16100827296unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.2726.20.79At1g03687839052-F:molecular_function unknown;P:biological_process unknown;C:unknown;BOPO.I.H.G.S.X.
0.2624.40.79At3g46960823849ATP binding / ATP-dependent helicase/ helicase/ hydrolase, acting on acid anhydrides, in phosphorus-containing anhydrides / nucleic acid bindingF:hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, helicase activity, ATP-dependent helicase activity, ATP binding, nucleic acid binding;P:biological_process unknown;C:vacuole;OBMFAPVO.I.H.G.S.X.
0.2522.60.80At1g08130837333ATLIG1 (ARABIDOPSIS THALIANA DNA LIGASE 1)Encodes the Arabidopsis DNA ligase 1 that provides the major DNA ligase activity in cells and plays a key role in both DNA replication and excision repair pathways. Indispensable for cell viability. AtLIG1 expresses one major and two minor mRNA transcripts differing only in the length of the 5' untranslated leader sequences preceding a common ORF. Translation from the first in-frame start codon produces an AtLIG1 isoform that is targeted exclusively to the mitochondria. Translation initiation from the second in-frame start codon produces an AtLIG1 isoform targeted only to the nucleus.O.I.H.G.S.X.
0.2522.60.81At1g59890842283SNL5 (SIN3-LIKE 5)F:molecular_function unknown;P:regulation of transcription, DNA-dependent;C:nucleus;MFPOBO.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
74.999.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
45.299.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.799.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.899.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.799.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.499.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
37.399.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.899.7GSM133759Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
34.599.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.499.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.199.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.799.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.299.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.299.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.099.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.599.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.699.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.399.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.099.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.899.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
30.799.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.799.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.899.7GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.099.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
25.599.7GSM284387Arabidopsis GSUS4bGSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
18.099.5GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.899.5GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.999.4E-MEXP-1138-raw-cel-1432773290
13.899.4GSM142736DH001_ATH1_A3-TCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
13.499.4GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
13.399.4GSM184477Lateral Root Cap root cells 2hr KCl control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
12.799.3GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
12.499.3E-MEXP-1138-raw-cel-1432773258
12.299.3GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.699.2GSM284386Arabidopsis GSUS3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.199.1E-MEXP-1138-raw-cel-1432773322
9.199.1GSM142739DH001_ATH1_A6-TCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
8.899.0GSM142740DH001_ATH1_A7-MPG1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
8.899.0GSM184483Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1447GO: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
0.0682GO: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
0.0411GO:0006271The process by which a DNA strand is synthesized from template DNA during replication by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.141603030DNA replicationLink to KEGG PATHWAY
0.108403430Mismatch repairLink to KEGG PATHWAY
0.067400240Pyrimidine 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



Back to the CoP portal site

Back to the KAGIANA project homepage