Co-expression analysis

Gene ID At1g20220
Gene name nucleic acid binding
Module size 37 genes
NF 0.48
%ile 68.5



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
0.6882.21.00At1g20220838610nucleic acid bindingF:nucleic acid binding;P:biological_process unknown;C:plant-type cell wall;MBOPFVAO.I.H.G.S.X.
0.7083.50.86At3g03110821074XPO1BEncodes 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.
0.6478.90.82At2g03270814856DNA-binding protein, putativeF:nucleoside-triphosphatase activity, DNA binding, nucleotide binding, ATP binding;P:unknown;C:cellular_component unknown;BMOFPAVO.I.H.G.S.X.
0.6378.10.86At5g49220834982unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.6277.30.86At3g12530820432PSF2F:molecular_function unknown;P:DNA replication;C:nucleus;MFOPO.I.H.G.S.X.
0.6075.70.84At1g05120839319SNF2 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.
0.6075.70.81At1g47570841166zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MOFPVO.I.H.G.S.X.
0.6075.70.81At5g65000836624nucleotide-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.
0.5773.80.83At1g71350843476eukaryotic translation initiation factor SUI1 family proteinF:RNA binding, translation initiation factor activity;P:translational initiation;C:unknown;MFOPAO.I.H.G.S.X.
0.5773.80.85At5g55300835623TOP1ALPHA (DNA TOPOISOMERASE I ALPHA)Encodes a type-I DNA topoisomerase I. Disruptions in this gene affect phyllotaxis and plant architecture suggesting that the gene plays a critical role in the maintenance of a regular pattern of organ initiation. Isolated as a protein oxidized during seed germination; proteomics approach revealed differences in de novo synthesis levels of this protein in condition with vs. without salicylic acid in the period from 0 to 40 hrs. following seed imbibition.O.I.H.G.S.X.
0.5673.00.86At1g03110839572transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:cellular_component unknown;MBFOPAO.I.H.G.S.X.
0.5570.60.83At2g30320817582tRNA pseudouridine synthase family proteinF:pseudouridine synthase activity;P:tRNA processing, pseudouridine synthesis;C:unknown;OBMFPAO.I.H.G.S.X.
0.5469.50.88At2g39760818561BPM3F:protein binding;P:biological_process unknown;C:unknown;MPOFVO.I.H.G.S.X.
0.5469.50.83At4g31400829267DNA-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.
0.5267.40.83At1g55915842042zinc ion bindingF:zinc ion binding;P:biological_process unknown;C:intracellular;FMOPO.I.H.G.S.X.
0.5166.30.82At1g04230839575unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPBVO.I.H.G.S.X.
0.5166.30.85At1g63160842620replication factor C 40 kDa, putativeF:in 6 functions;P:DNA replication;C:DNA replication factor C complex;BOMFAPVO.I.H.G.S.X.
0.4963.50.82At5g53150835396heat 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.
0.4963.50.85At1g67630843086POLA2 (DNA POLYMERASE ALPHA 2)F:DNA binding, DNA-directed DNA polymerase activity;P:DNA replication;C:mitochondrion;MFOPO.I.H.G.S.X.
0.4862.50.83At5g41880834193POLA3F:DNA primase activity;P:DNA replication, synthesis of RNA primer, DNA replication;C:unknown;MFOAPO.I.H.G.S.X.
0.4761.20.86At3g02920821187replication protein-relatedF:nucleic acid binding;P:biological_process unknown;C:unknown;MFPOO.I.H.G.S.X.
0.4761.20.83At4g11560826760bromo-adjacent homology (BAH) domain-containing proteinF:DNA binding;P:transcription;C:cellular_component unknown;MOFPVBAO.I.H.G.S.X.
0.4761.20.84At1g04790839412zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVO.I.H.G.S.X.
0.4558.30.85At1g47490841157ATRBP47C (ARABIDOPSIS THALIANA RNA-BINDING PROTEIN 47C)F:RNA binding;P:unknown;C:unknown;MPFOBVAO.I.H.G.S.X.
0.4558.30.83At5g18420831960unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPO.I.H.G.S.X.
0.4355.30.82At3g03970819552bindingF:binding;P:spliceosome assembly, nuclear mRNA splicing, via spliceosome;C:cellular_component unknown;PO.I.H.G.S.X.
0.4355.30.86At5g66010836731RNA 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.
0.4253.90.83At1g71800843510cleavage stimulation factor, putativeF:protein binding, RNA binding;P:biological_process unknown;C:cellular_component unknown;MPFOBAO.I.H.G.S.X.
0.4253.90.82At2g28320817379pleckstrin homology (PH) domain-containing protein / lipid-binding START domain-containing proteinF:phosphoinositide binding;P:signal transduction;C:plasma membrane;PMOO.I.H.G.S.X.
0.4152.40.83At3g24200822006FAD binding / monooxygenase/ oxidoreductase/ oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygenF:oxidoreductase activity, monooxygenase activity, FAD binding, oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen;P:ubiquinone biosynthetic process, metabolic process;C:unknown;BOFMPAO.I.H.G.S.X.
0.3846.70.85At4g17060827414unknown 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.
0.3846.70.81At3g24740822072-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.3643.60.83At4g16100827296unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.3541.60.81At1g05380837039DNA bindingF:DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;MPOFABO.I.H.G.S.X.
0.3439.80.84At5g04110830289DNA 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.
0.3439.80.82At3g46960823849ATP 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.
0.3032.10.83At1g77180844055chromatin protein familyEncodes a protein with a putative role in mRNA splicing.O.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
78.599.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
60.399.8GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
40.799.8GSM184477Lateral Root Cap root cells 2hr KCl control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
31.599.7GSM184480Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
30.799.7GSM284387Arabidopsis GSUS4bGSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
28.899.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.599.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.599.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
25.299.6GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.699.6GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.199.6GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.499.6GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.199.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.999.6GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.899.6GSM184483Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
22.099.6GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
21.599.6GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
21.099.6GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.099.6GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
19.899.6GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
19.599.6GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
16.399.5GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
16.299.5GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
16.099.5GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
15.899.5GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
12.299.3GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
11.599.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
11.099.2GSM284386Arabidopsis GSUS3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
10.099.2GSM184481Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.099.2GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
9.899.1GSM184893Arabidopsis, root cells, columella root cap, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.299.1GSM184894Arabidopsis, root cells, columella root cap, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.199.1GSM266668Arabidopsis, root cells, columella root cap, -Fe, replicate 3GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0934GO: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
0.0742GO:0006265The process by which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.Link to AmiGO
0.0672GO:0006259The chemical reactions and pathways involving DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.108403030DNA replicationLink to KEGG PATHWAY
0.063203430Mismatch repairLink to KEGG PATHWAY
0.045203420Nucleotide excision repairLink 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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