Co-expression analysis

Gene ID At5g55300
Gene name TOP1ALPHA (DNA TOPOISOMERASE I ALPHA)
Module size 29 genes
NF 0.58
%ile 79.5



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
0.7184.21.00At5g55300835623TOP1ALPHA (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.
0.7486.10.91At1g04790839412zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVO.I.H.G.S.X.
0.7284.80.90At1g04230839575unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPBVO.I.H.G.S.X.
0.7083.50.91At3g24200822006FAD 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.
0.6882.20.88At5g53150835396heat 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.
0.6882.20.89At5g65000836624nucleotide-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.
0.6680.10.89At4g16100827296unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.6680.10.89At5g18420831960unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPO.I.H.G.S.X.
0.6579.60.89At3g59380825107FTA (FARNESYLTRANSFERASE A)Encodes the alpha-subunit shared between protein farnesyltransferase and protein geranylgeranyltransferase-I. Involved in protein prenylation: covalent attachment of the C-15 isoprene farnesyl or the C-20 isoprene geranylgeranyl groups to the C-terminal end of some proteins. Involved in shoot and flower meristem homeostasis, and response to ABA and drought. Also regulates leaf cell shape. Mutant is epistatic to era1.O.I.H.G.S.X.
0.6579.60.94At5g53440835425unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cytosol;MOFBPVAO.I.H.G.S.X.
0.6378.10.92At2g39760818561BPM3F:protein binding;P:biological_process unknown;C:unknown;MPOFVO.I.H.G.S.X.
0.6176.70.90At4g11560826760bromo-adjacent homology (BAH) domain-containing proteinF:DNA binding;P:transcription;C:cellular_component unknown;MOFPVBAO.I.H.G.S.X.
0.6075.70.87At5g49610835023F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.5873.80.91At5g49220834982unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.5873.80.90At1g13350837895protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:nucleus, cytoplasm;MOFPBVAO.I.H.G.S.X.
0.5673.00.90At3g54380824604SAC3/GANP family proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;MFPOO.I.H.G.S.X.
0.5570.60.87At1g56560842110beta-fructofuranosidase, putative / invertase, putative / saccharase, putative / beta-fructosidase, putativeF:catalytic activity, beta-fructofuranosidase activity;P:biological_process unknown;C:unknown;OPBO.I.H.G.S.X.
0.5570.60.91At3g03110821074XPO1BEncodes 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.
0.5570.60.89At2g34690818034ACD11 (ACCELERATED CELL DEATH 11)Gene product transports the glycolipid precursor sphingosine between membranes in vitro. Mutant constitutively expresses defense-related genes that accompany the hypersensitive response normally triggered by avirulent pathogens.O.I.H.G.S.X.
0.5368.60.88At4g17060827414unknown 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.
0.5368.60.89At1g13450837905DNA binding protein GT-1F:transcription factor activity;P:regulation of transcription;C:nucleus;PMFOBO.I.H.G.S.X.
0.5267.40.88At1g71800843510cleavage stimulation factor, putativeF:protein binding, RNA binding;P:biological_process unknown;C:cellular_component unknown;MPFOBAO.I.H.G.S.X.
0.5166.30.88At1g07910837306RNL (RNA LIGASE)Encodes a tRNA ligase that resembles the yeast Trl1 RNA ligase in structure and function but very different in sequence. Like Trl1, AtRNL consists of two domains — an N-terminal ligase component and a C-terminal 5'-kinase/2',3'-cyclic phosphodiesterase (CPD) component— that can function in tRNA splicing in vivo when expressed as separate polypeptides. Requires a 2'-PO4 end for tRNA splicing in vivo.O.I.H.G.S.X.
0.4963.50.90At1g05120839319SNF2 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.
0.4862.50.89At1g09060837427transcription factor jumonji (jmjC) domain-containing proteinF:protein binding, transcription factor activity, zinc ion binding;P:unknown;C:unknown;PMOFO.I.H.G.S.X.
0.4862.50.90At3g21290821683dentin sialophosphoprotein-relatedF:molecular_function unknown;P:biological_process unknown;C:chloroplast;BMOFPVAO.I.H.G.S.X.
0.4659.80.88At1g04830839404RabGAP/TBC domain-containing proteinF:RAB GTPase activator activity;P:regulation of Rab GTPase activity;C:intracellular;MOFPBO.I.H.G.S.X.
0.4558.30.91At2g16370816134THY-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.
0.4355.30.90At3g10030820164aspartate/glutamate/uridylate kinase family proteinF:DNA binding;P:amino acid biosynthetic process;C:cytoplasm;BOPAMFO.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
85.599.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
56.799.8GSM133759Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
54.799.8GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
34.299.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink 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
26.899.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.799.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.199.7GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
25.199.6GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.599.6GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
23.299.6GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.199.6GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.199.6GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.999.6GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.099.6GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
21.699.6GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
21.199.6GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
20.999.6GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
20.999.6GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.799.6GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.699.6GSM184477Lateral Root Cap root cells 2hr KCl control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
18.699.5E-MEXP-1138-raw-cel-1432773290
18.499.5GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
17.299.5GSM184552Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
17.099.5GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
15.899.5GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
15.199.4GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
14.599.4E-MEXP-1138-raw-cel-1432773258
14.199.4GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
13.899.4GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.699.4GSM184483Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.299.4GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.199.4GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.399.3GSM184480Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.799.2GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.699.2GSM184893Arabidopsis, root cells, columella root cap, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
10.299.2E-MEXP-1138-raw-cel-1432773322
10.199.2GSM184894Arabidopsis, root cells, columella root cap, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.699.1GSM266668Arabidopsis, 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
0.0671GO:0018347The covalent attachment of a farnesyl moiety to a protein amino acid.Link to AmiGO
0.0651GO:0008360Any process that modulates the surface configuration of a cell.Link to AmiGO
0.0651GO:0009257The chemical reactions and pathways resulting in the formation of 10-formyltetrahydrofolate, the formylated derivative of tetrahydrofolate.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.057100790Folate biosynthesisLink to KEGG PATHWAY
0.043100670One carbon pool by folateLink to KEGG PATHWAY
0.037100130Ubiquinone and other terpenoid-quinone biosynthesisLink 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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