Co-expression analysis

Gene ID At2g31650
Gene name ATX1 (ARABIDOPSIS HOMOLOGUE OF TRITHORAX)
Module size 54 genes
NF 0.59
%ile 80.8



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
1.00100.01.00At2g31650817721ATX1 (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.
0.8391.40.93At3g58800825049unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PVOO.I.H.G.S.X.
0.7989.10.88At1g17040838274SHA (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.
0.7989.10.91At2g44660819074transferase, transferring glycosyl groups / transferase, transferring hexosyl groupsF:transferase activity, transferring hexosyl groups, transferase activity, transferring glycosyl groups;P:biological_process unknown;C:endomembrane system, endoplasmic reticulum membrane;MFOPBO.I.H.G.S.X.
0.7888.60.92At2g31270817684CDT1A (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.
0.7888.60.90At2g02090814740ETL1F:helicase activity, DNA binding, ATP binding, nucleic acid binding;P:unknown;C:chloroplast;BMOFPVAO.I.H.G.S.X.
0.7788.00.91At5g02910831746F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBOO.I.H.G.S.X.
0.7788.00.92At3g59550825124SYN3Encodes 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.
0.7788.00.89At1g16330838202CYCB3core cell cycle genesO.I.H.G.S.X.
0.7687.40.91At3g54750824640unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOO.I.H.G.S.X.
0.7486.10.87At3g03970819552bindingF:binding;P:spliceosome assembly, nuclear mRNA splicing, via spliceosome;C:cellular_component unknown;PO.I.H.G.S.X.
0.7385.50.90At1g47490841157ATRBP47C (ARABIDOPSIS THALIANA RNA-BINDING PROTEIN 47C)F:RNA binding;P:unknown;C:unknown;MPFOBVAO.I.H.G.S.X.
0.7385.50.89At1g15800838149unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7284.80.88At5g58760835990DDB2 (damaged DNA-binding 2)F:nucleotide binding, zinc ion binding, nucleic acid binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFOBPAO.I.H.G.S.X.
0.7284.80.91At2g45490819157AtAUR3 (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.
0.7184.20.89At2g26470817188unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OBMFAPVO.I.H.G.S.X.
0.7184.20.90At3g07400819928lipase class 3 family proteinF:triacylglycerol lipase activity;P:lipid metabolic process;C:cellular_component unknown;PFOMBO.I.H.G.S.X.
0.7083.50.92At1g05380837039DNA bindingF:DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;MPOFABO.I.H.G.S.X.
0.6882.20.90At5g25380832610CYCA2core cell cycle genesO.I.H.G.S.X.
0.6781.60.92At4g02730828189transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MFOPBAVO.I.H.G.S.X.
0.6781.60.87At3g12140820389emsy N terminus domain-containing protein / ENT domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.6680.10.89At3g06190819793BPM2 (BTB-POZ AND MATH DOMAIN 2)F:protein binding;P:biological_process unknown;C:cellular_component unknown;MPOFO.I.H.G.S.X.
0.6579.60.88At3g14890820718phosphoesteraseF:DNA binding, catalytic activity, zinc ion binding;P:unknown;C:unknown;MOFPVBAO.I.H.G.S.X.
0.6579.60.89At4g02060828153PRL (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.
0.6579.60.90At5g64930836617CPR5 (CONSTITUTIVE EXPRESSION OF PR GENES 5)Regulator of expression of pathogenesis-related (PR) genes. Participates in signal transduction pathways involved in plant defense (systemic acquired resistance -SAR).O.I.H.G.S.X.
0.6075.70.87At1g12640837820membrane bound O-acyl transferase (MBOAT) family proteinF:acyltransferase activity;P:biological_process unknown;C:plasma membrane, membrane;MBOFPO.I.H.G.S.X.
0.6075.70.91At5g41880834193POLA3F:DNA primase activity;P:DNA replication, synthesis of RNA primer, DNA replication;C:unknown;MFOAPO.I.H.G.S.X.
0.5974.70.89At5g11080830975ubiquitin family proteinF:molecular_function unknown;P:protein modification process;C:cellular_component unknown;MPOFVBO.I.H.G.S.X.
0.5974.70.91At1g35530840448DEAD/DEAH box helicase, putativeF:in 6 functions;P:unknown;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.5873.80.87At3g20040821543ATHXK4F: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.
0.5873.80.92At3g07020819887UDP-glucose:sterol glucosyltransferase (UGT80A2)F:transferase activity, transferring glycosyl groups;P:lipid glycosylation, carbohydrate metabolic process, metabolic process;C:plasma membrane, membrane;BMFPOVO.I.H.G.S.X.
0.5873.80.87At1g11100837651SNF2 domain-containing protein / helicase domain-containing protein / zinc finger protein-relatedF:in 6 functions;P:unknown;C:unknown;MBFOPVAO.I.H.G.S.X.
0.5570.60.88At5g54280835516ATM2 (ARABIDOPSIS THALIANA MYOSIN 2)Type VII myosin geneO.I.H.G.S.X.
0.5469.50.90At5g58510835964unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;MPOBO.I.H.G.S.X.
0.5469.50.89At4g31420829269zinc finger (C2H2 type) family proteinF:transcription factor activity;P:regulation of transcription;C:intracellular;MFOPO.I.H.G.S.X.
0.5368.60.90At3g10180820180kinesin motor protein-relatedF:microtubule motor activity, ATP binding;P:microtubule-based movement;C:microtubule associated complex;MOBFPAVO.I.H.G.S.X.
0.5267.40.91At5g05130830395SNF2 domain-containing protein / helicase domain-containing protein / RING finger domain-containing proteinF:in 7 functions;P:unknown;C:unknown;MOBFPVAO.I.H.G.S.X.
0.5267.40.88At3g48440824003zinc 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.
0.4963.50.87At1g0721083723230S ribosomal protein S18 familyF:structural constituent of ribosome;P:translation;C:ribosome, intracellular;BOPMFO.I.H.G.S.X.
0.4963.50.89At2g30320817582tRNA pseudouridine synthase family proteinF:pseudouridine synthase activity;P:tRNA processing, pseudouridine synthesis;C:unknown;OBMFPAO.I.H.G.S.X.
0.4963.50.89At1g70590843396F-box family proteinF:binding;P:biological_process unknown;C:chloroplast;BOFMPVO.I.H.G.S.X.
0.4862.50.88At4g32440829379agenet domain-containing proteinF:RNA binding;P:biological_process unknown;C:unknown;PO.I.H.G.S.X.
0.4862.50.89At2g30580817608DRIP2 (DREB2A-INTERACTING PROTEIN 2)Encodes a C3HC4 RING-domain-containing ubiquitin E3 ligase capable of interacting with DREB2A. DRIP2 seems to be involved in regulating stress-related transcriptional changes and drought tolerance.O.I.H.G.S.X.
0.4862.50.89At2g25560817094DNAJ heat shock N-terminal domain-containing proteinF:unfolded protein binding, heat shock protein binding;P:protein folding;C:cellular_component unknown;BOMPFAVO.I.H.G.S.X.
0.4761.20.87At5g16630831525RAD4F:damaged DNA binding;P:nucleotide-excision repair;C:nucleus, chloroplast;MFOPO.I.H.G.S.X.
0.4761.20.88At1g79950844335helicase-relatedF:in 6 functions;P:regulation of transcription, DNA-dependent, nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;C:mitochondrion;MBOFAPVO.I.H.G.S.X.
0.4761.20.90At5g07810830674SNF2 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.
0.4558.30.90At1g05120839319SNF2 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.
0.4457.20.88At2g28320817379pleckstrin 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.
0.4355.30.88At3g03110821074XPO1BEncodes 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.
0.4152.40.91At5g49220834982unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.3745.00.88At5g65000836624nucleotide-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.
0.3338.10.88At5g55300835623TOP1ALPHA (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.
0.2830.30.87At5g63630836483DEAD 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.

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
66.799.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
66.599.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
49.799.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
45.099.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.999.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
42.299.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.799.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.999.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.999.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.799.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.499.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.099.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.899.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.599.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.599.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.299.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.399.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.199.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.199.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
31.699.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.999.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.799.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.499.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.499.7GSM311289Laser 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
28.899.7GSM184477Lateral Root Cap root cells 2hr KCl control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
28.199.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.699.7GSM311290Laser 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
25.799.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.499.6GSM184480Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.999.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
17.199.5GSM258004LMPC-derived phloem_3GSE10247Transcriptome analysis of the Arabidopsis phloemLink to GEO
15.799.5GSM184483Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.699.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
15.099.4GSM133945Murray_2-1_T0-APH_Rep1_ATH1GSE5747Genome-wide cell cycle studiesLink to GEO
14.499.4GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
13.699.4E-ATMX-35-raw-cel-1574334816
13.399.4E-ATMX-35-raw-cel-1574334800
13.399.4E-ATMX-35-raw-cel-1574334832
11.099.2GSM67087Arabidopsis_Stigma03GSE3056Arabidopsis Pollination StudyLink to GEO
11.099.2GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
10.599.2GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.799.1GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
9.399.1GSM67086Arabidopsis_Stigma02GSE3056Arabidopsis Pollination StudyLink to GEO
8.899.0GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0532GO:0010182The process by which a change in the level of a mono- or disaccharide such as glucose, fructose or sucrose triggers the expression of genes controlling metabolic and developmental processes.Link to AmiGO
0.0392GO: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
0.0361GO:0006269The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.044203030DNA replicationLink to KEGG PATHWAY
0.038203420Nucleotide excision repairLink to KEGG PATHWAY
0.024100510N-Glycan 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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