Co-expression analysis

Gene ID At5g28040
Gene name transcription regulator
Module size 24 genes
NF 0.30
%ile 37.3



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
1.00100.01.00At5g28040832874transcription regulatorF:transcription regulator activity;P:unknown;C:unknown;PMBOFO.I.H.G.S.X.
0.5166.30.93At4g33890829532unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PFOO.I.H.G.S.X.
0.4558.30.92At2g22090816744UBP1 interacting protein 1a (UBA1a)encodes a nuclear protein that binds to RNA with a specificity for oligouridylates in vitro. As with UBP1, transient overexpression of UBA1a in protoplasts increases the steady-state levels of reporter mRNAs in a promoter-dependent manner. Along with UBP1 and UBA2a, it may act as a component of a complex recognizing U-rich sequences in plant 3'-UTRs and contributing to the stabilization of mRNAs in the nucleus.O.I.H.G.S.X.
0.4558.30.91At4g09580826542-F:unknown;P:biological_process unknown;C:endoplasmic reticulum;BOMPFAO.I.H.G.S.X.
0.4355.30.91At3g29270822584ubiquitin-protein ligaseF:ubiquitin-protein ligase activity;P:unknown;C:unknown;MPOO.I.H.G.S.X.
0.4050.80.91At2g18915816408LKP2 (LOV KELCH PROTEIN 2)encodes a member of F-box proteins that includes two other proteins in Arabidopsis (ZTL and FKF1). These proteins contain a unique structure containing a PAS domain at their N-terminus, an F-box motif, and 6 kelch repeats at their C-terminus. Overexpression results in arrhythmic phenotypes for a number of circadian clock outputs in both constant light and constant darkness, long hypocotyls under multiple fluences of both red and blue light, and a loss of photoperiodic control of flowering time. Although this the expression of this gene itself is not regulated by circadian clock, it physically interacts with Dof transcription factors that are transcriptionally regulated by circadian rhythm. LKP2 interacts with Di19, CO/COL family proteins.O.I.H.G.S.X.
0.3846.70.92At1g54115841851CCX4 (CATION CALCIUM EXCHANGER 4)Involved in cation (Na and K) homeostasis.O.I.H.G.S.X.
0.3541.60.91At4g21350827885PUB8 (PLANT U-BOX 8)Encodes a U-box/ARM repeat protein required fore self-incompatibility.O.I.H.G.S.X.
0.3235.70.91At1g69980843335unknown proteinF:unknown;P:unknown;C:endomembrane system;PO.I.H.G.S.X.
0.3032.10.91At1g22020838807SHM6 (serine hydroxymethyltransferase 6)Encodes a putative serine hydroxymethyltransferase.O.I.H.G.S.X.
0.3032.10.92At2g05170815065ATVPS11Homologous to yeast VPS11. Forms a complex with VCL1 and AtVPS33. Involved in vacuolar biogenesis.O.I.H.G.S.X.
0.2830.30.91At4g24200828521-F:unknown;P:unknown;C:mitochondrion;OBMFPO.I.H.G.S.X.
0.2624.40.91At1g27190839608leucine-rich repeat transmembrane protein kinase, putativeF:protein serine/threonine kinase activity, kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:nucleus, plasma membrane;PMOBFVAO.I.H.G.S.X.
0.2624.40.91At3g61790825352seven in absentia (SINA) family proteinF:ubiquitin-protein ligase activity, protein binding, zinc ion binding;P:multicellular organismal development, ubiquitin-dependent protein catabolic process, protein ubiquitination;C:nucleus;MPOFO.I.H.G.S.X.
0.2319.30.91At1g27850839678unknown proteinF:molecular_function unknown;P:biological_process unknown;C:plasma membrane;MOFBPVAO.I.H.G.S.X.
0.2217.50.92At3g03740821170ATBPM4 (BTB-POZ and MATH domain 4)F:protein binding;P:biological_process unknown;C:unknown;MPOFVO.I.H.G.S.X.
0.2014.40.91At5g64090836530-F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;MOPFO.I.H.G.S.X.
0.2014.40.91At1g21630838765calcium-binding EF hand family proteinF:calcium ion binding;P:unknown;C:cytosol, plasma membrane;BMOFPVAO.I.H.G.S.X.
0.1912.70.91At3g54860824651vacuolar protein sorting protein, putativeHomologous to yeast VPS33. Forms a complex with VCL1 and AtVPS11. Involved in vacuolar biogenesis.O.I.H.G.S.X.
0.1912.70.91At5g55500835643XYLT (ARABIDOPSIS THALIANA BETA-1,2-XYLOSYLTRANSFERASE)Encodes a beta-1,2-xylosyltransferase that is glycosylated at two positions.O.I.H.G.S.X.
0.1912.70.91At3g25800822171PP2AA2 (PROTEIN PHOSPHATASE 2A SUBUNIT A2)one of three genes encoding the protein phosphatase 2A regulatory subunitO.I.H.G.S.X.
0.1811.40.91At5g18190831937protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MBOPFVAO.I.H.G.S.X.
0.1811.40.91At3g01340821216protein transport protein SEC13 family protein / WD-40 repeat family proteinF:nucleotide binding;P:intracellular protein transport, membrane budding;C:cellular_component unknown;MFBOPAO.I.H.G.S.X.
0.157.80.91At5g35430833507bindingF:binding;P:biological_process unknown;C:cellular_component unknown;MPOBFO.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
61.199.8GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
48.099.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.999.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.299.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.099.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.799.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
42.699.8GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
42.399.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.399.8GSM311290Laser 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
40.599.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.999.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.099.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.999.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.599.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.999.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.899.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.799.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.099.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.899.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.299.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.799.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.399.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.999.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.099.7GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
25.299.6GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
24.499.6GSM311289Laser 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
22.099.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.999.6GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.099.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
18.799.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
17.399.5GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
17.199.5GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.399.5GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.599.4GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.999.3GSM133767Lindsey_1-19_torpedo-basal_Rep4_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
11.899.3GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
10.699.2GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1252GO:0007033A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole.Link to AmiGO
0.0801GO:0031204The process by which a protein translocates through the ER membrane posttranslationally.Link to AmiGO
0.0771GO:0006900The evagination of a membrane, resulting in formation of a vesicle.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.049100670One carbon pool by folateLink to KEGG PATHWAY
0.043100460Cyanoamino acid metabolismLink to KEGG PATHWAY
0.038104712Circadian rhythm - plantLink 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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