Co-expression analysis

Gene ID At3g01300
Gene name protein kinase, putative
Module size 41 genes
NF 0.29
%ile 35.9



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
1.00100.01.00At3g01300820989protein kinase, putativeF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVAO.I.H.G.S.X.
0.5065.30.91At3g54190824586-F:molecular_function unknown;P:biological_process unknown;C:unknown;POO.I.H.G.S.X.
0.4558.30.91At5g37380833712DNAJ heat shock N-terminal domain-containing proteinF:unfolded protein binding, heat shock protein binding;P:protein folding;C:unknown;BOMFPAVO.I.H.G.S.X.
0.4355.30.91At3g22990821873LFR (LEAF AND FLOWER RELATED)Armadillo-repeat containing protein. Involved in leaf and flower development. Located in nucleus. Broadly expressed throughout vegetative and floral tissues.O.I.H.G.S.X.
0.4253.90.92At2g05230815071DNAJ heat shock N-terminal domain-containing proteinF:heat shock protein binding;P:protein folding;C:cellular_component unknown;BOMPFAVO.I.H.G.S.X.
0.3948.40.91At4g02720828193unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;MOBFPVAO.I.H.G.S.X.
0.3846.70.91At2g01220814650nucleotidyltransferaseF:nucleotidyltransferase activity;P:biosynthetic process;C:chloroplast envelope;OPBAFO.I.H.G.S.X.
0.3846.70.92At1g54490841891XRN4 (EXORIBONUCLEASE 4)Involved in the ethylene response. XRN4 does not appear to regulate ethylene signaling via an RNA-INDUCED SILENCING COMPLEX-based RNA silencing mechanism but acts by independent means. Endogenous suppressor of posttranscriptional gene silencing.O.I.H.G.S.X.
0.3745.00.91At4g00830827998RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MOFPBVAO.I.H.G.S.X.
0.3745.00.91At1g50200841442ALATS (ALANYL-TRNA SYNTHETASE)F:alanine-tRNA ligase activity, ligase activity, forming aminoacyl-tRNA and related compounds, nucleotide binding, nucleic acid binding, ATP binding;P:alanyl-tRNA aminoacylation, response to cadmium ion;C:mitochondrion, chloroplast;OBMAFPO.I.H.G.S.X.
0.3541.60.92At1g08620837384transcription factorF:transcription factor activity;P:regulation of transcription;C:nucleus;MFPOO.I.H.G.S.X.
0.3541.60.91At5g64610836582HAM1 (HISTONE ACETYLTRANSFERASE OF THE MYST FAMILY 1)Encodes an enzyme with histone acetyltransferase activity. HAM1 primarily acetylate histone H4, but also display some ability to acetylate H3. Prior acetylation of lysine 5 on histone H4 reduces radioactive acetylation by either HAM1. HAM1 acetylates histone H4 lysine 5.O.I.H.G.S.X.
0.3439.80.91At3g06670819852bindingF:binding;P:biological_process unknown;C:cellular_component unknown;MOFPBVO.I.H.G.S.X.
0.3439.80.91At1g55150841958DEAD box RNA helicase, putative (RH20)F:helicase activity, ATP-dependent helicase activity, ATP binding, nucleic acid binding;P:unknown;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.3439.80.91At3g26560822264ATP-dependent RNA helicase, putativeF:in 6 functions;P:unknown;C:cytosol, mitochondrion;MOBFPVAO.I.H.G.S.X.
0.3338.10.92At1g09730837501Ulp1 protease family proteinF:cysteine-type peptidase activity;P:proteolysis;C:cellular_component unknown;MOFPBVAO.I.H.G.S.X.
0.3338.10.91At1g54610841903protein kinase family proteinF:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:plasma membrane;MPOFBVAO.I.H.G.S.X.
0.3235.70.91At2g44950819104HUB1 (HISTONE MONO-UBIQUITINATION 1)The gene encodes one of two orthologous E3 ubiquitin ligases in Arabidopsis that are involved in monoubiquitination of histone H2B.O.I.H.G.S.X.
0.3235.70.91At1g80930844433MIF4G domain-containing protein / MA3 domain-containing proteinF:protein binding, RNA binding, binding;P:translation, RNA metabolic process;C:cytosol, nucleus;MOFBPVAO.I.H.G.S.X.
0.3133.80.91At2g20000816519HBT (HOBBIT)Required for cell division and cell differentiation in meristems. Encodes a homolog of the CDC27 subunit of the anaphase-promoting complex (APC). Unlike other CDC27 homologs in Arabidopsis, its transcription is cell cycle regulated. Strong hbt mutants give rise to seedlings that lack an anatomically recognizable quiescent center and differentiated columella root cap cells, the cell types derived from the wild-type hypophysis. Furthermore, they have no mitotically active root meristem and lack a differentiated lateral root cap.O.I.H.G.S.X.
0.3133.80.91At3g51310824294VPS35C (VPS35 HOMOLOG C)Homolog of yeast retromer subunit VPS35. Part of a retromer-like protein complex involved in endosome to lysosome protein transport.O.I.H.G.S.X.
0.3133.80.91At3g60250825196CKB3Regulatory (beta) subunit of the protein kinase CK2. Involved in regulation of the circadian clock in ArabidopsisO.I.H.G.S.X.
0.3032.10.91At3g59990825169MAP2B (METHIONINE AMINOPEPTIDASE 2B)Encodes a MAP2 like methionine aminopeptidaseO.I.H.G.S.X.
0.3032.10.91At5g28850833004calcium-binding EF hand family proteinF:calcium ion binding;P:biological_process unknown;C:endomembrane system;MOPFO.I.H.G.S.X.
0.3032.10.91At1g52420841673glycosyl transferase family 1 proteinF:transferase activity, transferring glycosyl groups;P:biosynthetic process;C:unknown;BOAPFMO.I.H.G.S.X.
0.3032.10.91At5g64830836606programmed cell death 2 C-terminal domain-containing proteinF:molecular_function unknown;P:apoptosis;C:cytoplasm;MFOPO.I.H.G.S.X.
0.3032.10.91At4g05420825890DDB1A (DAMAGED DNA BINDING PROTEIN 1A)Structurally similar to damaged DNA binding proteins.DDB1a is part of a 350 KDa nuclear localized DET1 protein complex. This complex may physically interact with histone tails and while bound to chromatin- repress transcription of genes involved in photomorphogenesis.O.I.H.G.S.X.
0.2930.30.91At5g07940830688-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFBPAO.I.H.G.S.X.
0.2830.30.91At3g62130825386epimerase-relatedF:pyridoxal phosphate binding, catalytic activity;P:metabolic process;C:cellular_component unknown;BOFPAMO.I.H.G.S.X.
0.2726.20.91At1g78150844151unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PFMO.I.H.G.S.X.
0.2624.40.91At3g45190823655SIT4 phosphatase-associated family proteinF:unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPAVO.I.H.G.S.X.
0.2522.60.91At1g18450838425ATARP4Encodes a gene similar to actin-related proteins in other organisms. Member of nuclear ARP family of genes. Component of chromatin remodeling complexes, involved in chromatin-mediated gene regulation. Phenotype of the arp4-1 mutant allele revealed partial sterility due to defects in anther development. Targeting the distinct, 3' UTR of AtARP4 transcripts with RNA interference caused a drastic reduction in the level of AtARP4 protein expression, and resulted in strong pleiotropic phenotypes such as altered organization of plant organs, early flowering, delayed flower senescence and high levels of sterility. Western blot analysis and immunolabelling demonstrated a clear correlation between reductions in the level of AtARP4 expression and severity of the phenotypes.O.I.H.G.S.X.
0.2522.60.91At1g62880842589cornichon family proteinF:molecular_function unknown;P:intracellular signaling cascade;C:endomembrane system, membrane;MFPOO.I.H.G.S.X.
0.2522.60.92At4g24490828551protein prenyltransferaseF:protein prenyltransferase activity;P:response to cadmium ion;C:unknown;MOFBPAVO.I.H.G.S.X.
0.2420.70.91At3g22170821781FHY3 (FAR-RED ELONGATED HYPOCOTYLS 3)A component of the PHYA signaling network, mediates the FR-HIR response to far-red light in concert with FAR1.O.I.H.G.S.X.
0.2420.70.91At5g63110836431HDA6 (HISTONE DEACETYLASE 6)RPD3-like histone deacetylase. HDA6 mutations specifically increase the expression of auxin-responsive transgenes, suggesting a role in transgene silencing.O.I.H.G.S.X.
0.168.80.91At1g71860843516PTP1 (PROTEIN TYROSINE PHOSPHATASE 1)Encodes a protein with tyrosine phosphatase activity that is downregulated in response to cold and upregulated in response to salt stress.O.I.H.G.S.X.
0.157.80.91At1g08660837388glycosyl transferase family 29 protein / sialyltransferase family proteinF:transferase activity, transferring glycosyl groups, sialyltransferase activity;P:protein amino acid glycosylation;C:Golgi apparatus, membrane;MPOVO.I.H.G.S.X.
0.146.80.91At5g63200836441tetratricopeptide repeat (TPR)-containing proteinF:binding;P:biological_process unknown;C:cellular_component unknown;OBMAFPO.I.H.G.S.X.
0.146.80.91At1g25280839112AtTLP10 (TUBBY LIKE PROTEIN 10)Member of TLP familyO.I.H.G.S.X.
0.124.90.91At1g32130840105-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBVAO.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
42.799.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.699.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.699.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.099.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.799.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.699.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.999.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.399.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.999.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
36.999.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.399.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.399.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.699.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.099.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.699.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.599.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.499.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.199.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.699.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.099.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
25.599.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.399.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.399.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
16.899.5GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.499.4GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.699.3GSM142739DH001_ATH1_A6-TCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
12.599.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
11.799.3GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.399.3GSM142736DH001_ATH1_A3-TCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
10.799.2E-MEXP-711-raw-cel-1563002902
9.499.1GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.499.1GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0481GO:0000291The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 5'-cap or the 3'-poly(A) tail.Link to AmiGO
0.0481GO:0006513Addition of a single ubiquitin moiety to a protein.Link to AmiGO
0.0481GO:0048505The process controlling the activation and/or rate at which relatively unspecialized cells acquire specialized features. Any process that modulates the rate, frequency or extent of the XXX at a consistent predetermined time point during its development.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.029204120Ubiquitin mediated proteolysisLink to KEGG PATHWAY
0.029104712Circadian rhythm - plantLink to KEGG PATHWAY
0.023100970Aminoacyl-tRNA 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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