Co-expression analysis

Gene ID At5g14640
Gene name SK13 (SHAGGY-LIKE KINASE 13)
Module size 22 genes
NF 0.28
%ile 33.2

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
1.00100.01.00At5g14640831316SK13 (SHAGGY-LIKE KINASE 13)F:protein serine/threonine kinase activity, protein kinase activity, ATP binding;P:response to salt stress, hyperosmotic response;C:cytosol;MPOFBVAO.I.H.G.S.X.
0.4355.30.85At5g64610836582HAM1 (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.
0.4050.80.85At4g37210829875tetratricopeptide repeat (TPR)-containing proteinF:binding;P:biological_process unknown;C:cellular_component unknown;MFOPBVAO.I.H.G.S.X.
0.3846.70.85At1g16900838261sugar binding / transferase, transferring glycosyl groupscurculin-like (mannose-binding) lectin family protein, very low similarity to Ser Thr protein kinase GI:2598067 from (Zea mays); contains Pfam lectin (probable mannose binding) domain PF01453 but not the protein kinase domain of the Z. mays proteinO.I.H.G.S.X.
0.3846.70.85At3g04610819619FLK (flowering locus KH domain)F:RNA binding, nucleic acid binding;P:positive regulation of flower development;C:nucleus;MOPFVBO.I.H.G.S.X.
0.3643.60.84At1g52310841661protein kinase family protein / C-type lectin domain-containing proteinF:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVAO.I.H.G.S.X.
0.3541.60.84At3g22520821823unknown proteinF:unknown;P:biological_process unknown;C:chloroplast stroma, chloroplast, chloroplast envelope;OMBFPAO.I.H.G.S.X.
0.3032.10.84At1g18450838425ATARP4Encodes 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.
0.2930.30.84At3g22990821873LFR (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.
0.2930.30.84At5g63110836431HDA6 (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.
0.2624.40.84At5g16050831462GRF5 (GENERAL REGULATORY FACTOR 5)Encodes GF14 upsilon chain, a 14-3-3 gene family member.O.I.H.G.S.X.
0.2624.40.85At1g54610841903protein 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.
0.2522.60.84At4g11790826785Ran-binding protein 1 domain-containing protein / RanBP1 domain-containing proteinF:molecular_function unknown;P:intracellular transport;C:cellular_component unknown;OMBFPVAO.I.H.G.S.X.
0.2522.60.84At1g04080839314PRP39F:binding;P:regulation of timing of transition from vegetative to reproductive phase;C:intracellular;MFBOPVO.I.H.G.S.X.
0.2420.70.84At1g16970838268KU70 (ARABIDOPSIS THALIANA KU70 HOMOLOG)Ku80 and ku70 form the heterodimer complex Ku, required for proper maintenance of the telomeric C strand. Ku regulates the extension of the telomeric G strand. Interacts with WEX, and this interaction stimulates the WEX exonuclease activity.O.I.H.G.S.X.
0.2319.30.85At3g13570820559SCL30aencodes an SC35-like splicing factor of 30 kD that is localized to the nuclear specks.O.I.H.G.S.X.
0.2319.30.84At5g01230830268FtsJ-like methyltransferase family proteinF:methyltransferase activity;P:rRNA methylation;C:cellular_component unknown;OBMFAVPO.I.H.G.S.X.
0.2115.80.84At2g30100817561ubiquitin family proteinF:protein binding;P:protein modification process;C:chloroplast;MPBOFAVO.I.H.G.S.X.
0.2014.40.84At5g04940830376SUVH1 (SU(VAR)3-9 HOMOLOG 1)Encodes a SU(VAR)3-9 homolog, a SET domain protein. Known SET domain proteins are involved in epigenetic control of gene expression and act as histone methyltransferases. There are 10 SUVH genes in Arabidopsis and members of this subfamily of the SET proteins have an additional conserved SRA domain.O.I.H.G.S.X.
0.1811.40.85At5g18580831976FASS (FASS 1)fass mutants have aberrant cell shapes due to defects in arrangement of cortical microtubules. Encodes a protein highly conserved in higher plants and similar in its C-terminal part to B' regulatory subunits of type 2A protein phosphatases. Interacts with an Arabidopsis type A subunit of PP2A in the yeast two-hybrid system.O.I.H.G.S.X. family protein / WD-40 repeat family proteinF:ubiquitin-protein ligase activity, nucleotide binding;P:response to cadmium ion;C:nucleolus, CUL4 RING ubiquitin ligase complex;MFOBPAO.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
25.799.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.299.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.099.6GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
19.199.6GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
19.099.5GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.999.5GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.899.5GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.599.5GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
16.599.5GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
15.999.5GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
15.799.5GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
14.999.4GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
14.999.4GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
14.099.4GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.899.4GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
13.499.4GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.499.4GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
12.499.3GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
11.399.3GSM142623MC002_ATH1_A1.1-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
10.799.2GSM142624MC002_ATH1_A1.2-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
10.699.2GSM142641MC002_ATH1_A7.1-dubos-wLhGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
10.599.2GSM142625MC002_ATH1_A1.3-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
10.599.2GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.699.1GSM131699ATGE_81_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.399.1GSM142642MC002_ATH1_A7.2-dubos-wLhGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
9.099.1GSM142646MC002_ATH1_A8.3-dubos-aihGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
8.899.0GSM142643MC002_ATH1_A7.3-dubos-wLhGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
8.699.0GSM142644MC002_ATH1_A8.1-dubos-aihGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0741GO:0048574A change from the vegetative to the reproductive phase as a result of detection of, or exposure to, a period of light that exceeds the critical day length. The critical day length varies between species. Although the term is long-day is used, most species actually respond to the duration of the night, so that the response will occur when a period of darkness falls short of the number of hours defined by 24 minus the critical day length.Link to AmiGO
0.0691GO:0006325Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.Link to AmiGO
0.0691GO:0016458Any transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.067103450Non-homologous end-joiningLink to KEGG PATHWAY
0.038100510N-Glycan biosynthesisLink to KEGG PATHWAY
0.017104120Ubiquitin mediated proteolysisLink to KEGG PATHWAY

Inter-species module comparison

Select a plant to compare co-expressed genes between species.

Back to the CoP portal site

Back to the KAGIANA project homepage