Co-expression analysis

Gene ID At2g34210
Gene name structural constituent of ribosome / transcription elongation regulator/ transcription initiation factor
Module size 29 genes
NF 0.33
%ile 42.8



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
0.6882.21.00At2g34210817982structural constituent of ribosome / transcription elongation regulator/ transcription initiation factorF:transcription elongation regulator activity, structural constituent of ribosome, transcription initiation factor activity;P:regulation of transcription from RNA polymerase II promoter, translation, positive regulation of RNA elongation from RNA polymerase II promoter;C:ribosome, intracellular;MOFAPBVO.I.H.G.S.X.
0.6277.30.58At3g61450825318SYP73 (SYNTAXIN OF PLANTS 73)syntaxin of plants 73 (SYP73)O.I.H.G.S.X.
0.5773.80.56At2g32630817823pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.5570.60.57At3g05780819747LON3 (LON PROTEASE 3)Encodes a member of the Lon protease-like proteins (Lon1/At5g26860, Lon2/At5g47040, Lon3/At3g05780, Lon4/At3g05790). Lon is a multifunctional ATP-dependent protease which exists in bacteria, archaea and within organelles in eukaryotic cells. Lon proteases are responsible for the degradation of abnormal, damaged and unstable proteins.O.I.H.G.S.X.
0.5368.60.61At2g43220818923DC1 domain-containing proteinF:protein binding, zinc ion binding;P:intracellular signaling cascade;C:unknown;PMOBO.I.H.G.S.X.
0.5368.60.59At5g52620835339F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.4659.80.62At5g01280831711-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBVPAO.I.H.G.S.X.
0.4558.30.58At1g02670839532DNA repair protein, putativeF:helicase activity, DNA binding, ATP binding, nucleic acid binding;P:DNA repair;C:cellular_component unknown;BMFOPVAO.I.H.G.S.X.
0.4457.20.66At2g01810814712PHD finger family proteinF:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:cellular_component unknown;MFPOO.I.H.G.S.X.
0.4457.20.60At5g36670833632PHD finger family proteinF:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:nucleus;MOPFBVO.I.H.G.S.X.
0.4253.90.60At4g29550829076unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.4253.90.58At1g07060837217unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PO.I.H.G.S.X.
0.3846.70.56At2g35160818083SUVH5 (SU(VAR)3-9 HOMOLOG 5)Encodes SU(var)3-9 homologue 5 (SUVH5). SUVH5 has histone methyltransferase (MTase) activity in vitro and contributes to the maintenance of H3 mK9 (methylation of histone H3 at Lys-9) and CMT3-mediated non-CG methylation in vivo. This is a member of a subfamily of SET proteins that shares a conserved SRA domain.O.I.H.G.S.X.
0.3643.60.55At3g57370824904transcription factor IIB (TFIIB) family proteinF:protein binding, RNA polymerase II transcription factor activity, transcription regulator activity, zinc ion binding, translation initiation factor activity;P:translational initiation, regulation of transcription, DNA-dependent, transcription initiation;C:transcription factor complex, nucleus;AOMFPVO.I.H.G.S.X.
0.3541.60.56At5g63720836492unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;MBOFPVO.I.H.G.S.X.
0.3541.60.56At3g21000821651unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PFMOO.I.H.G.S.X.
0.2830.30.55At5g11080830975ubiquitin family proteinF:molecular_function unknown;P:protein modification process;C:cellular_component unknown;MPOFVBO.I.H.G.S.X.
0.2830.30.57At1g14680838030unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAVO.I.H.G.S.X.
0.2522.60.57At1g11100837651SNF2 domain-containing protein / helicase domain-containing protein / zinc finger protein-relatedF:in 6 functions;P:unknown;C:unknown;MBFOPVAO.I.H.G.S.X.
0.2420.70.56At1g35530840448DEAD/DEAH box helicase, putativeF:in 6 functions;P:unknown;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.2319.30.56At3g59550825124SYN3Encodes 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.
0.2319.30.58At5g22750832338RAD5DNA repair gene. gamma-radiation hypersensitive (RAD5) involved in stable transformation and T-DNA transferO.I.H.G.S.X.
0.2319.30.56At2g21930816729F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.2319.30.58At1g16330838202CYCB3core cell cycle genesO.I.H.G.S.X.
0.2217.50.55At2g43270818929F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.2217.50.58At3g16650820917PP1/PP2A phosphatases pleiotropic regulator 2 (PRL2)F:nucleotide binding;P:response to salt stress;C:CUL4 RING ubiquitin ligase complex;MFOBPAO.I.H.G.S.X.
0.2014.40.56At2g46040819212ARID/BRIGHT DNA-binding domain-containing protein / ELM2 domain-containing proteinF:DNA binding;P:biological_process unknown;C:intracellular;PMOFO.I.H.G.S.X.
0.103.40.57At3g18720821403F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PO.I.H.G.S.X.
0.061.40.62At1g27860839679unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.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
78.999.9GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
60.499.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
50.899.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.399.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.399.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
41.899.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.999.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.699.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.799.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.899.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.799.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.399.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.999.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.599.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.499.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.199.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.599.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.599.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.199.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
32.999.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.699.7GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
30.299.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.399.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.699.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.199.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.299.7GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
26.099.7GSM142750MJ001_ATH1_A1-jones-WT1GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
21.899.6GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
20.099.6GSM142751MJ001_ATH1_A2-jones-WT2GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
17.499.5GSM133984Birnbaum_1-14_StageIII-3_Rep3_ATH1GSE5749A gene expression map of the Arabidopsis rootLink to GEO
16.599.5GSM184910Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
15.599.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
14.999.4GSM154506Arabidopsis hydrated pollen grains rep2GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
14.899.4GSM184911Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
14.799.4GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
14.599.4GSM184912Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
11.899.3GSM226549Slice7JWGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
11.599.3GSM184844Arabidopsis, root, longitudinal zone 3, standard conditions, NaCl, replicate 2GSE7639Expression analysis of root developmental zones after treatment with saltLink to GEO
11.499.3GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.599.2E-MEXP-509-raw-cel-829148561
10.399.2GSM142754MJ001_ATH1_A5-jones-WT-Rep3GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
9.699.1GSM184908Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.499.1GSM142739DH001_ATH1_A6-TCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
8.999.0GSM131591ATGE_36_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
8.699.0GSM131593ATGE_36_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0631GO:0006357Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.Link to AmiGO
0.0631GO:0032968Any process that activates or increases the frequency, rate or extent of RNA elongation, the extension of an RNA molecule after transcription initiation by the addition of ribonucleotides, catalyzed by RNA polymerase II.Link to AmiGO
0.0611GO:0031048Repression of transcription by conversion of large regions of DNA into heterochromatin, directed by small RNAs sharing sequence identity to the repressed region.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.026104130SNARE interactions in vesicular transportLink 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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