Co-expression analysis

Gene ID At3g04770
Gene name RPSAb (40S ribosomal protein SA B)
Module size 26 genes
NF 0.46
%ile 65.1



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
0.5368.61.00At3g04770819637RPSAb (40S ribosomal protein SA B)F:structural constituent of ribosome;P:translation;C:cytosolic small ribosomal subunit, cytosolic ribosome, chloroplast, membrane;BMOAFPO.I.H.G.S.X.
0.7184.20.90At3g57940824963unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BMOFAPVO.I.H.G.S.X.
0.6277.30.92At4g05410825889transducin family protein / WD-40 repeat family proteinF:nucleotide binding, nucleic acid binding;P:mitochondrial fission;C:nucleolus, small nucleolar ribonucleoprotein complex, anaphase-promoting complex, CUL4 RING ubiquitin ligase complex;MFOBPVAO.I.H.G.S.X.
0.6075.70.90At1g69070843239-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MBOFPVAO.I.H.G.S.X.
0.5773.80.91At1g63810842684-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPAO.I.H.G.S.X.
0.5673.00.91At3g09720820129DEAD/DEAH box helicase, putativeF:helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding;P:unknown;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.5570.60.90At3g57660824935NRPA1Encodes a subunit of RNA polymerase I (aka RNA polymerase A).O.I.H.G.S.X.
0.5469.50.90At5g11240830994transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:endomembrane system;BMFOPAO.I.H.G.S.X.
0.5368.60.91At3g15460820785brix domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPO.I.H.G.S.X.
0.5267.40.89At5g06550830543-F:molecular_function unknown;P:cell surface receptor linked signal transduction;C:unknown;MBOFPO.I.H.G.S.X.
0.4963.50.92At5g65900836719DEAD/DEAH box helicase, putativeF:helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding;P:unknown;C:cellular_component unknown;MOBFPVAO.I.H.G.S.X.
0.4862.50.89At4g28450828962nucleotide binding / protein bindingThis gene is predicted to encode a protein with a DWD motif. It can bind to DDB1a in Y2H assays and may be involved in the formation of a CUL4-based E3 ubiquitin ligaseO.I.H.G.S.X.
0.4761.20.91At5g61770836299PPAN (PETER PAN-LIKE PROTEIN)F:unknown;P:unknown;C:cellular_component unknown;MOFPVBO.I.H.G.S.X.
0.4659.80.90At5g64420836563DNA polymerase V familyF:DNA-directed DNA polymerase activity, DNA binding;P:DNA replication, transcription;C:cellular_component unknown;MOFBPVO.I.H.G.S.X.
0.4457.20.90At1g31660840053-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBO.I.H.G.S.X.
0.4355.30.90At4g01560828136MEE49 (maternal effect embryo arrest 49)F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;FMOPAO.I.H.G.S.X.
0.4253.90.91At3g18600821391DEAD/DEAH box helicase, putativeF:helicase activity, ATP binding, ATP-dependent helicase activity, nucleic acid binding;P:unknown;C:nucleolus;BOMFPAVO.I.H.G.S.X.
0.4050.80.90At5g57280835833methyltransferaseF:methyltransferase activity;P:metabolic process;C:unknown;BOMFPAO.I.H.G.S.X.
0.3948.40.90At5g66540836786-F:molecular_function unknown;P:rRNA processing;C:cytosol, nucleolus, nucleus;MOFBPVAO.I.H.G.S.X.
0.3643.60.91At3g15080820738exonuclease family proteinF:exonuclease activity, nucleic acid binding;P:unknown;C:intracellular;MFOPBO.I.H.G.S.X.
0.3439.80.91At5g14050831254transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;BMOFPAVO.I.H.G.S.X.
0.3338.10.91At1g10490837589unknown proteinF:unknown;P:unknown;C:cellular_component unknown;BMOFAPO.I.H.G.S.X.
0.3338.10.90At1g16280838197DEAD/DEAH box helicase, putativeF:helicase activity, ATP binding, ATP-dependent helicase activity, nucleic acid binding;P:unknown;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.3235.70.90At1g18850838466unknown proteinF:molecular_function unknown;P:biological_process unknown;C:nucleolus;PO.I.H.G.S.X.
0.3133.80.90At5g15810831438N2,N2-dimethylguanosine tRNA methyltransferase family proteinF:RNA binding, tRNA (guanine-N2-)-methyltransferase activity;P:tRNA processing;C:cellular_component unknown;OMAFBPO.I.H.G.S.X.
0.3133.80.90At2g34260817987transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MBFOPAO.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
63.399.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
60.299.8GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
59.099.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
54.799.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
53.899.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
53.799.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
53.599.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
53.299.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
52.699.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
52.499.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
51.599.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
50.999.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.299.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
49.999.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
49.899.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
49.799.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
49.499.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
48.599.8E-MEXP-807-raw-cel-1173273252
44.999.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.699.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.299.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.399.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.499.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
29.099.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
26.899.7E-MEXP-807-raw-cel-1173273144
21.099.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.099.6GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
20.899.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
20.299.6E-MEXP-807-raw-cel-1173273170
16.999.5GSM131608ATGE_42_DGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
16.299.5E-MEXP-1138-raw-cel-1432772650
15.499.5E-MEXP-509-raw-cel-829148525
15.299.4E-MEXP-807-raw-cel-1173273060
15.299.4GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
14.999.4GSM154507Arabidopsis growing pollen tubes rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
14.099.4GSM154503Arabidopsis desiccated mature pollen grains rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
13.399.4E-MEXP-1138-raw-cel-1432772522
12.499.3GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.399.3E-MEXP-1138-raw-cel-1432772586
11.699.3E-MEXP-509-raw-cel-829148561
11.499.3GSM131606ATGE_42_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
10.099.2GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.199.1GSM131607ATGE_42_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.199.1GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.099.1E-MEXP-807-raw-cel-1173273116
8.799.0GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0691GO:0007166Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell.Link to AmiGO
0.0651GO:0000266The division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.Link to AmiGO
0.0412GO:0006350The synthesis of either RNA on a template of DNA or DNA on a template of RNA.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.036103020RNA polymeraseLink to KEGG PATHWAY
0.020100240Pyrimidine metabolismLink to KEGG PATHWAY
0.015100230Purine metabolismLink 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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