Co-expression analysis

Gene ID At2g30260
Gene name U2B'' (U2 small nuclear ribonucleoprotein B)
Module size 31 genes
NF 0.27
%ile 30.7



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
0.8693.11.00At2g30260817576U2B'' (U2 small nuclear ribonucleoprotein B)encodes U2B", which is a component of the U2 snRNP complex. Its precise role in pre-mRNA splicing is still unknown. It has been suggested that U2B0 may not be required for the splicing reaction itself but may have a role in U2 snRNP biogenesis. Deletion analysis of the U2B0 gene fusion has identified the N-terminal RNP-80 motif as sufficient for localization to the coiled body and the nucleus.O.I.H.G.S.X.
0.4050.80.92At3g1358082056060S ribosomal protein L7 (RPL7D)F:structural constituent of ribosome, transcription regulator activity;P:translation;C:cytosolic ribosome, cytosolic large ribosomal subunit, chloroplast, large ribosomal subunit, membrane;MOFAPO.I.H.G.S.X.
0.3439.80.93At1g09760837505U2A' (U2 small nuclear ribonucleoprotein A)F:protein binding;P:nuclear mRNA splicing, via spliceosome, response to cold;C:in 6 components;MBOFPVO.I.H.G.S.X.
0.3338.10.91At5g55190835612RAN3 (RAN GTPASE 3)A member of RAN GTPase gene family. Encodes a small soluble GTP-binding protein. Likely to be involved in nuclear translocation of proteins. May also be involved in cell cycle progression.O.I.H.G.S.X.
0.3235.70.92At1g04190839442tetratricopeptide repeat (TPR)-containing proteinF:binding;P:biological_process unknown;C:cellular_component unknown;OBMPFAO.I.H.G.S.X.
0.3133.80.92At1g7405084374460S ribosomal protein L6 (RPL6C)F:structural constituent of ribosome;P:translation;C:cytosolic large ribosomal subunit, ribosome, intracellular, plasma membrane, membrane;MOFPAO.I.H.G.S.X.
0.3032.10.93At2g33340817897nucleotide binding / ubiquitin-protein ligaseF:ubiquitin-protein ligase activity, nucleotide binding;P:protein ubiquitination;C:cell wall, chloroplast, CUL4 RING ubiquitin ligase complex;MFOBPAO.I.H.G.S.X.
0.2830.30.91At3g1460082068860S ribosomal protein L18A (RPL18aC)F:structural constituent of ribosome;P:N-terminal protein myristoylation, translation, ribosome biogenesis;C:cytosolic ribosome, cytosolic large ribosomal subunit, ribosome, membrane;MOFPO.I.H.G.S.X.
0.2830.30.93At4g2709082881760S ribosomal protein L14 (RPL14B)F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:in 8 components;MOFPAO.I.H.G.S.X.
0.2726.20.93At4g3467082961940S ribosomal protein S3A (RPS3aB)F:structural constituent of ribosome;P:translation;C:in 6 components;MOAPFBO.I.H.G.S.X.
0.2726.20.91At1g25350839120OVA9 (ovule abortion 9)F:glutamine-tRNA ligase activity;P:glutamyl-tRNA aminoacylation, translation, ovule development;C:cytosol;BOMFAPO.I.H.G.S.X.
0.2624.40.92At1g02780839407emb2386 (embryo defective 2386)F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation, ribosome biogenesis;C:in 6 components;MAOFPO.I.H.G.S.X.
0.2522.60.92At1g04080839314PRP39F:binding;P:regulation of timing of transition from vegetative to reproductive phase;C:intracellular;MFBOPVO.I.H.G.S.X.
0.2522.60.91At2g46230819231-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPAO.I.H.G.S.X.
0.2522.60.92At3g05070819669-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPVO.I.H.G.S.X.
0.2420.70.92At1g30230839903elongation factor 1-beta / EF-1-betaF:translation elongation factor activity;P:translational elongation, response to cadmium ion;C:plasma membrane, eukaryotic translation elongation factor 1 complex;MOFPO.I.H.G.S.X.
0.2420.70.92At5g10360830900EMB3010 (embryo defective 3010)F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation;C:cytosolic small ribosomal subunit, cytosolic ribosome, plasma membrane;MAOFPO.I.H.G.S.X.
0.2420.70.92At1g03330839526small nuclear ribonucleoprotein D, putative / snRNP core SM-like protein, putative / U6 snRNA-associated Sm-like protein, putativeF:molecular_function unknown;P:unknown;C:small nucleolar ribonucleoprotein complex, nucleus;MFOPAO.I.H.G.S.X.
0.2420.70.91At2g39990818587EIF2translation initiation factor eIF2 p47 subunit homologO.I.H.G.S.X.
0.2319.30.92At1g69620843298RPL34 (RIBOSOMAL PROTEIN L34)putative 60S ribosomal protein L34O.I.H.G.S.X.
0.2319.30.92At1g0836083735660S ribosomal protein L10A (RPL10aA)F:structural constituent of ribosome, RNA binding;P:translation, RNA processing;C:cytosolic ribosome, cytosolic large ribosomal subunit, ribosome, plasma membrane;BOMPAFO.I.H.G.S.X.
0.2217.50.92At4g09800826569RPS18C (S18 RIBOSOMAL PROTEIN)encodes a ribosomal protein S18C, a constituent of the small subunit of the ribosomal complexO.I.H.G.S.X.
0.2217.50.92At2g34520818015RPS14 (mitochondrial ribosomal protein S14)nuclear-encoded mitochondrial ribosomal protein S14O.I.H.G.S.X.
0.2217.50.92At3g04610819619FLK (flowering locus KH domain)F:RNA binding, nucleic acid binding;P:positive regulation of flower development;C:nucleus;MOPFVBO.I.H.G.S.X.
0.2217.50.91At3g02220821238unknown proteinF:unknown;P:biological_process unknown;C:cellular_component unknown;MOPFBAO.I.H.G.S.X.
0.2115.80.91At3g12390820418nascent polypeptide associated complex alpha chain protein, putative / alpha-NAC, putativeF:unknown;P:response to salt stress;C:cytosolic ribosome;MOFBPVAO.I.H.G.S.X.
0.2115.80.91At1g04510839503transducin 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.
0.2014.40.91At3g6287082546260S ribosomal protein L7A (RPL7aB)F:structural constituent of ribosome;P:translation;C:cytosolic ribosome, cytosolic large ribosomal subunit, plasma membrane, membrane;MOFAPO.I.H.G.S.X.
0.2014.40.92At2g43770818980transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MFOBPAVO.I.H.G.S.X.
0.1710.20.92At5g57020835805NMT1 (MYRISTOYL-COA:PROTEIN N-MYRISTOYLTRANSFERASE)Arabidopsis thaliana myristoyl-CoA:protein N-myristoyltransferase.O.I.H.G.S.X.
0.168.80.92At1g52380841668Ran-binding protein 1 domain-containing protein / RanBP1 domain-containing proteinF:molecular_function unknown;P:intracellular transport;C:cytosol, nucleus;MFOPBVO.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
17.099.5GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.799.5GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
15.599.5GSM10441WT Ovule 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
15.599.5GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.199.4GSM10442WT Ovule 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
14.999.4GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.699.4GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.599.4GSM62704arf6 arf8 flowers_stage 13-14GSE2848Auxin Response Factor mediated flower gene expressionLink to GEO
14.599.4GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.499.4GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.399.4GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.199.4GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
13.999.4GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
13.799.4GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.699.4GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.399.4GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.199.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.199.4GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.099.4GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.499.3GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
12.199.3GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
11.999.3GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
11.999.3GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
11.799.3GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
11.399.3GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
10.799.2GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
10.799.2GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.299.1GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0631GO:0000354Assembly of a spliceosomal complex containing the intact pre-mRNA and all of the spliceosomal snRNPs. This occurs when the tri-snRNP associates with the pre-mRNA and associated snRNPs in an ATP-dependent manner.Link to AmiGO
0.0631GO:0010064The process by which the anatomical structures of embryonic shoot are generated and organized. Morphogenesis pertains to the creation of form.Link to AmiGO
0.0611GO:0006499The covalent or non-covalent attachment of a myristoyl moiety to the N-terminal amino acid residue of a protein.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.0841103010RibosomeLink to KEGG PATHWAY
0.031204120Ubiquitin mediated proteolysisLink to KEGG PATHWAY
0.026100970Aminoacyl-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



Back to the CoP portal site

Back to the KAGIANA project homepage