Co-expression analysis

Gene ID At5g58130
Gene name RNA recognition motif (RRM)-containing protein
Module size 45 genes
NF 0.41
%ile 57.6



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
0.7888.61.00At5g58130835925RNA recognition motif (RRM)-containing proteinF:nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.6680.10.93At1g03910839371-F:unknown;P:unknown;C:unknown;MOFPBVAO.I.H.G.S.X.
0.6478.90.93At2g41500818748EMB2776Encodes LACHESIS (LIS), a protein with seven WD40 repeats. LIS is homologous to the yeast splicing factor PRP4 which is associated with the U4/U6 complex of the spliceosome. LIS is involved in a mechanism that prevents accessory cells from adopting gametic cell fate: lis mutant forms supernumerary egg cells.O.I.H.G.S.X.
0.5570.60.93At3g04610819619FLK (flowering locus KH domain)F:RNA binding, nucleic acid binding;P:positive regulation of flower development;C:nucleus;MOPFVBO.I.H.G.S.X.
0.5368.60.93At3g54540824619ATGCN4member of GCN subfamilyO.I.H.G.S.X.
0.5267.40.92At2g41620818760nucleoporin interacting component family proteinF:molecular_function unknown;P:transport;C:nucleolus;MFPOO.I.H.G.S.X.
0.5267.40.92At1g04080839314PRP39F:binding;P:regulation of timing of transition from vegetative to reproductive phase;C:intracellular;MFBOPVO.I.H.G.S.X.
0.5166.30.92At3g44600823585CYP71 (CYCLOPHILIN71)Cyclophilin71 is a WD40 domain cyclophilin, which functions in gene repression, organogenesis and meristem development. CYP71 physically interacts with histone H3.O.I.H.G.S.X.
0.5166.30.93At3g62310825404RNA helicase, putativeF:RNA helicase activity, helicase activity, ATP binding, nucleic acid binding;P:unknown;C:nucleolus;MBOFVPAO.I.H.G.S.X.
0.4963.50.92At2g33340817897nucleotide 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.
0.4862.50.93At1g29350839809-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBVO.I.H.G.S.X.
0.4862.50.92At5g47680834819-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFBPVAO.I.H.G.S.X.
0.4761.20.91At2g47250819338RNA helicase, putativeF:in 7 functions;P:unknown;C:membrane, chloroplast envelope;MBOFVPO.I.H.G.S.X.
0.4659.80.91At3g19740821511ATP binding / ATPase/ nucleoside-triphosphatase/ nucleotide bindingF:nucleoside-triphosphatase activity, ATPase activity, nucleotide binding, ATP binding;P:biological_process unknown;C:mitochondrion;BOMFPAVO.I.H.G.S.X.
0.4659.80.92At5g49530835014SIN-like family proteinF:DNA-directed RNA polymerase activity;P:transcription;C:nucleus;MOFPBO.I.H.G.S.X.
0.4558.30.93At3g26560822264ATP-dependent RNA helicase, putativeF:in 6 functions;P:unknown;C:cytosol, mitochondrion;MOBFPVAO.I.H.G.S.X.
0.4558.30.92At5g28740832986transcription-coupled DNA repair protein-relatedF:binding;P:RNA processing;C:intracellular;MFOPBAO.I.H.G.S.X.
0.4457.20.91At4g26870828794aspartyl-tRNA synthetase, putative / aspartate--tRNA ligase, putativeF:aspartate-tRNA ligase activity, nucleotide binding, aminoacyl-tRNA ligase activity, nucleic acid binding, ATP binding;P:response to cadmium ion, tRNA aminoacylation for protein translation;C:cytoplasm;BOMFAPO.I.H.G.S.X.
0.4457.20.92At5g48120834864bindingF:binding;P:unknown;C:cellular_component unknown;MFOPO.I.H.G.S.X.
0.4457.20.91At3g63400825515peptidyl-prolyl cis-trans isomerase cyclophilin-type family proteinF:peptidyl-prolyl cis-trans isomerase activity;P:protein folding, RNA splicing;C:cellular_component unknown;MOBFPVAO.I.H.G.S.X.
0.4457.20.92At4g02720828193unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;MOBFPVAO.I.H.G.S.X.
0.4355.30.91At1g18450838425ATARP4Encodes 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.
0.4355.30.93At4g10760826670MTA (MRNA ADENOSINE METHYLASE)F:S-adenosylmethionine-dependent methyltransferase activity, methyltransferase activity;P:embryonic development ending in seed dormancy, mRNA methylation;C:nuclear speck, chloroplast;MOBPFAVO.I.H.G.S.X.
0.4152.40.91At5g27540832814MIRO1 (Miro-related GTP-ase 1)Encodes a protein with similarity to GTPases that is localized to the mitochondrion. Involved in embryogenesis, pollen tube growth and required for mitochondrial development.O.I.H.G.S.X.
0.4050.80.92At1g14850838050NUP155Encodes a protein similar to nucleoporin, a a major component of the nuclear pore complex (NPC) involved in cellular nucleo-cytoplasmic transportO.I.H.G.S.X.
0.4050.80.93At4g00830827998RNA 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.
0.4050.80.92At5g165053770617transposable element geneF:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.3846.70.91At1g20960838690emb1507 (embryo defective 1507)F:in 6 functions;P:embryonic development ending in seed dormancy;C:nucleolus, membrane;OBMFAPVO.I.H.G.S.X.
0.3846.70.91At4g11790826785Ran-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.
0.3846.70.92At1g64550842763ATGCN3member of GCN subfamilyO.I.H.G.S.X.
0.3745.00.92At5g64960836620CDKC2 (Cyclin dependent kinase group C 2)Encodes CDKC;2, part of a CDKC kinase complex that is targeted by Cauliflower mosaic virus (CaMV) for transcriptional activation of viral genes. Also regulates plant growth and development. Co-localizes with spliceosomal components in a manner dependent on the transcriptional status of the cells and on CDKC2-kinase activity. Expression of CDKC2 modifies the location of spliceosomal components.O.I.H.G.S.X.
0.3745.00.91At2g17510816257EMB2763 (EMBRYO DEFECTIVE 2763)F:ribonuclease activity, RNA binding;P:unknown;C:unknown;BOMFPAVO.I.H.G.S.X.
0.3745.00.92At3g069403768779transposable element geneF:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.3643.60.91At2g16940816197RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:mRNA processing;C:nucleus;MOFPBVAO.I.H.G.S.X.
0.3439.80.92At4g28200828935-F:molecular_function unknown;P:RNA processing;C:intracellular;FMOPO.I.H.G.S.X.
0.3338.10.92At5g49930835056emb1441 (embryo defective 1441)F:zinc ion binding, nucleic acid binding;P:embryonic development ending in seed dormancy;C:cellular_component unknown;OMBFAPVO.I.H.G.S.X.
0.3235.70.92At1g80930844433MIF4G 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.
0.3235.70.92At4g37210829875tetratricopeptide repeat (TPR)-containing proteinF:binding;P:biological_process unknown;C:cellular_component unknown;MFOPBVAO.I.H.G.S.X.
0.3133.80.92At1g25350839120OVA9 (ovule abortion 9)F:glutamine-tRNA ligase activity;P:glutamyl-tRNA aminoacylation, translation, ovule development;C:cytosol;BOMFAPO.I.H.G.S.X.
0.2930.30.92At5g64610836582HAM1 (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.
0.2726.20.92At2g05230815071DNAJ heat shock N-terminal domain-containing proteinF:heat shock protein binding;P:protein folding;C:cellular_component unknown;BOMPFAVO.I.H.G.S.X.
0.2726.20.91At2g25740817117ATP-dependent protease La (LON) domain-containing proteinF:ATP-dependent peptidase activity;P:N-terminal protein myristoylation, ATP-dependent proteolysis;C:cellular_component unknown;BOMPFO.I.H.G.S.X.
0.2726.20.92At4g11420826746EIF3A (EUKARYOTIC TRANSLATION INITIATION FACTOR 3A)Encodes a subunit of eukaryotic initiation factor 3 (eIF3), a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilization of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits.O.I.H.G.S.X.
0.2624.40.92At1g73720843707transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFOBPAVO.I.H.G.S.X.
0.2522.60.92At1g04510839503transducin 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
44.699.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.399.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.199.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.199.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.599.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.199.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.099.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.499.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.199.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.299.7GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
37.099.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.999.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.799.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.899.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.399.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.299.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.299.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.099.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
33.799.7GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
32.499.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.899.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.799.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
30.699.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.199.7GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
29.099.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.399.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
22.399.6GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.499.6GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
19.799.6GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
17.099.5GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.399.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
15.299.4GSM133962Fukuda_1-7_6A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
15.199.4GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.199.4GSM133963Fukuda_1-8_6B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
12.999.3E-MEXP-1443-raw-cel-1581869573
11.399.3GSM10441WT Ovule 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
11.199.2GSM10442WT Ovule 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
11.199.2GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
10.199.2GSM62704arf6 arf8 flowers_stage 13-14GSE2848Auxin Response Factor mediated flower gene expressionLink to GEO
8.899.0GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
8.799.0GSM258003LMPC-derived phloem_2GSE10247Transcriptome analysis of the Arabidopsis phloemLink to GEO
8.799.0GSM290758root - 01% oxygen - 48h - AGSE11558transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plantsLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0672GO:0048440The process whose specific outcome is the progression of the carpel over time, from its formation to the mature structure. A carpel is an organ (generally believed to be a modified foliar unit) at the centre of a flower, bearing one or more ovules and having its margins fused together or with other carpels to enclose the ovule in an ovary, and consisting also of a stigma and usually a style.Link to AmiGO
0.0582GO:0006397Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.Link to AmiGO
0.0482GO:0008380The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.043200970Aminoacyl-tRNA biosynthesisLink to KEGG PATHWAY
0.028204120Ubiquitin mediated proteolysisLink to KEGG PATHWAY
0.022103018RNA degradationLink 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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