Co-expression analysis

Gene ID At2g41500
Gene name EMB2776
Module size 34 genes
NF 0.43
%ile 61.3



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
0.6882.21.00At2g41500818748EMB2776Encodes 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.
0.7184.20.93At1g03910839371-F:unknown;P:unknown;C:unknown;MOFPBVAO.I.H.G.S.X.
0.6982.90.93At5g58130835925RNA recognition motif (RRM)-containing proteinF:nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.5368.60.93At3g04610819619FLK (flowering locus KH domain)F:RNA binding, nucleic acid binding;P:positive regulation of flower development;C:nucleus;MOPFVBO.I.H.G.S.X.
0.5368.60.92At1g29350839809-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBVO.I.H.G.S.X.
0.5166.30.93At5g42920834304unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOO.I.H.G.S.X.
0.5065.30.93At2g33340817897nucleotide 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.
0.5065.30.92At1g04080839314PRP39F:binding;P:regulation of timing of transition from vegetative to reproductive phase;C:intracellular;MFBOPVO.I.H.G.S.X.
0.4963.50.93At3g54540824619ATGCN4member of GCN subfamilyO.I.H.G.S.X.
0.4862.50.93At1g52380841668Ran-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.
0.4761.20.92At3g44600823585CYP71 (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.
0.4761.20.94At4g00830827998RNA 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.
0.4761.20.92At3g62310825404RNA helicase, putativeF:RNA helicase activity, helicase activity, ATP binding, nucleic acid binding;P:unknown;C:nucleolus;MBOFVPAO.I.H.G.S.X.
0.4761.20.92At5g64960836620CDKC2 (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.
0.4761.20.94At1g18450838425ATARP4Encodes 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.
0.4659.80.93At3g26560822264ATP-dependent RNA helicase, putativeF:in 6 functions;P:unknown;C:cytosol, mitochondrion;MOBFPVAO.I.H.G.S.X.
0.4659.80.94At5g165053770617transposable element geneF:unknown;P:unknown;C:unknownO.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.
0.4457.20.93At5g47680834819-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFBPVAO.I.H.G.S.X.
0.4253.90.92At4g11790826785Ran-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.
0.4253.90.93At5g27540832814MIRO1 (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.
0.3948.40.92At3g069403768779transposable element geneF:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.3948.40.93At2g16940816197RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:mRNA processing;C:nucleus;MOFPBVAO.I.H.G.S.X.
0.3745.00.93At2g17510816257EMB2763 (EMBRYO DEFECTIVE 2763)F:ribonuclease activity, RNA binding;P:unknown;C:unknown;BOMFPAVO.I.H.G.S.X.
0.3745.00.93At1g80930844433MIF4G 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.
0.3643.60.93At1g64550842763ATGCN3member of GCN subfamilyO.I.H.G.S.X.
0.3439.80.92At3g22990821873LFR (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.
0.3439.80.92At5g64610836582HAM1 (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.
0.3338.10.92At2g25970817137KH domain-containing proteinF:RNA binding, nucleic acid binding;P:unknown;C:unknown;MBFOPVAO.I.H.G.S.X.
0.3338.10.92At4g15900827272PRL1 (PLEIOTROPIC REGULATORY LOCUS 1)Mutations confer hypersensitivity to glucose and sucrose and augments sensitivity to cytokinin, ethylene, ABA and auxin. Encodes a nuclear WD40 protein that is imported into the nucleus. Essential for plant innate immunity. Interacts with MOS4 and AtCDC5. It is also predicted to have two DWD motifs. It can bind to DDB1a in Y2H assays, and DDB1b in co-IP assays, and may be involved in the formation of a CUL4-based E3 ubiquitin ligase, and may affect the stability of AKIN10.O.I.H.G.S.X.
0.3133.80.92At4g28200828935-F:molecular_function unknown;P:RNA processing;C:intracellular;FMOPO.I.H.G.S.X.
0.2930.30.92At2g05230815071DNAJ heat shock N-terminal domain-containing proteinF:heat shock protein binding;P:protein folding;C:cellular_component unknown;BOMPFAVO.I.H.G.S.X.
0.2930.30.92At2g25740817117ATP-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.
0.2420.70.92At5g64200836541ATSC35encodes an SC35-like splicing factor of 35 kD localized to the nuclear specks.O.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
42.499.8GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
40.299.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.699.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.499.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.399.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
38.299.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
37.599.7GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
37.399.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.399.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.599.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.199.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.099.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.599.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
34.799.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.699.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.099.7GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
33.899.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.899.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.499.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.399.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.899.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.699.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.699.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.699.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
31.399.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.599.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.299.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.699.7GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
25.599.7GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
23.499.6GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.199.6GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
17.399.5GSM133962Fukuda_1-7_6A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
17.299.5E-MEXP-1443-raw-cel-1581869573
15.099.4GSM133963Fukuda_1-8_6B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
14.699.4GSM10441WT Ovule 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
14.399.4GSM10442WT Ovule 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
13.199.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.099.4GSM62704arf6 arf8 flowers_stage 13-14GSE2848Auxin Response Factor mediated flower gene expressionLink to GEO
11.499.3GSM258003LMPC-derived phloem_2GSE10247Transcriptome analysis of the Arabidopsis phloemLink to GEO
11.099.2GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
10.999.2GSM258002LMPC-derived phloem_1GSE10247Transcriptome analysis of the Arabidopsis phloemLink to GEO
10.199.2E-MEXP-1443-raw-cel-1581869515
9.199.1GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
8.999.0GSM133965Fukuda_1-10_8B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0952GO:0046907The directed movement of substances within a cell.Link to AmiGO
0.0822GO: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
0.0692GO: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

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.024103018RNA degradationLink to KEGG PATHWAY
0.015104120Ubiquitin mediated proteolysisLink 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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