Co-expression analysis

Gene ID At1g01040
Gene name DCL1 (DICER-LIKE 1)
Module size 24 genes
NF 0.54
%ile 74.9



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
0.5873.81.00At1g01040839574DCL1 (DICER-LIKE 1)Encodes a Dicer homolog. Dicer is a RNA helicase involved in microRNA processing. Mutations in this locus can result in embryo lethality. Embryo shape at seed maturity is globular-elongate. Other mutants convert the floral meristems to an indeterminate state, others yet show defects in ovule development. mRNA is expressed in all shoot tissues. DCL1 is able to produce miRNAs and siRNAs.O.I.H.G.S.X.
0.7586.90.89At3g54230824590nucleic acid binding / nucleotide binding / zinc ion bindingF:nucleotide binding, zinc ion binding, nucleic acid binding;P:unknown;C:intracellular;MOFPBAVO.I.H.G.S.X.
0.7586.90.83At5g51410835215LUC7 N_terminus domain-containing proteinF:RNA binding;P:biological_process unknown;C:cellular_component unknown;MOFPBVAO.I.H.G.S.X.
0.6781.60.85At3g21060821658transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:heterotrimeric G-protein complex;MFBOPAO.I.H.G.S.X.
0.6579.60.85At5g55670835661RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MBOFPVAO.I.H.G.S.X.
0.6075.70.85At1g31870840077unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cytosol, nucleus;MOFPBVAO.I.H.G.S.X.
0.6075.70.86At2g29210817470splicing factor PWI domain-containing proteinF:unknown;P:RNA splicing;C:unknown;MOFBPVAO.I.H.G.S.X.
0.5873.80.82At5g55660835660-F:unknown;P:unknown;C:mitochondrion;MOFBPVAO.I.H.G.S.X.
0.5673.00.81At5g47690834820bindingF:binding;P:biological_process unknown;C:mitochondrion, nucleus, chloroplast;MOFPBVAO.I.H.G.S.X.
0.5673.00.82At1g17130838283cell cycle control protein-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBVO.I.H.G.S.X.
0.5570.60.84At3g24490822039transcription factorF:transcription factor activity;P:regulation of transcription;C:cellular_component unknown;MOPFBVO.I.H.G.S.X.
0.5469.50.84At1g18950838476aminoacyl-tRNA synthetase familyF:aminoacyl-tRNA ligase activity;P:biological_process unknown;C:unknown;MOFBPVAO.I.H.G.S.X.
0.5267.40.84At3g50080824170VFB2 (VIER F-BOX PROTEINE 2)Encodes an F-box protein. Based on genetic analysis appears to be functionally redundant with VFB1,3, and 4. When expression of all 4 genes is reduced plants show defects in growth and reduced expression of auxin response genes.O.I.H.G.S.X.
0.5166.30.84At2g06210815177ELF8 (EARLY FLOWERING 8)Encodes a yeast CTR9 homolog that is involved in the control of flowering time by elevating FLC expression to a level that creates the vernalization-responsive, winter-annual habit. Yeast CTR9 is a component of a five-member PAF1 complex that associates with RNA pol II and is thought to regulate gene expression by recruiting SET1 (a histone 3 Lys 4 [H3-K4] methyl transferase) to the initially transcribed [5'] regions of target chromatin. Mutants display reduced H3-K4 methylation in both FLC and FLM chromatin.O.I.H.G.S.X.
0.5065.30.82At4g33690829511unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;MOFPO.I.H.G.S.X.
0.4659.80.81At1g79940844334ATERDJ2AJ domain protein localized in ER membrane. Mutants have defective pollen germination.O.I.H.G.S.X.
0.4659.80.84At2g27285817271unknown proteinF:unknown;P:unknown;C:unknown;MOBFPAVO.I.H.G.S.X.
0.4659.80.81At5g58000835911-F:unknown;P:unknown;C:endoplasmic reticulum, chloroplast;MOPFVBO.I.H.G.S.X.
0.4659.80.85At5g44180834441homeobox transcription factor, putativeF:transcription factor activity;P:regulation of transcription, DNA-dependent, regulation of transcription;C:nucleus;MOBFPVAO.I.H.G.S.X.
0.4659.80.83At5g65720836701NFS1cysteine desulfurase whose activity is dependent on AtSufE activation.O.I.H.G.S.X.
0.4457.20.84At2g35530818118bZIP transcription factor family proteinF:transcription factor activity;P:regulation of transcription, DNA-dependent, transcription, DNA-dependent, regulation of transcription;C:nucleus, chloroplast;MOPFBVAO.I.H.G.S.X.
0.4253.90.84At5g01270831743CPL2Encodes CPL2, a carboxyl-terminal domain (CTD) phosphatase that dephosphorylates CTD Ser5-PO4 of the RNA polymerase II complex. Regulates plant growth, stress and auxin responses.O.I.H.G.S.X.
0.4152.40.80At4g37120829866SMP2Encodes a zinc finger containing protein similar to step II splicing factors that is similar to SMP1. SMP2 is also reduced in SMP1 epigenetic alleles; plants make smaller organs having reduced cell numbers but increased cell size.O.I.H.G.S.X.
0.4152.40.84At1g09770837506ATCDC5 (ARABIDOPSIS THALIANA CELL DIVISION CYCLE 5)Member of MYB3R- and R2R3- type MYB- encoding genes. Essential for plant innate immunity. Interacts with MOS4 and PRL1.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
196.1100.0GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
70.699.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
66.899.8GSM284396Arabidopsis GPSc2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
61.899.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
61.199.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
60.099.8GSM284388Arabidopsis GMPE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
55.499.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
54.799.8GSM284389Arabidopsis GMPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
51.099.8GSM284395Arabidopsis GPSc1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
34.799.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
30.599.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.499.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.199.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.199.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.399.6GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.399.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
24.699.6GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.699.6GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
24.299.6GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.199.6GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.199.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.099.6GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.899.6GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.799.6GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.199.6GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
21.599.6GSM142750MJ001_ATH1_A1-jones-WT1GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
19.799.6GSM142751MJ001_ATH1_A2-jones-WT2GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
19.099.5GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
17.399.5GSM311282Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
17.099.5GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
16.999.5GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
16.899.5GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
16.399.5GSM311275Laser capture microdissected (LCM) micropylar endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
15.099.4GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
14.399.4GSM311279Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
14.199.4GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.599.4GSM142754MJ001_ATH1_A5-jones-WT-Rep3GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
12.699.3GSM284387Arabidopsis GSUS4bGSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
12.199.3GSM311276Laser capture microdissected (LCM) micropylar endospermr at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
11.299.2GSM311291Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
11.199.2GSM131277AtGen_6-1521_Cold(4°C)-Roots-12.0h_Rep1GSE5621AtGenExpress: Stress Treatments (Cold stress)Link to GEO
10.599.2GSM311281Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
10.399.2GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
10.199.2GSM284386Arabidopsis GSUS3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
10.199.2GSM311292Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
9.699.1GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.599.1GSM131278AtGen_6-1522_Cold(4°C)-Roots-12.0h_Rep2GSE5621AtGenExpress: Stress Treatments (Cold stress)Link to GEO
9.099.1GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
8.799.0GSM184837Arabidopsis, root, longitudinal zone 4, standard conditions, replicate 7GSE7639Expression analysis of root developmental zones after treatment with saltLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0741GO:0010599Cleavage of double-stranded RNA to form lsiRNA (long small interfering RNA), a class of siRNAs 30 to 40 nt in length. lsiRNAs are induced by pathogen infection or under specific growth conditions.Link to AmiGO
0.0711GO:0010098The process whose specific outcome is the progression of the suspensor over time, from its formation to the mature structure. The suspensor is the extension at the base of the embryo that anchors the embryo in the embryo sac and pushes it into the endosperm.Link to AmiGO
0.0711GO:0031053Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.067100730Thiamine 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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