Co-expression analysis

Gene ID At3g55770
Gene name LIM domain-containing protein
Module size 10 genes
NF 0.48
%ile 67.3



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
0.6176.71.00At3g55770824743LIM domain-containing proteinF:zinc ion binding;P:biological_process unknown;C:cellular_component unknown;MOPFO.I.H.G.S.X.
0.7083.50.94At5g65430836668GRF8 (GENERAL REGULATORY FACTOR 8)member of 14-3-3 proteins. This protein is reported to interact with the BZR1 transcription factor involved in brassinosteroid signaling and may affect the nucleocytoplasmic shuttling of BZR1O.I.H.G.S.X.
0.5368.60.94At1g14400838002UBC1 (UBIQUITIN CARRIER PROTEIN 1)ubiquitin carrier proteinO.I.H.G.S.X.
0.5065.30.95At5g10450830909GRF6 (G-box regulating factor 6)Encodes a member of the 14-3-3 gene family that is a lambda isoform (14-3-3λ). Interacts with APX3 (ascorbate peroxidase) and AKR2 , suggesting a role in mediating oxidative metabolism in stress response. This protein was shown to colocalize and interact with SERK1 by which it is phosphorylated. This protein is also reported to interact with the phosphorylated form of the BZR1 transcription factor involved in brassinosteroid signaling and may affect the nucleocytoplasmic shuttling of BZR1.O.I.H.G.S.X.
0.4761.20.93At2g20120816531COV1 (CONTINUOUS VASCULAR RING)Encodes an integral membrane protein of unknown function, highly conserved between plants and bacteria; is likely to be involved in a mechanism that negatively regulates the differentiation of vascular tissue in the stem. Mutants display a dramatic increase in vascular tissue development in the stem in place of the interfascicular region that normally separates the vascular bundles.O.I.H.G.S.X.
0.4659.80.93At2g28370817385-F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;PO.I.H.G.S.X.
0.4355.30.93At3g11530820326vacuolar protein sorting 55 family protein / VPS55 family proteinF:transporter activity;P:transport;C:vacuole;FMPOO.I.H.G.S.X.
0.4355.30.94At1g16240838193SYP51 (SYNTAXIN OF PLANTS 51)Encodes one of 24 Arabidopsis syntaxins. Its mRNA has been shown to be expressed.O.I.H.G.S.X.
0.3846.70.93At2g45980819206unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.3338.10.93At1g76920844027F-box family protein (FBX3)F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:unknown;PO.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
157.099.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
150.899.9GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
135.299.9GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
98.599.9GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
87.399.9GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
87.099.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
75.699.9GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
69.199.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
68.899.9GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
47.299.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.599.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.999.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.599.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.099.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.699.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.099.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.999.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.199.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.999.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.699.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.499.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.999.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.199.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.999.7GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
33.999.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.799.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.499.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.299.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.399.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
24.899.6GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
21.699.6GSM154507Arabidopsis growing pollen tubes rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
18.699.5GSM154508Arabidopsis growing pollen tubes rep2GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
18.399.5GSM154505Arabidopsis hydrated pollen grains rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
17.099.5GSM154503Arabidopsis desiccated mature pollen grains rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
15.899.5E-MEXP-1138-raw-cel-1432772906
15.399.4E-MEXP-1138-raw-cel-1432772874
14.599.4GSM184922Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
14.399.4E-MEXP-1138-raw-cel-1432772842
13.699.4E-MEXP-1138-raw-cel-1432772586
13.599.4E-MEXP-1138-raw-cel-1432772650
13.499.4E-MEXP-1138-raw-cel-1432772938
13.299.4E-MEXP-1138-raw-cel-1432773002
12.599.3E-MEXP-1138-raw-cel-1432772810
12.399.3E-MEXP-1138-raw-cel-1432772618
11.799.3E-MEXP-1138-raw-cel-1432772682
11.599.3GSM226536L6SBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
11.399.3E-MEXP-1138-raw-cel-1432772554
11.299.2E-MEXP-1138-raw-cel-1432772778
11.199.2E-MEXP-1138-raw-cel-1432773130
11.199.2GSM62696Columbia flowers_stage 13-14GSE2848Auxin Response Factor mediated flower gene expressionLink to GEO
10.599.2E-ATMX-35-raw-cel-1574334880
10.499.2E-MEXP-1138-raw-cel-1432773034
10.499.2E-MEXP-1138-raw-cel-1432772522
10.399.2E-MEXP-1138-raw-cel-1432772746
10.399.2E-MEXP-1138-raw-cel-1432772714
10.199.2GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.099.2GSM131608ATGE_42_DGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
10.099.2E-MEXP-285-raw-cel-440782791
9.899.1E-MEXP-1138-raw-cel-1432772970
9.899.1E-ATMX-35-raw-cel-1574334864
9.699.1E-MEXP-285-raw-cel-440782725
9.699.1E-MEXP-1138-raw-cel-1432773066
9.599.1GSM131606ATGE_42_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.399.1GSM239251Columbia glabrous (C24) wild type pollenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
9.299.1E-MEXP-1138-raw-cel-1432773194
8.699.0GSM131607ATGE_42_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1671GO:0010222Vascular tissue pattern formation as it occurs in the stem of vascular plants.Link to AmiGO
0.1431GO:0033523The modification of histone H2B by addition of ubiquitin groups.Link to AmiGO
0.1112GO:0009742A series of molecular signals mediated by the detection of brassinosteroid.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.034104130SNARE interactions in vesicular transportLink to KEGG PATHWAY
0.018104120Ubiquitin 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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