Co-expression analysis

Gene ID At3g24480
Gene name leucine-rich repeat family protein / extensin family protein
Module size 6 genes
NF 0.42
%ile 58.2



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
0.2115.81.00At3g24480822038leucine-rich repeat family protein / extensin family proteinF:structural constituent of cell wall, protein binding;P:unknown;C:cell wall, plant-type cell wall;PMOBFVAO.I.H.G.S.X.
0.8391.40.73At2g37260818303TTG2 (TRANSPARENT TESTA GLABRA 2)Encodes a protein similar to WRKY transcription factors that is expressed in the seed integument and endosperm. Mutants are defective in proanthocyanidin synthesis and seed mucilate deposition. Seeds are yellow colored. Seed size is also affected; seeds are reduced in size but only when the mutant allele is transmitted through the female parent.O.I.H.G.S.X.
0.6781.60.71At3g13540820556ATMYB5 (MYB DOMAIN PROTEIN 5)Encodes a member of the MYB family of transcriptional regulators. MYB5 act as a negative regulator of trichome branching and play a role in the correct formation of the seed coat and possibly the formation the underlying endosperm layers. Loss of function mutations have defects in seed coat mucilage and columella cells as well as trichome defects (smaller and reduced number of branches).O.I.H.G.S.X.
0.6075.70.74At1g20550838643unknown proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion;PO.I.H.G.S.X.
0.4457.20.72At3g07980819989MAPKKK6MAP3K epsilon protein kinase 2 is functionally redundant with MAP3Ke1. Required for pollen development but not essential.O.I.H.G.S.X.
0.2726.20.73At3g49050824066lipase class 3 family protein / calmodulin-binding heat-shock protein, putativeF:triacylglycerol lipase activity, calmodulin binding;P:lipid catabolic process, lipid metabolic process;C:endomembrane system;MPOFBO.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
88.499.9E-MEXP-1474-raw-cel-1593932737
82.999.9E-MEXP-1474-raw-cel-1593932641
61.899.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
55.899.8E-MEXP-1474-raw-cel-1593932769
55.299.8E-MEXP-1474-raw-cel-1593932897
49.699.8GSM133758Lindsey_1-11_heart-stage-root_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
37.599.7GSM133760Lindsey_1-12_heart-stage-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
29.499.7E-MEXP-1474-raw-cel-1593932705
28.999.7E-MEXP-1474-raw-cel-1593932801
25.299.6GSM133781Lindsey_1-6_globular-basal_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
24.799.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.499.6GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.399.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
21.399.6GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.299.6GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
20.299.6E-MEXP-1474-raw-cel-1593932609
19.999.6GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
18.299.5GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
15.999.5GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.799.5GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
15.399.4GSM75509Col-0 2h NAA replicate 1GSE3350SLR/IAA14-dependent auxin induced lateral root initiationLink to GEO
14.799.4GSM75513Col-0 2h NAA replicate 2GSE3350SLR/IAA14-dependent auxin induced lateral root initiationLink to GEO
14.799.4GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.599.4GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.399.4GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
14.299.4GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.199.4GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.099.4GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
13.999.4E-MEXP-1474-raw-cel-1593932545
13.899.4E-MEXP-1474-raw-cel-1593932513
13.799.4GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.299.4GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.099.4GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
13.099.4GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
12.399.3GSM133304RIKEN-NAKABAYASHI1BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
12.199.3E-MEXP-1474-raw-cel-1593932865
11.699.3E-MEXP-1474-raw-cel-1593932929
11.599.3GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
11.399.3GSM133719Deeken_A-1-Deeke-Tum_SLD_REP1GSE5725Agrobacterium tumefaciens-induced tumour development of Arabidopsis thalianaLink to GEO
10.899.2GSM133773Lindsey_1-25_torpedo-meristem_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.199.2GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
10.099.2GSM75517slr-1 2h NAA replicate 1GSE3350SLR/IAA14-dependent auxin induced lateral root initiationLink to GEO
9.399.1GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
9.299.1GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
9.199.1GSM133775Lindsey_1-27_torpedo-meristem_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
8.999.0GSM75521slr-1 6h NAA replicate 2GSE3350SLR/IAA14-dependent auxin induced lateral root initiationLink to GEO
8.799.0GSM75508Col-0 0h NAA replicate 1GSE3350SLR/IAA14-dependent auxin induced lateral root initiationLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.2862GO:0010214The process whose specific outcome is the progression of the seed coat over time, from its formation to the mature structure.Link to AmiGO
0.2501GO:0007009A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane.Link to AmiGO
0.2501GO:0048354The chemical reactions and pathways resulting in the formation of mucilage that occur during seed coat development; mucilage is normally synthesized during seed coat development.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG

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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