Co-expression analysis

Gene ID At3g18390
Gene name EMB1865 (embryo defective 1865)
Module size 5 genes
NF 0.59
%ile 80.6



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
0.5065.31.00At3g18390821368EMB1865 (embryo defective 1865)F:RNA binding;P:embryonic development ending in seed dormancy;C:chloroplast;OPMFVBAO.I.H.G.S.X.
0.7385.50.94At3g49140824075-F:unknown;P:unknown;C:unknown;PBMOFVAO.I.H.G.S.X.
0.6781.60.93At3g23070821881RNA bindingF:RNA binding;P:unknown;C:chloroplast;PMOFBAVO.I.H.G.S.X.
0.5065.30.94At3g01370821288ATCFM2 (CRM FAMILY MEMBER 2)Encodes a protein containing a CRM domain that is involved in group I and group II intron splicing.O.I.H.G.S.X.
0.5065.30.95At5g03940830273CPSRP54 (CHLOROPLAST SIGNAL RECOGNITION PARTICLE 54 KDA SUBUNIT)mutant has Yellow first leaves; Chloroplast Signal Recognition Particle SubunitO.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
152.999.9E-ATMX-35-raw-cel-1574334816
112.299.9E-ATMX-35-raw-cel-1574334832
110.699.9E-ATMX-35-raw-cel-1574334800
22.099.6GSM142630MC002_ATH1_A3.2-dubos-6kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
20.799.6GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.299.6GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.899.5GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.299.5GSM142653MC002_ATH1_A11.1-dubos-mxhGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
17.499.5GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
16.899.5GSM142655MC002_ATH1_A11.3-dubos-mxhGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
16.899.5GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
16.699.5GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
16.299.5GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
16.199.5GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
15.999.5GSM142625MC002_ATH1_A1.3-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
15.399.4GSM131703ATGE_83_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
15.099.4GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
14.799.4GSM142654MC002_ATH1_A11.2-dubos-mxhGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
14.599.4GSM142631MC002_ATH1_A3.3-dubos-6kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
13.999.4GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.699.4GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.399.4GSM142624MC002_ATH1_A1.2-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
13.099.4GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
13.099.4GSM131705ATGE_83_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
12.599.3GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
12.499.3GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
11.899.3GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
11.799.3GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
11.699.3E-ATMX-31-raw-cel-1516948018
11.499.3GSM131704ATGE_83_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
11.499.3E-ATMX-31-raw-cel-1516948001
11.299.2GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
10.999.2GSM142629MC002_ATH1_A3.1-dubos-6kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
10.699.2GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
10.599.2GSM189112HSP90_Reduced_RNAi-A3_Biological_Replicate_2_Technical_Replicate_1GSE7796Phenotypic Diversity and Altered Environmental Plasticity in Arabidopsis thaliana with Reduced HSP90 LevelsLink to GEO
10.399.2GSM142623MC002_ATH1_A1.1-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
9.599.1GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.199.1GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
8.999.0GSM131698ATGE_81_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.3642GO:0000373The splicing of Group II introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group II introns and containing splice site consensus sequences, that is involved in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions (mechanistically similar to those for splicing of nuclear mRNAs) initiated by a bulged adenosine residue within the intron sequence as the initiating nucleophile. The intron is excised as a lariat.Link to AmiGO
0.3331GO:0000372The splicing of Group I introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group I introns and involved in determining the locations of the splice sites (there do not appear to be consensus splice site sequences) as well as having a role in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions, generally with exogenous guanosine as the initiating nucleophile. The intron is excised as a linear piece (though it may subsequently circularize).Link to AmiGO
0.2221GO:0006617The process by which SRP binds to the signal peptide in a nascent protein, causing protein elongation to pause, during cotranslational membrane targeting.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.065103060Protein exportLink 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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