Co-expression analysis

Gene ID At3g05680
Gene name EMB2016 (embryo defective 2016)
Module size 5 genes
NF 0.11
%ile 7.9



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
0.4253.91.00At3g05680819736EMB2016 (embryo defective 2016)F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;MOFPBVO.I.H.G.S.X.
0.2217.50.84At1g64570842765-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.146.80.86At1g76320843965FRS4 (FAR1-related sequence 4)F:zinc ion binding;P:response to red or far red light;C:cellular_component unknown;PFMO.I.H.G.S.X.
0.071.90.85At1g64050842709unknown proteinF:unknown;P:biological_process unknown;C:cellular_component unknown;OMBFPO.I.H.G.S.X.
0.030.60.84At2g38410818422VHS domain-containing protein / GAT domain-containing proteinF:protein transporter activity;P:intracellular protein transport, intra-Golgi vesicle-mediated transport;C:Golgi stack, plasma membrane;MOFPBVAO.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
243.7100.0GSM284389Arabidopsis GMPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
224.6100.0GSM311275Laser 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
155.899.9GSM311276Laser 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
113.099.9GSM284388Arabidopsis GMPE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
82.299.9GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
81.599.9GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
75.199.9GSM184892Arabidopsis, root cells, columella root cap, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
70.999.9GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
68.999.9GSM266668Arabidopsis, root cells, columella root cap, -Fe, replicate 3GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
67.999.9GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
67.899.9GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
63.699.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
63.099.8GSM226531L1SBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
60.899.8GSM266667Arabidopsis, root cells, columella root cap, -Fe, replicate 2GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
60.199.8GSM266666Arabidopsis, root cells, columella root cap, -Fe, replicate 1GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
59.899.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
57.699.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
57.499.8GSM265414Arabidopsis, root cells, -Fe, replicate 1GSE10496Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)Link to GEO
55.699.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
55.599.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
53.899.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
49.599.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
49.299.8GSM133969Birnbaum_1-20_LRC-2_Rep2_ATH1GSE5749A gene expression map of the Arabidopsis rootLink to GEO
47.999.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.199.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.199.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.899.8GSM184910Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
41.599.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.199.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.399.7GSM133968Birnbaum_1-19_LRC-1_Rep1_ATH1GSE5749A gene expression map of the Arabidopsis rootLink to GEO
33.899.7GSM184911Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
33.099.7GSM184894Arabidopsis, root cells, columella root cap, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
32.699.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.199.7GSM184893Arabidopsis, root cells, columella root cap, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
29.499.7GSM184912Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
27.399.7GSM284386Arabidopsis GSUS3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
27.199.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
22.399.6GSM128676Underwood_1-29_DC3000-10e8-7h_Rep2_ATH1GSE5520Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interactionLink to GEO
21.499.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.699.6GSM184839Arabidopsis, root, longitudinal zone 1, standard conditions, NaCl, replicate 1GSE7639Expression analysis of root developmental zones after treatment with saltLink to GEO
19.099.5GSM184832Arabidopsis, root, longitudinal zone 1, standard conditions, replicate 2GSE7639Expression analysis of root developmental zones after treatment with saltLink to GEO
18.799.5GSM184831Arabidopsis, root, longitudinal zone 1, standard conditions, replicate 1GSE7639Expression analysis of root developmental zones after treatment with saltLink to GEO
18.799.5GSM265415Arabidopsis, root cells, -Fe, replicate 2GSE10496Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)Link to GEO
18.499.5GSM252687Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (8 dpg) rep1GSE9996Organ regeneration in plants is independent of stem cell niche activityLink to GEO
17.799.5GSM184840Arabidopsis, root, longitudinal zone 1, standard conditions, NaCl, replicate 2GSE7639Expression analysis of root developmental zones after treatment with saltLink to GEO
17.599.5GSM252689Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (8 dpg) rep3GSE9996Organ regeneration in plants is independent of stem cell niche activityLink to GEO
17.199.5GSM252688Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (8 dpg) rep2GSE9996Organ regeneration in plants is independent of stem cell niche activityLink to GEO
17.099.5GSM284387Arabidopsis GSUS4bGSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
16.699.5GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.299.5GSM128675Underwood_1-28_DC3000-10e8-7h_Rep1_ATH1GSE5520Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interactionLink to GEO
16.299.5GSM184907Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
15.399.4GSM265416Arabidopsis, root cells, -Fe, replicate 3GSE10496Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)Link to GEO
12.299.3GSM252686Arabidopsis Root from tip to 130 mm proximal to tip (cut 8dpg) rep3GSE9996Organ regeneration in plants is independent of stem cell niche activityLink to GEO
12.099.3GSM252685Arabidopsis Root from tip to 130 mm proximal to tip (cut 8dpg) rep2GSE9996Organ regeneration in plants is independent of stem cell niche activityLink to GEO
11.499.3GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.099.2GSM266664Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 3GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
10.999.2GSM266662Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 1GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
10.399.2GSM252684Arabidopsis Root from tip to 130 mm proximal to tip (cut 8dpg) rep1GSE9996Organ regeneration in plants is independent of stem cell niche activityLink to GEO
10.399.2GSM184909Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.999.1GSM133976Birnbaum_1-6_StageI-3_Rep3_ATH1GSE5749A gene expression map of the Arabidopsis rootLink to GEO
9.199.1GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
9.099.1GSM184908Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
8.999.0GSM266665Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 4GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0911GO:0006891The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).Link to AmiGO
0.0531GO:0009639A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a red or far red light stimulus. Red light is electromagnetic radiation of wavelength of 580-700nm. Far red light is electromagnetic radiation of wavelength 700-800nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.Link to AmiGO
0.0121GO:0006886The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.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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