Co-expression analysis

Gene ID At1g28300
Gene name LEC2 (LEAFY COTYLEDON 2)
Module size 35 genes
NF 0.55
%ile 76.2



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
1.00100.01.00At1g28300839724LEC2 (LEAFY COTYLEDON 2)Transcription factor that contains a B3 domain, a DNA-binding motif unique to plants and characteristic of several transcription factors. Plays critical roles both early and late during embryo development. LEC2 RNA accumulates primarily during seed development. LEC2 is required for the maintenance of suspensor morphology, specification of cotyledon identity, progression through the maturation phase, and suppression of premature germination. It establishes a cellular environment sufficient to initiate embryo development - ectopic, postembryonic expression of LEC2 in transgenic plants induces the formation of somatic embryos and other organ-like structures and often confers embryonic characteristics to seedlings and to reproductive and vegetative organs of mature plants.O.I.H.G.S.X.
0.9296.00.72At1g20520838640unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.8994.60.71At1g76210843954unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7989.10.56At4g08040826317ACS11encodes an aminotransferase that belongs to ACC synthase gene family structurallyO.I.H.G.S.X.
0.7989.10.60At5g59580836077UGT76E1 (UDP-GLUCOSYL TRANSFERASE 76E1)F:quercetin 3-O-glucosyltransferase activity, quercetin 7-O-glucosyltransferase activity, UDP-glycosyltransferase activity;P:metabolic process;C:unknown;PMBVOFO.I.H.G.S.X.
0.7284.80.57At1g44830841047AP2 domain-containing transcription factor TINY, putativeencodes a member of the DREB subfamily A-5 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 15 members in this subfamily including RAP2.1, RAP2.9 and RAP2.10.O.I.H.G.S.X.
0.6982.90.65At3g09870820145auxin-responsive family proteinF:molecular_function unknown;P:response to auxin stimulus;C:endomembrane system;POO.I.H.G.S.X.
0.6882.20.58At4g38420829999sks9 (SKU5 Similar 9)F:oxidoreductase activity, copper ion binding;P:unknown;C:plant-type cell wall;FBPMOAO.I.H.G.S.X.
0.6882.20.58At4g37770829933ACS8Encodes an auxin inducible ACC synthase.O.I.H.G.S.X.
0.6781.60.56At5g45630834603unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6378.10.60At1g30135839893JAZ8 (JASMONATE-ZIM-DOMAIN PROTEIN 8)F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6378.10.57At5g58750835989wound-responsive protein-relatedF:binding, catalytic activity;P:metabolic process;C:cellular_component unknown;BPFOO.I.H.G.S.X.
0.6176.70.60At2g34600818025JAZ7 (JASMONATE-ZIM-DOMAIN PROTEIN 7)F:molecular_function unknown;P:response to jasmonic acid stimulus, response to chitin;C:cellular_component unknown;PO.I.H.G.S.X.
0.5974.70.60At2g201422745551transmembrane receptorF:transmembrane receptor activity;P:signal transduction, innate immune response;C:intrinsic to membrane;PO.I.H.G.S.X.
0.5974.70.51At1g52830841717IAA6 (INDOLE-3-ACETIC ACID 6)An extragenic dominant suppressor of the hy2 mutant phenotype. Also exhibits aspects of constitutive photomorphogenetic phenotype in the absence of hy2. Mutants have dominant leaf curling phenotype shortened hypocotyls and reduced apical hook. Induced by indole-3-acetic acid.O.I.H.G.S.X.
0.5873.80.64At1g33760840267AP2 domain-containing transcription factor, putativeencodes a member of the DREB subfamily A-4 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 17 members in this subfamily including TINY.O.I.H.G.S.X.
0.5673.00.56At5g66620836794DAR6 (DA1-RELATED PROTEIN 6)F:zinc ion binding;P:unknown;C:unknown;MOBFPVAO.I.H.G.S.X.
0.5570.60.52At1g56520842105disease resistance protein (TIR-NBS-LRR class), putativeF:transmembrane receptor activity, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:signal transduction, defense response, apoptosis, innate immune response;C:intrinsic to membrane;PMBOFVAO.I.H.G.S.X.
0.5469.50.56At1g51620841587protein kinase family proteinF:protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVAO.I.H.G.S.X.
0.5469.50.56At2g01300814658unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PO.I.H.G.S.X.
0.5469.50.56At1g61260842420unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;POO.I.H.G.S.X.
0.5469.50.52At2g20350816554AP2 domain-containing transcription factor, putativeencodes a member of the ERF (ethylene response factor) subfamily B-6 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 12 members in this subfamily including RAP2.11.O.I.H.G.S.X.
0.5469.50.59At5g66640836796DAR3 (DA1-RELATED PROTEIN 3)F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMBFO.I.H.G.S.X.
0.5368.60.50At1g61460842440S-locus protein kinase, putativeF:in 6 functions;P:protein amino acid phosphorylation, recognition of pollen;C:unknown;MPOBFVAO.I.H.G.S.X.
0.4862.50.55At2g27320817275unknown proteinF:unknown;P:biological_process unknown;C:endomembrane system;PFBO.I.H.G.S.X.
0.4761.20.51At5g56980835800unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PMO.I.H.G.S.X.
0.4761.20.49At4g26200828726ACS7Member of a family of proteins in Arabidopsis that encode 1-Amino-cyclopropane-1-carboxylate synthase, an enzyme involved in ethylene biosynthesis. Not expressed in response to IAA.O.I.H.G.S.X.
0.4253.90.49At1g066208371712-oxoglutarate-dependent dioxygenase, putativeencodes a protein whose sequence is similar to a 2-oxoglutarate-dependent dioxygenaseO.I.H.G.S.X.
0.4152.40.53At2g14290815916F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBO.I.H.G.S.X.
0.4050.80.49At1g30370839917lipase class 3 family proteinF:triacylglycerol lipase activity;P:lipid metabolic process;C:unknown;PBOFMVO.I.H.G.S.X.
0.3745.00.52At1g20310838619unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PO.I.H.G.S.X.
0.3643.60.51At5g51190835193AP2 domain-containing transcription factor, putativeencodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 18 members in this subfamily including ATERF-1, ATERF-2, AND ATERF-5.O.I.H.G.S.X.
0.3439.80.49At5g42380834244CML37 (CALMODULIN LIKE 37)F:calcium ion binding;P:response to ozone;C:chloroplast;MPOFBVO.I.H.G.S.X.
0.3338.10.51At5g47220834768ERF2 (ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 2)Encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family (ATERF-2). The protein contains one AP2 domain. Functions as activator of GCC box–dependent transcription. Positive regulator of JA-responsive defense genes and resistance to F. oxysporum and enhances JA inhibition of root elongation.O.I.H.G.S.X.
0.2420.70.49At3g05320819696unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMFO.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
90.999.9GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
71.499.9GSM311291Laser 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
70.399.9GSM311292Laser 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
61.299.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
54.399.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
51.799.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
50.699.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
49.499.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.099.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
45.199.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
44.799.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.699.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.699.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.599.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.499.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.499.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
41.399.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.599.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.299.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.299.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.299.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.099.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.999.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.999.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.899.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.899.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.599.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.799.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
22.099.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.299.6GSM311288Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
17.899.5GSM311287Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
16.099.5GSM311290Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
15.799.5GSM311289Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
14.899.4GSM10453WT Mature Green Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
13.299.4GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
12.499.3GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
11.899.3GSM133755Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
11.599.3GSM265431Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
10.799.2GSM133756Lindsey_1-10_heart-stage-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.599.2GSM284398Arabidopsis GGSc2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
10.299.2GSM311296Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
8.899.0GSM265423Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
8.699.0GSM311293Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1093GO:0009693The chemical reactions and pathways resulting in the formation of ethylene (C2-H4, ethene), a simple hydrocarbon gas that can function in plants as a growth regulator.Link to AmiGO
0.0561GO:0010601Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of auxins, plant hormones that regulate aspects of plant growth.Link to AmiGO
0.0541GO:0010431A process in seed development that occurs after embryogenesis by which a quiescent state is established in a seed. Seed maturation is characterized by storage compound accumulation, acquisition of desiccation tolerance, growth arrest and the entry into a dormancy period of variable length that is broken upon germination.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.020100270Cysteine and methionine metabolismLink to KEGG PATHWAY
0.006101070Biosynthesis of plant hormonesLink 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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