Co-expression analysis

Gene ID	At5g28650
Gene name	WRKY74
Module size	5 genes
NF	0.39
%ile	53.4

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : 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
0.43	55.3	1.00	At5g28650	832971	WRKY74	member of WRKY Transcription Factor; Group II-d	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.50	65.3	0.75	At1g49320	841355	BURP domain-containing protein	F:molecular_function unknown;P:unknown;C:endomembrane system;P	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.50	65.3	0.72	At4g37970	829953	CAD6 (CINNAMYL ALCOHOL DEHYDROGENASE 6)	F:oxidoreductase activity, binding, catalytic activity, zinc ion binding;P:oxidation reduction, metabolic process;C:cellular_component unknown;BOPFMAV	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.32	35.7	0.75	At4g33450	829482	MYB69 (MYB DOMAIN PROTEIN 69)	Member of the R2R3 factor gene family.	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.31	33.8	0.75	At4g00940	827952	Dof-type zinc finger domain-containing protein	F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;POM	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)

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
106.1	99.9	GSM184556	Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
82.6	99.9	GSM311296	Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
65.6	99.8	GSM284396	Arabidopsis GPSc2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
55.6	99.8	GSM284395	Arabidopsis GPSc1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
50.4	99.8	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
49.9	99.8	GSM311281	Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
45.9	99.8	GSM184906	Arabidopsis, root cells, protophloem, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
45.1	99.8	GSM284398	Arabidopsis GGSc2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
45.0	99.8	GSM184904	Arabidopsis, root cells, protophloem, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
44.7	99.8	GSM311294	Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
41.8	99.8	GSM311293	Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
36.8	99.7	GSM184923	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
35.7	99.7	GSM184905	Arabidopsis, root cells, protophloem, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
33.1	99.7	GSM311282	Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
31.2	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
30.4	99.7	GSM311292	Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
28.2	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
27.8	99.7	GSM311295	Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
27.5	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
27.5	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
26.5	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
25.8	99.7	GSM284397	Arabidopsis GGSc1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
25.3	99.6	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
25.1	99.6	GSM284390	Arabidopsis GPE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
23.9	99.6	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
23.7	99.6	GSM311291	Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
23.6	99.6	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.4	99.6	GSM133775	Lindsey_1-27_torpedo-meristem_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
23.1	99.6	GSM311289	Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
22.3	99.6	GSM284391	Arabidopsis GPE3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
21.8	99.6	GSM284384	Arabidopsis GEP5	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
21.3	99.6	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
21.2	99.6	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.0	99.6	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.9	99.6	GSM284394	Arabidopsis GCE3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
20.1	99.6	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
19.1	99.6	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.8	99.5	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.1	99.5	GSM311277	Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
18.0	99.5	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.7	99.5	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.6	99.5	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
17.4	99.5	GSM284392	Arabidopsis GCE1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
16.8	99.5	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
16.7	99.5	GSM311286	Laser capture microdissected (LCM) whole seed sections at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
16.3	99.5	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.2	99.5	GSM284393	Arabidopsis GCE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
16.2	99.5	GSM311284	Laser capture microdissected (LCM) general seed coat at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
15.9	99.5	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.4	99.5	GSM311279	Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
15.3	99.4	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.1	99.4	GSM284385	Arabidopsis GEP6	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
15.1	99.4	GSM311278	Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
14.3	99.4	GSM311274	Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
12.7	99.3	GSM184917	Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
12.5	99.3	GSM284388	Arabidopsis GMPE1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
12.4	99.3	GSM311290	Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
12.2	99.3	GSM184924	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
12.0	99.3	GSM184551	Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
11.4	99.3	GSM284386	Arabidopsis GSUS3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
11.2	99.2	GSM284389	Arabidopsis GMPE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
10.6	99.2	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
10.1	99.2	GSM311283	Laser capture microdissected (LCM) general seed coat at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
10.0	99.2	GSM184900	Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
9.9	99.1	GSM311285	Laser capture microdissected (LCM) whole seed sections at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
9.4	99.1	E-ATMX-33-raw-cel-1562596197
9.2	99.1	GSM131690	ATGE_77_F	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
9.2	99.1	GSM131689	ATGE_77_E	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
8.7	99.0	GSM131688	ATGE_77_D	GSE5634	AtGenExpress: Developmental series (siliques and seeds)

Biological processes inferred to relate to the module

SF	Genes	GO ID	Process Name	Link to AmiGO
0.056	1	GO:0048316	The process whose specific outcome is the progression of the seed over time, from its formation to the mature structure. A seed is a propagating organ formed in the sexual reproductive cycle of gymnosperms and angiosperms, consisting of a protective coat enclosing an embryo and food reserves.
0.043	1	GO:0009809	The chemical reactions and pathways resulting in the formation of lignins, a class of polymers formed by the dehydrogenetive radical polymerization of various phenylpropanoid monomers.
0.016	1	GO:0055114	The process of removal or addition of one or more electrons with or without the concomitant removal or addition of a proton or protons.

KEGG PATHWAY inferred to related to the module

SF	Genes	KEGG ID	Pathway name	Link 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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