Co-expression analysis

Gene ID	At5g02260
Gene name	ATEXPA9 (ARABIDOPSIS THALIANA EXPANSIN A9)
Module size	5 genes
NF	0.31
%ile	40.0

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
0.20	14.4	1.00	At5g02260	831736	ATEXPA9 (ARABIDOPSIS THALIANA EXPANSIN A9)	member of Alpha-Expansin Gene Family. Naming convention from the Expansin Working Group (Kende et al, 2004. Plant Mol Bio)	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)
0.57	73.8	0.66	At2g47780	819390	rubber elongation factor (REF) protein-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;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)
0.55	70.6	0.63	At5g67060	836841	HEC1 (HECATE 1)	F:transcription factor activity;P:transmitting tissue development, carpel formation, regulation of transcription;C:nucleus;PMBOFA	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)
0.40	50.8	0.62	At3g48700	824031	ATCXE13 (ARABIDOPSIS THALIANA CARBOXYESTERASE 13)	F:hydrolase activity;P:metabolic process;C:cellular_component unknown;BMOPFAV	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)
0.33	38.1	0.62	At3g21720	821726	ICL (ISOCITRATE LYASE)	Encodes a glyoxylate cycle enzyme isocitrate lyase (ICL).	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
159.6	99.9	GSM284389	Arabidopsis GMPE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
127.3	99.9	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
98.8	99.9	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
86.2	99.9	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
84.8	99.9	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
84.5	99.9	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
75.1	99.9	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
73.4	99.9	GSM284387	Arabidopsis GSUS4b	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
72.5	99.9	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.0	99.9	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
67.8	99.9	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
66.7	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
65.1	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
64.3	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
56.6	99.8	GSM284392	Arabidopsis GCE1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
56.4	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
55.6	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
53.3	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
50.5	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
46.2	99.8	GSM13784	Cycloheximide - replicate	GSE911	Identification of LEAFY targets during reproductive transition
45.3	99.8	GSM284390	Arabidopsis GPE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
44.7	99.8	GSM13779	Dexamethasone plus cycloheximide	GSE911	Identification of LEAFY targets during reproductive transition
43.7	99.8	GSM13780	Cycloheximide	GSE911	Identification of LEAFY targets during reproductive transition
43.6	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
42.3	99.8	GSM13783	Dexamethasone plus cycloheximide - replicate	GSE911	Identification of LEAFY targets during reproductive transition
41.8	99.8	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
41.6	99.8	GSM284386	Arabidopsis GSUS3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
40.9	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
40.3	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
40.1	99.8	GSM284394	Arabidopsis GCE3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
39.0	99.8	E-MEXP-807-raw-cel-1173273088
38.2	99.8	GSM311275	Laser capture microdissected (LCM) micropylar endosperm at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
35.2	99.7	E-MEXP-807-raw-cel-1173273223
32.5	99.7	GSM131325	AtGen_6-3521_Saltstress-Roots-12.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
32.0	99.7	GSM131321	AtGen_6-3421_Saltstress-Roots-6.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
31.9	99.7	E-MEXP-807-raw-cel-1173273116
31.3	99.7	E-MEXP-807-raw-cel-1173273252
31.2	99.7	E-MEXP-807-raw-cel-1173273196
31.1	99.7	GSM311276	Laser capture microdissected (LCM) micropylar endospermr at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
31.0	99.7	GSM284393	Arabidopsis GCE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
30.7	99.7	GSM284388	Arabidopsis GMPE1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
30.5	99.7	E-MEXP-807-raw-cel-1173273170
29.3	99.7	E-MEXP-807-raw-cel-1173273060
29.0	99.7	GSM131322	AtGen_6-3422_Saltstress-Roots-6.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
29.0	99.7	GSM184893	Arabidopsis, root cells, columella root cap, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
27.7	99.7	E-MEXP-807-raw-cel-1173273144
27.1	99.7	E-MEXP-807-raw-cel-1173272948
26.6	99.7	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
26.5	99.7	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
21.6	99.6	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
21.6	99.6	GSM131318	AtGen_6-3322_Saltstress-Roots-3.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
21.2	99.6	GSM131317	AtGen_6-3321_Saltstress-Roots-3.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
20.4	99.6	GSM131329	AtGen_6-3621_Saltstress-Roots-24.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
19.8	99.6	GSM266668	Arabidopsis, root cells, columella root cap, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
18.1	99.5	GSM184520	Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
17.3	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
15.9	99.5	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
15.6	99.5	GSM184912	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
15.3	99.4	GSM131330	AtGen_6-3622_Saltstress-Roots-24.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
14.5	99.4	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
14.1	99.4	GSM184894	Arabidopsis, root cells, columella root cap, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
13.5	99.4	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
12.1	99.3	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.9	99.3	GSM133776	Lindsey_1-1_globular-apical_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.6	99.3	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.5	99.3	GSM184892	Arabidopsis, root cells, columella root cap, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
11.3	99.3	GSM184909	Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
11.0	99.2	GSM184530	Stele root cells 2hr continuous KNO3 treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.6	99.2	GSM311280	Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
10.3	99.2	GSM147963	WT Globular Stage Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
9.9	99.1	GSM184519	Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.9	99.1	GSM147965	lec1-1 Globular Stage Seed 1	GSE1051	Seed development in LEAFY COTYLEDON1 mutants
9.7	99.1	GSM184516	Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.4	99.1	GSM184521	Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.0	99.1	GSM147964	WT Globular Stage Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
8.7	99.0	GSM184908	Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
8.6	99.0	GSM184910	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt

Biological processes inferred to relate to the module

SF	Genes	GO ID	Process Name	Link to AmiGO
0.250	1	GO:0010500	The process whose specific outcome is the progression of the transmitting tract over time, from its formation to the mature structure. The transmitting tissue is the tissue in the style of a carpel through which the pollen tube grows; it connects the stigma and the inside of ovary.
0.250	1	GO:0048462	The process that gives rise to the carpel. This process pertains to the initial formation of a structure from unspecified parts.
0.200	1	GO:0019752	The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).

KEGG PATHWAY inferred to related to the module

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.054	1	00630	Glyoxylate and dicarboxylate metabolism
0.002	1	01100	Metabolic pathways

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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