Co-expression analysis

Gene ID	At5g12940
Gene name	leucine-rich repeat family protein
Module size	5 genes
NF	0.58
%ile	79.3

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
0.50	65.3	1.00	At5g12940	831134	leucine-rich repeat family protein	F:protein binding;P:signal transduction;C:endomembrane system;PMOBFA	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)
0.89	94.6	0.80	At1g02810	838078	pectinesterase family protein	F:enzyme inhibitor activity, pectinesterase activity;P:cell wall modification;C:endomembrane system, cell wall, plant-type cell wall;PBFMO	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)
0.75	86.9	0.76	At5g59070	836024	glycosyl transferase family 1 protein	F:transferase activity, transferring glycosyl groups;P:biosynthetic process;C:endomembrane system;BOAPMF	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)
0.67	81.6	0.79	At2g45400	819146	BEN1	involved in the regulation of brassinosteroid metabolic pathway	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	0.74	At4g00080	828192	UNE11 (unfertilized embryo sac 11)	F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:double fertilization forming a zygote and endosperm;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)

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
67.8	99.9	GSM265423	Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
43.5	99.8	GSM284384	Arabidopsis GEP5	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
31.9	99.7	GSM157323	Hammond_3-16_Control-root_Rep3_ATH1	GSE6825	Differential gene expression patterns in potassium-starved and Caesium-treated plants
31.2	99.7	E-MEXP-1592-raw-cel-1617526848
27.3	99.7	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
26.7	99.7	E-MEXP-1592-raw-cel-1617526912
25.9	99.7	E-MEXP-1592-raw-cel-1617526880
25.0	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
24.9	99.6	E-MEXP-1592-raw-cel-1617526944
23.5	99.6	GSM142725	CH001_ATH1_A004-Hampt-c1a	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
23.4	99.6	GSM62694	Columbia flowers_stage 1-10	GSE2848	Auxin Response Factor mediated flower gene expression
23.4	99.6	GSM142732	CH001_ATH1_A011-Hampt-c4c	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
23.4	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
23.4	99.6	GSM142723	CH001_ATH1_A002-Hampt-aka	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
21.9	99.6	GSM142729	CH001_ATH1_A008-Hampt-c1b	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
21.9	99.6	GSM47019	Ler 9	GSE2473	Small RNA biogenesis mutants
21.8	99.6	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.0	99.6	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.0	99.6	GSM157315	Hammond_3-5_Potassium-starved-root_Rep1_ATH1	GSE6825	Differential gene expression patterns in potassium-starved and Caesium-treated plants
20.6	99.6	E-MEXP-1592-raw-cel-1617526976
20.3	99.6	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.9	99.6	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
19.8	99.6	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
19.7	99.6	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.6	99.6	GSM284387	Arabidopsis GSUS4b	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
19.4	99.6	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
19.0	99.5	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.6	99.5	GSM142730	CH001_ATH1_A009-Hampt-wsc_repeat	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
18.4	99.5	GSM62698	arf6/arf6 ARF8/arf8 flowers_stage 1-10	GSE2848	Auxin Response Factor mediated flower gene expression
18.4	99.5	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.4	99.5	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.3	99.5	GSM142724	CH001_ATH1_A003-Hampt-c4a_repeat	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
18.2	99.5	GSM253199	Nontransgenic(ga1-3rgargl2)-DEX-REP1	GSE10019	Identification of RGA downstream genes by using steroid-inducible system
18.2	99.5	GSM253201	Nontransgenic(ga1-3rgargl2)-DEX-REP3	GSE10019	Identification of RGA downstream genes by using steroid-inducible system
18.1	99.5	GSM311287	Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
17.0	99.5	E-MEXP-828-raw-cel-1156922905
16.9	99.5	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.5	99.5	GSM311288	Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
16.4	99.5	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.2	99.5	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.2	99.5	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.2	99.5	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.0	99.5	E-MEXP-849-raw-cel-1181980958
15.9	99.5	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.8	99.5	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.4	99.5	GSM128732	Hennig_1-4_flower-buds-CK_021114_1_B_Rep2_ATH1	GSE5526	Transcriptional Programs of Early Reproductive Stages in Arabidopsis
15.2	99.4	GSM231204	chl1 at T0.5, biological rep3	GSE9148	Expression data of 10-day-old wild-type and chl1-5 plants exposed to 25 mM nitrate for 0h or 0.5h
14.8	99.4	GSM231198	wild-type at T0.5, biological rep3	GSE9148	Expression data of 10-day-old wild-type and chl1-5 plants exposed to 25 mM nitrate for 0h or 0.5h
14.6	99.4	GSM284395	Arabidopsis GPSc1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
14.5	99.4	E-MEXP-849-raw-cel-1181980966
14.4	99.4	GSM142721	CH001_ATH1_A001-Hampt-wsa	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
14.2	99.4	GSM142728	CH001_ATH1_A007-Hampt-c4b	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
13.8	99.4	GSM232889	Wt.3-1.0	GSE9201	Identification of genes responding to the activity of the Arabidopsis cytochrome P450 KLUH/CYP78A5
13.8	99.4	GSM133891	Schroeder_1-3_JS45-control-48h_Rep1_ATH1	GSE5744	Response to potassium starvation in roots
13.8	99.4	GSM131579	ATGE_32_A2	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
13.7	99.4	GSM131580	ATGE_32_B2	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
13.7	99.4	GSM157314	Hammond_3-4_Control-root_Rep1_ATH1	GSE6825	Differential gene expression patterns in potassium-starved and Caesium-treated plants
13.5	99.4	GSM75510	Col-0 6h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
13.3	99.4	GSM253200	Nontransgenic(ga1-3rgargl2)-DEX-REP2	GSE10019	Identification of RGA downstream genes by using steroid-inducible system
13.3	99.4	GSM131581	ATGE_32_C2	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
13.1	99.4	GSM47018	Ler 8	GSE2473	Small RNA biogenesis mutants
12.7	99.3	GSM311273	Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
12.7	99.3	E-MEXP-849-raw-cel-1181980910
12.6	99.3	GSM231203	chl1 at T0.5, biological rep2	GSE9148	Expression data of 10-day-old wild-type and chl1-5 plants exposed to 25 mM nitrate for 0h or 0.5h
12.3	99.3	GSM62702	arf6 arf8 flowers_stage 1-10	GSE2848	Auxin Response Factor mediated flower gene expression
12.3	99.3	E-MEXP-1592-raw-cel-1617526824
11.8	99.3	E-MEXP-849-raw-cel-1181980942
11.6	99.3	GSM253197	RGA-GR-MOCK-REP3	GSE10019	Identification of RGA downstream genes by using steroid-inducible system
11.2	99.2	E-MEXP-1592-raw-cel-1617526888
11.2	99.2	E-MEXP-849-raw-cel-1181980934
11.1	99.2	E-MEXP-1592-raw-cel-1617526816
11.1	99.2	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
11.0	99.2	E-MEXP-849-raw-cel-1181980894
11.0	99.2	E-MEXP-849-raw-cel-1181980950
10.9	99.2	GSM253194	RGA-GR-DEX-REP1	GSE10019	Identification of RGA downstream genes by using steroid-inducible system
10.9	99.2	GSM131639	ATGE_92_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
10.8	99.2	GSM253195	RGA-GR-MOCK-REP2	GSE10019	Identification of RGA downstream genes by using steroid-inducible system
10.7	99.2	GSM142726	CH001_ATH1_A005-Hampt-wsb_repeat	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
10.6	99.2	E-MEXP-1592-raw-cel-1617526952
10.6	99.2	GSM232886	Wt.4-3.90	GSE9201	Identification of genes responding to the activity of the Arabidopsis cytochrome P450 KLUH/CYP78A5
10.5	99.2	GSM232882	Mut.3-2.90	GSE9201	Identification of genes responding to the activity of the Arabidopsis cytochrome P450 KLUH/CYP78A5
10.3	99.2	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
10.3	99.2	E-MEXP-849-raw-cel-1181980974
10.3	99.2	E-MEXP-849-raw-cel-1181980902
10.3	99.2	E-MEXP-1592-raw-cel-1617526984
10.2	99.2	GSM284394	Arabidopsis GCE3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
10.2	99.2	GSM253193	RGA-GR-MOCK-REP1	GSE10019	Identification of RGA downstream genes by using steroid-inducible system
10.2	99.2	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
10.2	99.2	GSM184894	Arabidopsis, root cells, columella root cap, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
9.9	99.1	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
9.9	99.1	E-MEXP-1592-raw-cel-1617526856
9.9	99.1	GSM131621	ATGE_55_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.7	99.1	E-MEXP-849-raw-cel-1181980886
9.7	99.1	GSM131640	ATGE_92_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.7	99.1	E-MEXP-849-raw-cel-1181980918
9.6	99.1	GSM133752	Turner_A-6-Turne-WT-Top2_SLD	GSE5729	Role of COV in vascular patterning
9.5	99.1	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
9.4	99.1	GSM131623	ATGE_55_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.2	99.1	GSM131622	ATGE_55_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.2	99.1	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.0	99.1	GSM157327	Hammond_3-11_Potassium-starved-root_Rep2_ATH1	GSE6825	Differential gene expression patterns in potassium-starved and Caesium-treated plants
9.0	99.1	GSM231197	wild-type at T0.5, biological rep2	GSE9148	Expression data of 10-day-old wild-type and chl1-5 plants exposed to 25 mM nitrate for 0h or 0.5h
8.8	99.0	GSM131641	ATGE_92_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
8.7	99.0	GSM265425	Arabidopsis, root, longitudinal zone 4, standard conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
8.6	99.0	GSM47017	Ler 7	GSE2473	Small RNA biogenesis mutants

Biological processes inferred to relate to the module

SF	Genes	GO ID	Process Name	Link to AmiGO
0.333	1	GO:0010422	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of brassinosteroids.
0.182	1	GO:0016131	The chemical reactions and pathways involving brassinosteroids, any of a group of steroid derivatives that occur at very low concentrations in plant tissues and may have hormone-like effects.
0.071	1	GO:0009567	Fertilization where one of the two sperm nuclei from the pollen tube fuses with the egg nucleus to form a 2n zygote, and the other fuses with the two polar nuclei to form the 3n primary endosperm nucleus and then develops into the endosperm. The ploidy level of the 2n zygote and 3n primary endosperm nucleus is determined by the ploidy level of the parents involved. An example of this component is found in Arabidopsis thaliana.

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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