Co-expression analysis

Gene ID	At5g03680
Gene name	PTL (PETAL LOSS)
Module size	5 genes
NF	0.09
%ile	6.0

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
0.61	76.7	1.00	At5g03680	831757	PTL (PETAL LOSS)	Recessive mutations are defective in organ initiation and orientation in the second whorl. This gene encodes a trihelix transcription factor whose expression is limited to margins of floral and vegetative organs. Overexpression and double mutant analyses suggest that this gene is involved in limiting lateral growth of organs.	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	0.71	At3g04510	819607	LSH2 (LIGHT SENSITIVE HYPOCOTYLS 2)	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PM	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	0.75	At5g28490	832941	LSH1 (LIGHT-DEPENDENT SHORT HYPOCOTYLS 1)	Encodes a nuclear protein that mediates light regulation of seedling development in a phytochrome-dependent manner.	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)
0.04	0.9	0.70	At4g29080	829029	PAP2 (PHYTOCHROME-ASSOCIATED PROTEIN 2)	phytochrome-associated protein 2 (PAP2)	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)
0.04	0.9	0.69	At1g70510	843388	KNAT2 (KNOTTED-LIKE FROM ARABIDOPSIS THALIANA 2)	A member of class I knotted1-like homeobox gene family (together with KNAT1). Similar to the knotted1 (kn1) homeobox gene of maize. KNAT2 acts synergistically with cytokinins and antagonistically with ethylene based on ectopic expression studies in different mutant backgrounds and hormone treatments. In addition, KNAT2 is negatively regulated by AS and YABBY genes. KNAT2 is strongly expressed in the shoot apex of seedlings, while in mature plants the gene is primarily expressed in flowers and inflorescence stems.	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
65.1	99.8	GSM184917	Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
47.5	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.5	99.8	E-MEXP-546-raw-cel-863289586
44.6	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.7	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.4	99.7	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
34.0	99.7	GSM184916	Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
31.9	99.7	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
31.8	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.4	99.7	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
31.0	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.5	99.7	GSM184900	Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
30.2	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.9	99.7	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
29.6	99.7	GSM266673	Arabidopsis, root cells, endodermis and quiescent center, -Fe, replicate 2	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
29.2	99.7	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.1	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
28.2	99.7	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
27.5	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
26.0	99.7	GSM265431	Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
26.0	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.0	99.6	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.6	99.6	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.5	99.6	GSM266674	Arabidopsis, root cells, endodermis and quiescent center, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
24.5	99.6	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
23.5	99.6	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
22.7	99.6	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
22.4	99.6	GSM134457	St.Clair_1-82_294_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1	GSE5758	Expression Level Polymorphism Project (ELP) - Mt-0
22.3	99.6	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
21.9	99.6	GSM184898	Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
21.7	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.5	99.6	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.2	99.6	GSM133029	BC482-1	GSE5684	AtGenExpress: Pathogen Series: Response to Botrytis cinerea infection
20.0	99.6	GSM134518	Col-0_4day_red illumination_-lincomycin_rep2	GSE5759	red illumination w/o lincomycin
19.2	99.6	GSM134513	Col-0_4day_dark_-lincomycin_rep1	GSE5759	red illumination w/o lincomycin
19.1	99.6	GSM133985	Birnbaum_1-15_StageIII-4_Rep4_ATH1	GSE5749	A gene expression map of the Arabidopsis root
18.7	99.5	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.7	99.5	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
17.4	99.5	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.3	99.5	GSM184899	Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
17.2	99.5	GSM184918	Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
16.0	99.5	GSM142750	MJ001_ATH1_A1-jones-WT1	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
15.8	99.5	GSM134519	Col-0_4day_red illumination_+lincomycin_rep1	GSE5759	red illumination w/o lincomycin
15.8	99.5	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.7	99.5	GSM266672	Arabidopsis, root cells, endodermis and quiescent center, -Fe, replicate 1	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
15.5	99.5	GSM265430	Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 1	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
15.3	99.4	GSM134517	Col-0_4day_red illumination_-lincomycin_rep1	GSE5759	red illumination w/o lincomycin
14.6	99.4	GSM133030	BC482-2	GSE5684	AtGenExpress: Pathogen Series: Response to Botrytis cinerea infection
14.5	99.4	GSM134516	Col-0_4day_dark_+lincomycin_rep2	GSE5759	red illumination w/o lincomycin
13.8	99.4	GSM131207	AtGen_D-41_3-DS_REP3_ATH1	GSE5617	AtGenExpress: Light treatments
13.4	99.4	GSM131208	AtGen_D-42_3-FS_REP3_ATH1	GSE5617	AtGenExpress: Light treatments
13.3	99.4	GSM244455	Arabidopsis AtMYB30-ox_6 h_ Xanthomonas inoculated_biological rep1_exp1	GSE9674	Expression data from Arabidopsis plants misexpressing AtMYB30 after Xanthomonas inoculation at early timepoints
13.3	99.4	GSM134514	Col-0_4day_dark_-lincomycin_rep2	GSE5759	red illumination w/o lincomycin
13.1	99.4	GSM131210	AtGen_D-44_3-RS_REP3_ATH1	GSE5617	AtGenExpress: Light treatments
12.9	99.3	GSM128662	Underwood_1-15_Cor-5x10e7-10h_Rep3_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
12.7	99.3	GSM184895	Arabidopsis, root cells, cortex, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
12.7	99.3	GSM226537	L7SB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
12.6	99.3	GSM184896	Arabidopsis, root cells, cortex, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
12.5	99.3	GSM131211	AtGen_D-45_3-BS_REP3_ATH1	GSE5617	AtGenExpress: Light treatments
12.3	99.3	GSM131209	AtGen_D-43_3-PS_REP3_ATH1	GSE5617	AtGenExpress: Light treatments
12.3	99.3	GSM266670	Arabidopsis, root cells, cortex, -Fe, replicate 2	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
12.1	99.3	GSM133778	Lindsey_1-2_globular-apical_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.9	99.3	GSM142751	MJ001_ATH1_A2-jones-WT2	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
11.9	99.3	GSM142753	MJ001_ATH1_A4-jones-rh2	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
11.7	99.3	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
11.6	99.3	GSM131178	AtGen_D-10_1-FS_REP1_ATH1	GSE5617	AtGenExpress: Light treatments
11.5	99.3	GSM226549	Slice7JW	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
11.4	99.3	GSM266676	Arabidopsis, root cells, stele, -Fe, replicate 2	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
11.4	99.3	GSM131184	AtGen_D-16_1-WS_REP1_ATH1	GSE5617	AtGenExpress: Light treatments
11.3	99.3	GSM131212	AtGen_D-46_3-AS_REP3_ATH1	GSE5617	AtGenExpress: Light treatments
11.2	99.2	GSM75513	Col-0 2h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
10.8	99.2	GSM131183	AtGen_D-15_1-US_REP1_ATH1	GSE5617	AtGenExpress: Light treatments
10.5	99.2	GSM131214	AtGen_D-48_3-WS_REP3_ATH1	GSE5617	AtGenExpress: Light treatments
10.4	99.2	GSM134515	Col-0_4day_dark_+lincomycin_rep1	GSE5759	red illumination w/o lincomycin
10.3	99.2	GSM131182	AtGen_D-14_1-AS_REP1_ATH1	GSE5617	AtGenExpress: Light treatments
10.2	99.2	GSM75509	Col-0 2h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
10.2	99.2	GSM292081	pif1-2, dark sample, biological rep3	GSE11594	Expression data from dark grown Arabidopsis Wild type (Wt, col-o) and pif1-2 (At2g20810, Salk_072677) mutant seedlings
10.1	99.2	GSM131213	AtGen_D-47_3-US_REP3_ATH1	GSE5617	AtGenExpress: Light treatments
10.1	99.2	GSM131180	AtGen_D-12_1-RS_REP1_ATH1	GSE5617	AtGenExpress: Light treatments
10.0	99.2	GSM142845	MG001_ATH1_A26-Torres-8N3	GSE6176	Impact of Type III effectors on plant defense responses
10.0	99.2	GSM170897	Col-0 +ABA repl1	GSE7112	Abscisic acid effect on wild type and the abh1 mutant
10.0	99.2	GSM131199	AtGen_D-33_3-DL_REP3_ATH1	GSE5617	AtGenExpress: Light treatments
9.7	99.1	GSM131181	AtGen_D-13_1-BS_REP1_ATH1	GSE5617	AtGenExpress: Light treatments
9.6	99.1	GSM266669	Arabidopsis, root cells, cortex, -Fe, replicate 1	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
9.6	99.1	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.5	99.1	GSM131203	AtGen_D-37_3-BL_REP3_ATH1	GSE5617	AtGenExpress: Light treatments
9.5	99.1	GSM131202	AtGen_D-36_3-RL_REP3_ATH1	GSE5617	AtGenExpress: Light treatments
9.5	99.1	GSM133984	Birnbaum_1-14_StageIII-3_Rep3_ATH1	GSE5749	A gene expression map of the Arabidopsis root
9.4	99.1	E-MEXP-509-raw-cel-829148561
9.3	99.1	E-MEXP-1468-raw-cel-1591138820
9.2	99.1	GSM131196	AtGen_D-30_2-AS_REP2_ATH1	GSE5617	AtGenExpress: Light treatments
9.0	99.1	GSM131195	AtGen_D-29_2-BS_REP2_ATH1	GSE5617	AtGenExpress: Light treatments
8.9	99.0	GSM131179	AtGen_D-11_1-PS_REP1_ATH1	GSE5617	AtGenExpress: Light treatments
8.9	99.0	GSM131105	Broadley_1-3_A3-Bo-P2-phosphate-starved_Rep2_ATH1	GSE5614	Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study)
8.9	99.0	GSM131206	AtGen_D-40_3-WL_REP3_ATH1	GSE5617	AtGenExpress: Light treatments
8.8	99.0	GSM134520	Col-0_4day_red illumination _+lincomycin_rep2	GSE5759	red illumination w/o lincomycin
8.7	99.0	GSM131106	Broadley_1-4_A4-Bo-P3-phosphate-starved_Rep3_ATH1	GSE5614	Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study)
8.7	99.0	GSM131108	Broadley_1-6_A6-Bo+P3-nutrient-replete_Rep3_ATH1	GSE5614	Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study)
8.6	99.0	E-MEXP-509-raw-cel-829148525

Biological processes inferred to relate to the module

SF	Genes	GO ID	Process Name	Link to AmiGO
0.333	1	GO:0010094	The process by which a floral organ primordium acquires the carpel identity. Identity is considered to be the aggregate of characteristics by which a structure is recognized.
0.333	1	GO:0048498	The process that determines the orientation of petals with reference to the central axis.
0.250	1	GO:0046621	Any process that stops, prevents or reduces the frequency, rate or extent of growth of an organ of an organism.

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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