Co-expression analysis

Gene ID	At1g28680
Gene name	transferase family protein
Module size	5 genes
NF	0.71
%ile	89.8

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
1.00	100.0	1.00	At1g28680	839768	transferase family protein	F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PF	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)
0.86	93.1	0.87	At2g37040	818280	pal1 (Phe ammonia lyase 1)	encodes a protein similar to phenylalanine ammonia-lyase	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)
0.73	85.5	0.89	At2g40890	818686	CYP98A3 (cytochrome P450, family 98, subfamily A, polypeptide 3)	encodes coumarate 3-hydroxylase (C3H), a P450-dependent monooxygenase. Involved in lignin biosynthesis and flavonoid biosynthesis. Also affects the biosynthesis of coumarins such as scopoletin and scopolin as a branching-out-pathway from the phenylpropanoid acid level.	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	0.87	At2g30490	817599	C4H (CINNAMATE-4-HYDROXYLASE)	Encodes a cinnamate-4-hydroxylase.	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	0.87	At4g34050	829551	caffeoyl-CoA 3-O-methyltransferase, putative	F:caffeoyl-CoA O-methyltransferase activity;P:coumarin biosynthetic process, response to cadmium ion;C:cytosol;BOPMFA	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
221.2	100.0	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
197.8	100.0	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
166.8	100.0	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
136.8	99.9	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
60.4	99.8	GSM265425	Arabidopsis, root, longitudinal zone 4, standard conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
59.8	99.8	GSM265422	Arabidopsis, root, longitudinal zone 3, standard conditions, rep1	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
58.7	99.8	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
52.6	99.8	GSM265424	Arabidopsis, root, longitudinal zone 4, standard conditions, rep 1	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
43.0	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
42.2	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
26.7	99.7	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
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
25.3	99.6	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
23.9	99.6	GSM265433	Arabidopsis, root, longitudinal zone 4, -Fe conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
23.8	99.6	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.4	99.6	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
23.2	99.6	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.2	99.6	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.4	99.6	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
22.2	99.6	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
22.1	99.6	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.3	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
20.2	99.6	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.0	99.6	GSM131588	ATGE_35_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
19.9	99.6	GSM106914	opr3_JA_8 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
19.6	99.6	GSM265432	Arabidopsis, root, longitudinal zone 4, -Fe conditions, rep 1	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
19.5	99.6	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.9	99.5	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.7	99.5	GSM131589	ATGE_35_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
18.6	99.5	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.5	99.5	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.4	99.5	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.2	99.5	GSM106911	opr2_JA_2 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
17.9	99.5	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.8	99.5	GSM226552	Slice10JW	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
17.6	99.5	GSM131590	ATGE_35_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
17.4	99.5	GSM265423	Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
17.1	99.5	GSM265430	Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 1	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
16.2	99.5	GSM106909	opr3-JA_2 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
15.0	99.4	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.9	99.4	GSM106970	opr3_OPDA_22 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
14.7	99.4	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
14.3	99.4	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.3	99.4	GSM133126	S0_2H_B	GSE5688	AtGenExpress: Response to sulfate limitation
14.2	99.4	GSM179958	Arabidopsis roots, air treatment, replica 1	GSE7432	Ethylene and auxin interactions in the roots of Arabidopsis seedlings
13.8	99.4	GSM142634	MC002_ATH1_A4.3-dubos-6kc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
13.5	99.4	GSM142633	MC002_ATH1_A4.2-dubos-6kc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
12.8	99.3	GSM133138	S1500_2H_B	GSE5688	AtGenExpress: Response to sulfate limitation
12.5	99.3	GSM179960	Arabidopsis roots, ethylene treatment, replica 1	GSE7432	Ethylene and auxin interactions in the roots of Arabidopsis seedlings
12.5	99.3	GSM142627	MC002_ATH1_A2.2-dubos-wtc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
12.4	99.3	GSM106966	opr3_OPDA_8 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
12.4	99.3	GSM106969	opr3_OPDA_22 hrs_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
12.4	99.3	E-MEXP-1443-raw-cel-1581869803
12.3	99.3	GSM133139	S1500_4H_A	GSE5688	AtGenExpress: Response to sulfate limitation
12.3	99.3	GSM106912	opr3_JA 8hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
12.2	99.3	GSM106967	opr3_OPDA_22 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.5	99.3	GSM67086	Arabidopsis_Stigma02	GSE3056	Arabidopsis Pollination Study
11.4	99.3	GSM106910	opr3_JA_2 hrs_rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.4	99.3	GSM265413	Arabidopsis, whole roots, -Fe, replicate 3	GSE10496	Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)
11.4	99.3	GSM142628	MC002_ATH1_A2.3-dubos-wtc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.2	99.2	GSM226554	Slice12JW	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
11.0	99.2	GSM106934	opr3_OPDA_8 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.0	99.2	GSM179977	Arabidopsis ein2 mutant roots, IAA treatment, replica 1	GSE7432	Ethylene and auxin interactions in the roots of Arabidopsis seedlings
10.9	99.2	GSM226541	L11SB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
10.6	99.2	GSM133130	S0_8H_B	GSE5688	AtGenExpress: Response to sulfate limitation
10.5	99.2	GSM179971	Arabidopsis roots, mock treatment, replica 1	GSE7432	Ethylene and auxin interactions in the roots of Arabidopsis seedlings
10.5	99.2	GSM142642	MC002_ATH1_A7.2-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.4	99.2	GSM226553	Slice11JW	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
10.4	99.2	GSM106924	opr3_OPDA_2 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
10.4	99.2	GSM142643	MC002_ATH1_A7.3-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.3	99.2	E-MEXP-828-raw-cel-1156922485
10.3	99.2	GSM179963	Arabidopsis aux1 mutant roots, air treatment, replica 1	GSE7432	Ethylene and auxin interactions in the roots of Arabidopsis seedlings
10.2	99.2	GSM106828	opr3_0 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
10.2	99.2	E-MEXP-828-raw-cel-1156922509
10.1	99.2	GSM179973	Arabidopsis roots, IAA treatment, replica 1	GSE7432	Ethylene and auxin interactions in the roots of Arabidopsis seedlings
10.0	99.2	GSM142644	MC002_ATH1_A8.1-dubos-aih	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.5	99.1	GSM133125	S0_2H_A	GSE5688	AtGenExpress: Response to sulfate limitation
9.4	99.1	GSM106908	opr3_JA_0.5 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.4	99.1	GSM133135	S1500_24H_A	GSE5688	AtGenExpress: Response to sulfate limitation
9.2	99.1	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
9.2	99.1	GSM142626	MC002_ATH1_A2.1-dubos-wtc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.2	99.1	GSM184838	Arabidopsis, root, longitudinal zone 4, standard conditions, replicate 8	GSE7639	Expression analysis of root developmental zones after treatment with salt
9.2	99.1	GSM133121	S0_12H_A	GSE5688	AtGenExpress: Response to sulfate limitation
9.0	99.1	GSM106921	opr3_OPDA_0.5 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
8.9	99.0	GSM75521	slr-1 6h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
8.9	99.0	GSM142640	MC002_ATH1_A6.3-dubos-5kc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.8	99.0	GSM179975	Arabidopsis ein2 mutant roots, mock treatment, replica 1	GSE7432	Ethylene and auxin interactions in the roots of Arabidopsis seedlings
8.7	99.0	GSM133137	S1500_2H_A	GSE5688	AtGenExpress: Response to sulfate limitation
8.6	99.0	GSM133983	Birnbaum_1-13_StageIII-2_Rep2_ATH1	GSE5749	A gene expression map of the Arabidopsis root
8.6	99.0	GSM179978	Arabidopsis ein2 mutant roots, IAA treatment, replica 2	GSE7432	Ethylene and auxin interactions in the roots of Arabidopsis seedlings

Biological processes inferred to relate to the module

SF	Genes	GO ID	Process Name	Link to AmiGO
0.500	2	GO:0009805	The chemical reactions and pathways resulting in the formation of coumarins, a class of compounds derived from the phenylacrylic skeleton of cinnamic acids.
0.375	3	GO:0009699	The chemical reactions and pathways resulting in the formation of aromatic derivatives of trans-cinnamic acid.
0.222	1	GO:0009808	The chemical reactions and pathways involving lignins, a class of polymers of phenylpropanoid units.

KEGG PATHWAY inferred to related to the module

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.286	3	00941	Flavonoid biosynthesis
0.087	1	00960	Tropane, piperidine and pyridine alkaloid biosynthesis
0.085	3	00945	Stilbenoid, diarylheptanoid and gingerol biosynthesis
0.075	4	00940	Phenylpropanoid biosynthesis
0.047	2	00360	Phenylalanine metabolism

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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