Co-expression analysis

Gene ID	At3g03980
Gene name	short-chain dehydrogenase/reductase (SDR) family protein
Module size	5 genes
NF	0.45
%ile	63.2

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
0.42	53.9	1.00	At3g03980	819553	short-chain dehydrogenase/reductase (SDR) family protein	F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:unknown;BOMFPAV	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	0.88	At2g25870	817128	haloacid dehalogenase-like hydrolase family protein	F:hydrolase activity, catalytic activity;P:metabolic process;C:unknown;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	0.89	At5g63040	836424	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PB	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)
0.44	57.2	0.90	At3g13800	820592	metallo-beta-lactamase family protein	F:hydrolase activity, catalytic activity;P:metabolic process;C:chloroplast;OBPAFM	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)
0.22	17.5	0.89	At4g31400	829267	DNA-directed DNA polymerase/ damaged DNA binding	F:damaged DNA binding, DNA-directed DNA polymerase activity;P:DNA repair;C:unknown;MFPOB	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
196.3	100.0	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
106.1	99.9	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
102.6	99.9	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
78.8	99.9	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
61.5	99.8	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
50.6	99.8	GSM142653	MC002_ATH1_A11.1-dubos-mxh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
48.3	99.8	GSM142654	MC002_ATH1_A11.2-dubos-mxh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
47.0	99.8	GSM142655	MC002_ATH1_A11.3-dubos-mxh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
46.9	99.8	E-ATMX-31-raw-cel-1516948018
40.9	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
39.6	99.8	E-ATMX-31-raw-cel-1516947984
39.5	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.9	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
38.8	99.8	GSM133957	Fukuda_1-2_0B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
38.4	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.8	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.7	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.5	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.4	99.7	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.0	99.7	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.7	99.7	GSM265474	Arabidopsis, whole roots, -Fe, 72 hour, rep 2	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
32.7	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.7	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.7	99.7	GSM142644	MC002_ATH1_A8.1-dubos-aih	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
32.2	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.5	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.2	99.7	GSM265473	Arabidopsis, whole roots, -Fe, 72 hour, rep 1	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
30.4	99.7	E-ATMX-31-raw-cel-1516948001
30.2	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.5	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
27.6	99.7	GSM142673	SF001_ATH1_A3-Fille-ANGR4-12	GSE6155	Nutritional control of plant development: molecular analysis of the NO3- response pathway in Arabidopsis roots.
26.4	99.7	GSM142641	MC002_ATH1_A7.1-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
24.8	99.6	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.6	99.6	GSM265470	Arabidopsis, whole roots, -Fe, 24 hour, rep 2	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
23.7	99.6	GSM142643	MC002_ATH1_A7.3-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
23.5	99.6	GSM142642	MC002_ATH1_A7.2-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
23.4	99.6	GSM142646	MC002_ATH1_A8.3-dubos-aih	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
21.1	99.6	GSM265472	Arabidopsis, whole roots, -Fe, 48 hour, rep 2	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
20.0	99.6	E-MEXP-635-raw-cel-912819824
18.5	99.5	GSM142623	MC002_ATH1_A1.1-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
18.5	99.5	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
18.2	99.5	GSM265467	Arabidopsis, whole roots, -Fe, 12 hour, rep 1	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
17.9	99.5	GSM265471	Arabidopsis, whole roots, -Fe, 48 hour, rep 1	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
17.7	99.5	GSM142645	MC002_ATH1_A8.2-dubos-aih	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
17.2	99.5	GSM75516	slr-1 0h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
17.0	99.5	E-MEXP-635-raw-cel-912819840
16.6	99.5	GSM157315	Hammond_3-5_Potassium-starved-root_Rep1_ATH1	GSE6825	Differential gene expression patterns in potassium-starved and Caesium-treated plants
16.3	99.5	GSM265469	Arabidopsis, whole roots, -Fe, 24 hour, rep 1	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
15.7	99.5	GSM157327	Hammond_3-11_Potassium-starved-root_Rep2_ATH1	GSE6825	Differential gene expression patterns in potassium-starved and Caesium-treated plants
15.3	99.4	GSM75511	Col-0 6h MOCK replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
15.2	99.4	GSM157324	Hammond_3-17_Potassium-starved-root_Rep3_ATH1	GSE6825	Differential gene expression patterns in potassium-starved and Caesium-treated plants
15.1	99.4	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.8	99.4	GSM265466	Arabidopsis, whole roots, -Fe, 6 hour, rep 2	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
14.4	99.4	GSM142633	MC002_ATH1_A4.2-dubos-6kc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
14.4	99.4	GSM142634	MC002_ATH1_A4.3-dubos-6kc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
14.1	99.4	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.0	99.4	GSM176879	AWP_Control_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
14.0	99.4	GSM75517	slr-1 2h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
13.9	99.4	GSM142628	MC002_ATH1_A2.3-dubos-wtc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
13.9	99.4	GSM142626	MC002_ATH1_A2.1-dubos-wtc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
13.8	99.4	GSM133963	Fukuda_1-8_6B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
13.3	99.4	E-MEXP-722-raw-cel-1062243390
13.2	99.4	GSM142627	MC002_ATH1_A2.2-dubos-wtc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
13.1	99.4	GSM142670	SF002_ATH1_A8-Fille-ANGR4-12+dex	GSE6155	Nutritional control of plant development: molecular analysis of the NO3- response pathway in Arabidopsis roots.
13.0	99.4	GSM75518	slr-1 6h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
12.9	99.3	GSM75520	slr-1 2h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
12.5	99.3	GSM142647	MC002_ATH1_A9.1-dubos-aah	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
12.4	99.3	GSM265468	Arabidopsis, whole roots, -Fe, 12 hour, rep 2	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
12.2	99.3	GSM133960	Fukuda_1-5_4A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
11.6	99.3	GSM142649	MC002_ATH1_A9.3-dubos-aah	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.3	99.3	GSM75519	slr-1 0h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
11.3	99.3	GSM142624	MC002_ATH1_A1.2-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.2	99.2	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.0	99.2	GSM75515	Col-0 6h MOCK replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
11.0	99.2	GSM142728	CH001_ATH1_A007-Hampt-c4b	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
11.0	99.2	GSM133962	Fukuda_1-7_6A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
10.9	99.2	GSM142629	MC002_ATH1_A3.1-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.8	99.2	GSM265461	Arabidopsis, whole roots, standard conditions, rep 1	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
10.7	99.2	GSM133964	Fukuda_1-9_8A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
10.6	99.2	GSM142733	CH001_ATH1_A012-Hampt-c1c	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
10.6	99.2	GSM142648	MC002_ATH1_A9.2-dubos-aah	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.5	99.2	GSM142730	CH001_ATH1_A009-Hampt-wsc_repeat	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
10.4	99.2	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.1	99.2	GSM142631	MC002_ATH1_A3.3-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.8	99.1	GSM142729	CH001_ATH1_A008-Hampt-c1b	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
9.8	99.1	GSM142652	MC002_ATH1_A10.3-dubos-wth	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.3	99.1	GSM75513	Col-0 2h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
9.2	99.1	E-MEXP-637-raw-cel-913038965
9.2	99.1	E-MEXP-722-raw-cel-1062242948
9.2	99.1	GSM142625	MC002_ATH1_A1.3-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.2	99.1	GSM142732	CH001_ATH1_A011-Hampt-c4c	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
9.1	99.1	GSM133966	Fukuda_1-11_10A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.0	99.1	GSM133967	Fukuda_1-12_10B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
8.9	99.0	GSM75514	Col-0 6h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
8.6	99.0	E-MEXP-828-raw-cel-1156922296

Biological processes inferred to relate to the module

SF	Genes	GO ID	Process Name	Link to AmiGO
0.019	1	GO:0006281	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.

KEGG PATHWAY inferred to related to the module

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.071	1	00061	Fatty acid biosynthesis
0.065	1	01040	Biosynthesis of unsaturated fatty acids
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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