CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g17420

Gene name LOX3

Module size 5 genes

NF 0.55

%ile 76.0

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
0.38 46.7 1.00 At1g17420 838314 LOX3 Lipoxygenase O.I. H.G. S.X.
0.75 86.9 0.70 At1g15010 838066 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;PB O.I. H.G. S.X.
0.73 85.5 0.71 At2g27690 817315 CYP94C1 Encodes a CYP94C1. Has highest omega-hydroxylase activity with 9,10-epoxystearic acid, while also metabolized lauric acid (C12:0) and C18 unsaturated fatty acids. Gene expression is induced in response to wounding and jasmonic acid treatment. O.I. H.G. S.X.
0.67 81.6 0.71 At2g38240 818403 oxidoreductase, 2OG-Fe(II) oxygenase family protein F:oxidoreductase activity;P:response to salt stress;C:unknown;POBFM O.I. H.G. S.X.
0.33 38.1 0.70 At4g32800 829416 AP2 domain-containing transcription factor TINY, putative encodes a member of the DREB subfamily A-4 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 17 members in this subfamily including TINY. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.38	46.7	1.00	At1g17420	838314	LOX3	Lipoxygenase	O.I.	H.G.	S.X.
0.75	86.9	0.70	At1g15010	838066	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;PB	O.I.	H.G.	S.X.
0.73	85.5	0.71	At2g27690	817315	CYP94C1	Encodes a CYP94C1. Has highest omega-hydroxylase activity with 9,10-epoxystearic acid, while also metabolized lauric acid (C12:0) and C18 unsaturated fatty acids. Gene expression is induced in response to wounding and jasmonic acid treatment.	O.I.	H.G.	S.X.
0.67	81.6	0.71	At2g38240	818403	oxidoreductase, 2OG-Fe(II) oxygenase family protein	F:oxidoreductase activity;P:response to salt stress;C:unknown;POBFM	O.I.	H.G.	S.X.
0.33	38.1	0.70	At4g32800	829416	AP2 domain-containing transcription factor TINY, putative	encodes a member of the DREB subfamily A-4 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 17 members in this subfamily including TINY.	O.I.	H.G.	S.X.

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
112.2 99.9 GSM13779 Dexamethasone plus cycloheximide GSE911 Identification of LEAFY targets during reproductive transition
100.3 99.9 GSM13784 Cycloheximide - replicate GSE911 Identification of LEAFY targets during reproductive transition
99.7 99.9 E-MEXP-807-raw-cel-1173273252
95.7 99.9 GSM13783 Dexamethasone plus cycloheximide - replicate GSE911 Identification of LEAFY targets during reproductive transition
92.4 99.9 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
81.3 99.9 GSM13780 Cycloheximide GSE911 Identification of LEAFY targets during reproductive transition
63.2 99.8 E-MEXP-807-raw-cel-1173273144
48.0 99.8 E-MEXP-739-raw-cel-1099467339
44.8 99.8 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
43.4 99.8 GSM266667 Arabidopsis, root cells, columella root cap, -Fe, replicate 2 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
39.9 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
37.5 99.7 GSM266668 Arabidopsis, root cells, columella root cap, -Fe, replicate 3 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
37.3 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
37.1 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.7 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.2 99.7 E-MEXP-828-raw-cel-1156922342
35.7 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.1 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.0 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.1 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.5 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.1 99.7 E-MEXP-739-raw-cel-1099467384
30.7 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
30.5 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.9 99.7 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.8 99.7 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.7 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.8 99.7 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.5 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
26.0 99.7 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
25.7 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
22.5 99.6 E-MEXP-739-raw-cel-1099467393
21.9 99.6 E-MEXP-739-raw-cel-1099467321
21.5 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
20.0 99.6 GSM266666 Arabidopsis, root cells, columella root cap, -Fe, replicate 1 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
16.3 99.5 E-MEXP-739-raw-cel-1099467375
14.8 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
14.1 99.4 GSM142839 MG001_ATH1_A18-Torres-6N6 GSE6176 Impact of Type III effectors on plant defense responses
14.0 99.4 GSM142829 GM001_ATH1_A11-Torres-5N3 GSE6176 Impact of Type III effectors on plant defense responses
13.4 99.4 GSM142853 MG001_ATH1_A6-Torres-2N6 GSE6176 Impact of Type III effectors on plant defense responses
12.4 99.3 E-MEXP-807-raw-cel-1173273088
12.4 99.3 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
11.4 99.3 GSM131281 AtGen_6-1621_Cold(4°C)-Roots-24.0h_Rep1 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
11.3 99.3 E-ATMX-13-raw-cel-1556149807
10.8 99.2 GSM131127 AtGen_B-13_1-6-4_REP1_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
10.8 99.2 GSM131139 AtGen_B-25_2-4-4_REP2_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
10.6 99.2 GSM184893 Arabidopsis, root cells, columella root cap, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
10.6 99.2 E-MEXP-807-raw-cel-1173273116
10.4 99.2 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
10.2 99.2 GSM131111 AtGen_B-39_3-4-4_REP3_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
10.0 99.2 GSM184480 Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
10.0 99.2 E-ATMX-13-raw-cel-1556149791
10.0 99.2 GSM133758 Lindsey_1-11_heart-stage-root_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.8 99.1 GSM184481 Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.8 99.1 GSM184477 Lateral Root Cap root cells 2hr KCl control treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.6 99.1 E-MEXP-739-raw-cel-1099467330
9.3 99.1 E-ATMX-13-raw-cel-1556149727
9.2 99.1 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.1 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
9.1 99.1 GSM131113 AtGen_B-41_3-6-4_REP3_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
8.7 99.0 GSM142852 MG001_ATH1_A5-Torres-2N3 GSE6176 Impact of Type III effectors on plant defense responses
8.6 99.0 E-ATMX-13-raw-cel-1556149855
8.6 99.0 GSM134514 Col-0_4day_dark_-lincomycin_rep2 GSE5759 red illumination w/o lincomycin

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
112.2	99.9	GSM13779	Dexamethasone plus cycloheximide	GSE911	Identification of LEAFY targets during reproductive transition
100.3	99.9	GSM13784	Cycloheximide - replicate	GSE911	Identification of LEAFY targets during reproductive transition
99.7	99.9	E-MEXP-807-raw-cel-1173273252
95.7	99.9	GSM13783	Dexamethasone plus cycloheximide - replicate	GSE911	Identification of LEAFY targets during reproductive transition
92.4	99.9	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
81.3	99.9	GSM13780	Cycloheximide	GSE911	Identification of LEAFY targets during reproductive transition
63.2	99.8	E-MEXP-807-raw-cel-1173273144
48.0	99.8	E-MEXP-739-raw-cel-1099467339
44.8	99.8	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
43.4	99.8	GSM266667	Arabidopsis, root cells, columella root cap, -Fe, replicate 2	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
39.9	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
37.5	99.7	GSM266668	Arabidopsis, root cells, columella root cap, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
37.3	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
37.1	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.7	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.2	99.7	E-MEXP-828-raw-cel-1156922342
35.7	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.1	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.0	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.1	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.5	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.1	99.7	E-MEXP-739-raw-cel-1099467384
30.7	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
30.5	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.9	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.8	99.7	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.7	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.8	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.5	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
26.0	99.7	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
25.7	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
22.5	99.6	E-MEXP-739-raw-cel-1099467393
21.9	99.6	E-MEXP-739-raw-cel-1099467321
21.5	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
20.0	99.6	GSM266666	Arabidopsis, root cells, columella root cap, -Fe, replicate 1	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
16.3	99.5	E-MEXP-739-raw-cel-1099467375
14.8	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
14.1	99.4	GSM142839	MG001_ATH1_A18-Torres-6N6	GSE6176	Impact of Type III effectors on plant defense responses
14.0	99.4	GSM142829	GM001_ATH1_A11-Torres-5N3	GSE6176	Impact of Type III effectors on plant defense responses
13.4	99.4	GSM142853	MG001_ATH1_A6-Torres-2N6	GSE6176	Impact of Type III effectors on plant defense responses
12.4	99.3	E-MEXP-807-raw-cel-1173273088
12.4	99.3	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
11.4	99.3	GSM131281	AtGen_6-1621_Cold(4°C)-Roots-24.0h_Rep1	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
11.3	99.3	E-ATMX-13-raw-cel-1556149807
10.8	99.2	GSM131127	AtGen_B-13_1-6-4_REP1_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
10.8	99.2	GSM131139	AtGen_B-25_2-4-4_REP2_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
10.6	99.2	GSM184893	Arabidopsis, root cells, columella root cap, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
10.6	99.2	E-MEXP-807-raw-cel-1173273116
10.4	99.2	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
10.2	99.2	GSM131111	AtGen_B-39_3-4-4_REP3_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
10.0	99.2	GSM184480	Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.0	99.2	E-ATMX-13-raw-cel-1556149791
10.0	99.2	GSM133758	Lindsey_1-11_heart-stage-root_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.8	99.1	GSM184481	Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.8	99.1	GSM184477	Lateral Root Cap root cells 2hr KCl control treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.6	99.1	E-MEXP-739-raw-cel-1099467330
9.3	99.1	E-ATMX-13-raw-cel-1556149727
9.2	99.1	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.1	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
9.1	99.1	GSM131113	AtGen_B-41_3-6-4_REP3_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
8.7	99.0	GSM142852	MG001_ATH1_A5-Torres-2N3	GSE6176	Impact of Type III effectors on plant defense responses
8.6	99.0	E-ATMX-13-raw-cel-1556149855
8.6	99.0	GSM134514	Col-0_4day_dark_-lincomycin_rep2	GSE5759	red illumination w/o lincomycin

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.111 1 GO:0040007 The increase in size or mass of an entire organism, a part of an organism or a cell.
0.071 1 GO:0009695 The chemical reactions and pathways resulting in the formation of jasmonic acid, a fatty acid derivative.
0.053 1 GO:0009620 A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a fungus.

SF	Genes	GO ID	Process Name
0.111	1	GO:0040007	The increase in size or mass of an entire organism, a part of an organism or a cell.
0.071	1	GO:0009695	The chemical reactions and pathways resulting in the formation of jasmonic acid, a fatty acid derivative.
0.053	1	GO:0009620	A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a fungus.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.059 1 00592 alpha-Linolenic acid metabolism
0.006 1 01070 Biosynthesis of plant hormones
0.002 1 01100 Metabolic pathways

SF	Genes	KEGG ID	Pathway name
0.059	1	00592	alpha-Linolenic acid metabolism
0.006	1	01070	Biosynthesis of plant hormones
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

Back to the CoP portal site

Back to the KAGIANA project homepage

Gene ID	At1g17420
Gene name	LOX3
Module size	5 genes
NF	0.55
%ile	76.0

Co-expression analysis

Gene ID At1g17420 Gene name LOX3 Module size 5 genes NF 0.55 %ile 76.0

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 More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Biological processes inferred to relate to the module

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG0.059100592alpha-Linolenic acid metabolism0.006101070Biosynthesis of plant hormones0.002101100Metabolic pathways

Inter-species module comparison

Select a plant to compare co-expressed genes between species.Glycine_maxHordeum_vulgareOryza_sativaPopulus_trichocarpaTriticum_aestivumVitis_viniferaZea_mays

Gene ID At1g17420

Gene name LOX3

Module size 5 genes

NF 0.55

%ile 76.0

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

SF Genes KEGG ID Pathway name Link to KEGG
0.059 1 00592 alpha-Linolenic acid metabolism
0.006 1 01070 Biosynthesis of plant hormones
0.002 1 01100 Metabolic pathways

Select a plant to compare co-expressed genes between species.
Glycine_max
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays