CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g02550

Gene name LBD41 (LOB DOMAIN-CONTAINING PROTEIN 41)

Module size 10 genes

NF 0.83

%ile 95.8

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 At3g02550 821112 LBD41 (LOB DOMAIN-CONTAINING PROTEIN 41) F:unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.95 97.0 0.81 At3g10040 820165 transcription factor F:transcription factor activity;P:regulation of transcription;C:unknown;OMFPBVA O.I. H.G. S.X.
0.89 94.6 0.87 At4g10270 826619 wound-responsive family protein F:molecular_function unknown;P:response to wounding;C:unknown;P O.I. H.G. S.X.
0.89 94.6 0.89 At5g39890 833986 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO O.I. H.G. S.X.
0.84 91.9 0.76 At1g33055 840201 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. H.G. S.X.
0.82 90.9 0.74 At4g24110 828511 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM O.I. H.G. S.X.
0.78 88.6 0.86 At5g15120 831364 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO O.I. H.G. S.X.
0.74 86.1 0.82 At4g33560 829495 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. H.G. S.X.
0.73 85.5 0.74 At5g66985 836833 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.71 84.2 0.85 At3g27220 822341 kelch repeat-containing protein F:unknown;P:biological_process unknown;C:Golgi apparatus;MBOVPFA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
1.00	100.0	1.00	At3g02550	821112	LBD41 (LOB DOMAIN-CONTAINING PROTEIN 41)	F:unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.95	97.0	0.81	At3g10040	820165	transcription factor	F:transcription factor activity;P:regulation of transcription;C:unknown;OMFPBVA	O.I.	H.G.	S.X.
0.89	94.6	0.87	At4g10270	826619	wound-responsive family protein	F:molecular_function unknown;P:response to wounding;C:unknown;P	O.I.	H.G.	S.X.
0.89	94.6	0.89	At5g39890	833986	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO	O.I.	H.G.	S.X.
0.84	91.9	0.76	At1g33055	840201	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	H.G.	S.X.
0.82	90.9	0.74	At4g24110	828511	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM	O.I.	H.G.	S.X.
0.78	88.6	0.86	At5g15120	831364	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO	O.I.	H.G.	S.X.
0.74	86.1	0.82	At4g33560	829495	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	H.G.	S.X.
0.73	85.5	0.74	At5g66985	836833	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.71	84.2	0.85	At3g27220	822341	kelch repeat-containing protein	F:unknown;P:biological_process unknown;C:Golgi apparatus;MBOVPFA	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
60.8 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
59.1 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
58.3 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.2 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
54.6 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.8 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.4 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
50.5 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.6 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.6 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.4 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.6 99.8 GSM284395 Arabidopsis GPSc1 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
45.2 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
42.5 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
40.9 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.3 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.2 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
34.7 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
34.7 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.0 99.7 GSM131281 AtGen_6-1621_Cold(4°C)-Roots-24.0h_Rep1 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
29.9 99.7 GSM131282 AtGen_6-1622_Cold(4°C)-Roots-24.0h_Rep2 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
26.8 99.7 GSM131278 AtGen_6-1522_Cold(4°C)-Roots-12.0h_Rep2 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
26.2 99.7 GSM131277 AtGen_6-1521_Cold(4°C)-Roots-12.0h_Rep1 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
25.9 99.7 GSM311293 Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
21.9 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
20.2 99.6 E-MEXP-1094-raw-cel-1379507273
17.7 99.5 GSM284396 Arabidopsis GPSc2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
17.1 99.5 GSM142847 MG001_ATH1_A28-Torres-9N1 GSE6176 Impact of Type III effectors on plant defense responses
16.5 99.5 E-MEXP-1094-raw-cel-1379507313
14.8 99.4 GSM131111 AtGen_B-39_3-4-4_REP3_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
14.3 99.4 GSM131140 AtGen_B-26_2-5-4_REP2_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
14.0 99.4 GSM142835 MG001_ATH1_A13-Torres-4N1 GSE6176 Impact of Type III effectors on plant defense responses
13.2 99.4 GSM142833 MG001_ATH1_A10-Torres-5N1 GSE6176 Impact of Type III effectors on plant defense responses
12.9 99.3 GSM131112 AtGen_B-40_3-5-4_REP3_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
12.9 99.3 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
12.9 99.3 GSM131113 AtGen_B-41_3-6-4_REP3_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
12.7 99.3 GSM131139 AtGen_B-25_2-4-4_REP2_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
12.1 99.3 GSM131141 AtGen_B-27_2-6-4_REP2_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
11.4 99.3 E-MEXP-1443-raw-cel-1581869573
11.4 99.3 GSM142834 MG001_ATH1_A12-Torres-5N6 GSE6176 Impact of Type III effectors on plant defense responses
11.1 99.2 GSM128664 Underwood_1-18_Cor-hrpS-5x10e7-10h_Rep3_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
11.0 99.2 GSM128672 Underwood_1-27_hrpA-10e8-7h_Rep3_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
10.9 99.2 GSM142836 MG001_ATH1_A15-Torres-4N6 GSE6176 Impact of Type III effectors on plant defense responses
10.2 99.2 GSM311294 Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 2 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
10.0 99.2 E-ATMX-33-raw-cel-1562596241
9.6 99.1 GSM128673 Underwood_1-25_hrpA-10e8-7h_Rep1_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
9.5 99.1 GSM142848 MG001_ATH1_A29-Torres-9N3 GSE6176 Impact of Type III effectors on plant defense responses
9.2 99.1 GSM131126 AtGen_B-12_1-5-4_REP1_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
8.8 99.0 GSM131127 AtGen_B-13_1-6-4_REP1_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
8.6 99.0 GSM128686 Underwood_1-39_E.coli-TUV86-2-fliC-10e8-7h_Rep2_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
60.8	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
59.1	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
58.3	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.2	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
54.6	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.8	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.4	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
50.5	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.6	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.6	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.4	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.6	99.8	GSM284395	Arabidopsis GPSc1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
45.2	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
42.5	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
40.9	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.3	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.2	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
34.7	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
34.7	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.0	99.7	GSM131281	AtGen_6-1621_Cold(4°C)-Roots-24.0h_Rep1	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
29.9	99.7	GSM131282	AtGen_6-1622_Cold(4°C)-Roots-24.0h_Rep2	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
26.8	99.7	GSM131278	AtGen_6-1522_Cold(4°C)-Roots-12.0h_Rep2	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
26.2	99.7	GSM131277	AtGen_6-1521_Cold(4°C)-Roots-12.0h_Rep1	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
25.9	99.7	GSM311293	Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
21.9	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
20.2	99.6	E-MEXP-1094-raw-cel-1379507273
17.7	99.5	GSM284396	Arabidopsis GPSc2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
17.1	99.5	GSM142847	MG001_ATH1_A28-Torres-9N1	GSE6176	Impact of Type III effectors on plant defense responses
16.5	99.5	E-MEXP-1094-raw-cel-1379507313
14.8	99.4	GSM131111	AtGen_B-39_3-4-4_REP3_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
14.3	99.4	GSM131140	AtGen_B-26_2-5-4_REP2_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
14.0	99.4	GSM142835	MG001_ATH1_A13-Torres-4N1	GSE6176	Impact of Type III effectors on plant defense responses
13.2	99.4	GSM142833	MG001_ATH1_A10-Torres-5N1	GSE6176	Impact of Type III effectors on plant defense responses
12.9	99.3	GSM131112	AtGen_B-40_3-5-4_REP3_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
12.9	99.3	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
12.9	99.3	GSM131113	AtGen_B-41_3-6-4_REP3_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
12.7	99.3	GSM131139	AtGen_B-25_2-4-4_REP2_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
12.1	99.3	GSM131141	AtGen_B-27_2-6-4_REP2_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
11.4	99.3	E-MEXP-1443-raw-cel-1581869573
11.4	99.3	GSM142834	MG001_ATH1_A12-Torres-5N6	GSE6176	Impact of Type III effectors on plant defense responses
11.1	99.2	GSM128664	Underwood_1-18_Cor-hrpS-5x10e7-10h_Rep3_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
11.0	99.2	GSM128672	Underwood_1-27_hrpA-10e8-7h_Rep3_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
10.9	99.2	GSM142836	MG001_ATH1_A15-Torres-4N6	GSE6176	Impact of Type III effectors on plant defense responses
10.2	99.2	GSM311294	Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
10.0	99.2	E-ATMX-33-raw-cel-1562596241
9.6	99.1	GSM128673	Underwood_1-25_hrpA-10e8-7h_Rep1_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
9.5	99.1	GSM142848	MG001_ATH1_A29-Torres-9N3	GSE6176	Impact of Type III effectors on plant defense responses
9.2	99.1	GSM131126	AtGen_B-12_1-5-4_REP1_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
8.8	99.0	GSM131127	AtGen_B-13_1-6-4_REP1_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
8.6	99.0	GSM128686	Underwood_1-39_E.coli-TUV86-2-fliC-10e8-7h_Rep2_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.014 1 GO:0009611 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 indicating damage to the organism.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.014	1	GO:0009611	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 indicating damage to the 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

Back to the CoP portal site

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Gene ID	At3g02550
Gene name	LBD41 (LOB DOMAIN-CONTAINING PROTEIN 41)
Module size	10 genes
NF	0.83
%ile	95.8

Co-expression analysis

Gene ID At3g02550 Gene name LBD41 (LOB DOMAIN-CONTAINING PROTEIN 41) Module size 10 genes NF 0.83 %ile 95.8

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 More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO0.0141GO:0009611A 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 indicating damage to the organism.

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG

Inter-species module comparison

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

Gene ID At3g02550

Gene name LBD41 (LOB DOMAIN-CONTAINING PROTEIN 41)

Module size 10 genes

NF 0.83

%ile 95.8

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

SF Genes GO ID Process Name Link to AmiGO
0.014 1 GO:0009611 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 indicating damage to the organism.

SF Genes KEGG ID Pathway name Link to KEGG

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