CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g78815

Gene name LSH7 (LIGHT SENSITIVE HYPOCOTYLS 7)

Module size 5 genes

NF 0.62

%ile 83.1

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
0.40 50.8 1.00 At1g78815 844218 LSH7 (LIGHT SENSITIVE HYPOCOTYLS 7) F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PM O.I. H.G. S.X.
0.80 89.8 0.75 At3g28360 822465 PGP16 (P-GLYCOPROTEIN 16) F:ATPase activity, coupled to transmembrane movement of substances;P:transport;C:integral to membrane;BOMAFPV O.I. H.G. S.X.
0.75 86.9 0.64 At1g21890 838791 nodulin MtN21 family protein F:unknown;P:unknown;C:membrane;BPOAM O.I. H.G. S.X.
0.67 81.6 0.88 At5g65040 836628 senescence-associated protein-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.46 59.8 0.70 At5g11930 831066 glutaredoxin family protein F:electron carrier activity, protein disulfide oxidoreductase activity;P:cell redox homeostasis;C:unknown;PMBO O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.40	50.8	1.00	At1g78815	844218	LSH7 (LIGHT SENSITIVE HYPOCOTYLS 7)	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PM	O.I.	H.G.	S.X.
0.80	89.8	0.75	At3g28360	822465	PGP16 (P-GLYCOPROTEIN 16)	F:ATPase activity, coupled to transmembrane movement of substances;P:transport;C:integral to membrane;BOMAFPV	O.I.	H.G.	S.X.
0.75	86.9	0.64	At1g21890	838791	nodulin MtN21 family protein	F:unknown;P:unknown;C:membrane;BPOAM	O.I.	H.G.	S.X.
0.67	81.6	0.88	At5g65040	836628	senescence-associated protein-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.46	59.8	0.70	At5g11930	831066	glutaredoxin family protein	F:electron carrier activity, protein disulfide oxidoreductase activity;P:cell redox homeostasis;C:unknown;PMBO	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
155.0 99.9 E-MEXP-1344-raw-cel-1559561683
133.0 99.9 E-MEXP-1344-raw-cel-1559561563
69.5 99.9 E-MEXP-1345-raw-cel-1559561199
54.4 99.8 E-MEXP-1345-raw-cel-1559561139
47.9 99.8 E-MEXP-1345-raw-cel-1559561169
42.7 99.8 E-MEXP-1344-raw-cel-1559561593
36.3 99.7 E-MEXP-1345-raw-cel-1559561289
29.7 99.7 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
29.2 99.7 E-MEXP-1344-raw-cel-1559561653
28.9 99.7 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
26.3 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
25.8 99.7 E-MEXP-1345-raw-cel-1559561229
22.3 99.6 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.2 99.6 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.1 99.6 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
22.0 99.6 E-MEXP-1344-raw-cel-1559561623
22.0 99.6 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
21.9 99.6 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
21.6 99.6 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.4 99.6 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
20.7 99.6 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.6 99.6 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.9 99.6 E-MEXP-1345-raw-cel-1559561259
19.2 99.6 E-MEXP-1344-raw-cel-1559561713
19.0 99.5 E-ATMX-35-raw-cel-1574334848
18.3 99.5 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.2 99.5 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.9 99.5 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.8 99.5 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.8 99.5 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
17.8 99.5 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.5 99.5 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.3 99.5 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.9 99.5 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
15.2 99.4 GSM128683 Underwood_1-36_E.coli-0157-H7-10e8-7h_Rep2_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
15.2 99.4 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.2 99.4 E-ATMX-35-raw-cel-1574334880
14.9 99.4 GSM128661 Underwood_1-14_Cor-5x10e7-10h_Rep2_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
14.2 99.4 GSM134208 Murray_3-4_D7-GROWTH_Rep1_ATH1 GSE5750 Growth of suspension-cultured cells
13.9 99.4 GSM128677 Underwood_1-30_DC3000-10e8-7h_Rep3_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
13.0 99.4 E-ATMX-35-raw-cel-1574334864
12.9 99.3 GSM142852 MG001_ATH1_A5-Torres-2N3 GSE6176 Impact of Type III effectors on plant defense responses
12.9 99.3 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
12.8 99.3 GSM142740 DH001_ATH1_A7-MPG1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
12.5 99.3 GSM128676 Underwood_1-29_DC3000-10e8-7h_Rep2_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
11.7 99.3 GSM142853 MG001_ATH1_A6-Torres-2N6 GSE6176 Impact of Type III effectors on plant defense responses
11.7 99.3 GSM128660 Underwood_1-13_Cor-5x10e7-10h_Rep1_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
11.6 99.3 E-MEXP-285-raw-cel-440782725
11.3 99.3 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
10.9 99.2 GSM128684 Underwood_1-37_E.coli-0157-H7-10e8-7h_Rep3_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
10.7 99.2 GSM128687 Underwood_1-40_E.coli-TUV86-2-fliC-10e8-7h_Rep3_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
10.6 99.2 GSM128685 Underwood_1-38_E.coli-TUV86-2-fliC-10e8-7h_Rep1_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
10.5 99.2 GSM239253 CaMV::DME pollen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
10.5 99.2 GSM239251 Columbia glabrous (C24) wild type pollen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
10.4 99.2 GSM244448 Arabidopsis wild-type_6 h_ Xanthomonas inoculated_biological rep1_exp1 GSE9674 Expression data from Arabidopsis plants misexpressing AtMYB30 after Xanthomonas inoculation at early timepoints
9.8 99.1 E-MEXP-285-raw-cel-440782791
9.7 99.1 GSM131637 ATGE_73_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
9.4 99.1 GSM131638 ATGE_73_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
9.4 99.1 GSM142849 MG001_ATH1_A2-Torres-1N3 GSE6176 Impact of Type III effectors on plant defense responses
9.4 99.1 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
9.2 99.1 E-MEXP-1094-raw-cel-1379507273
9.0 99.1 GSM142850 MG001_ATH1_A3-Torres-1N6 GSE6176 Impact of Type III effectors on plant defense responses
9.0 99.1 GSM142851 MG001_ATH1_A4-Torres-2N1 GSE6176 Impact of Type III effectors on plant defense responses
8.6 99.0 GSM131636 ATGE_73_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
155.0	99.9	E-MEXP-1344-raw-cel-1559561683
133.0	99.9	E-MEXP-1344-raw-cel-1559561563
69.5	99.9	E-MEXP-1345-raw-cel-1559561199
54.4	99.8	E-MEXP-1345-raw-cel-1559561139
47.9	99.8	E-MEXP-1345-raw-cel-1559561169
42.7	99.8	E-MEXP-1344-raw-cel-1559561593
36.3	99.7	E-MEXP-1345-raw-cel-1559561289
29.7	99.7	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
29.2	99.7	E-MEXP-1344-raw-cel-1559561653
28.9	99.7	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
26.3	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
25.8	99.7	E-MEXP-1345-raw-cel-1559561229
22.3	99.6	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.2	99.6	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.1	99.6	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
22.0	99.6	E-MEXP-1344-raw-cel-1559561623
22.0	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.9	99.6	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.6	99.6	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.4	99.6	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
20.7	99.6	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.6	99.6	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.9	99.6	E-MEXP-1345-raw-cel-1559561259
19.2	99.6	E-MEXP-1344-raw-cel-1559561713
19.0	99.5	E-ATMX-35-raw-cel-1574334848
18.3	99.5	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.2	99.5	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.9	99.5	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.8	99.5	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.8	99.5	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
17.8	99.5	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.5	99.5	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.3	99.5	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.9	99.5	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
15.2	99.4	GSM128683	Underwood_1-36_E.coli-0157-H7-10e8-7h_Rep2_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
15.2	99.4	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.2	99.4	E-ATMX-35-raw-cel-1574334880
14.9	99.4	GSM128661	Underwood_1-14_Cor-5x10e7-10h_Rep2_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
14.2	99.4	GSM134208	Murray_3-4_D7-GROWTH_Rep1_ATH1	GSE5750	Growth of suspension-cultured cells
13.9	99.4	GSM128677	Underwood_1-30_DC3000-10e8-7h_Rep3_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
13.0	99.4	E-ATMX-35-raw-cel-1574334864
12.9	99.3	GSM142852	MG001_ATH1_A5-Torres-2N3	GSE6176	Impact of Type III effectors on plant defense responses
12.9	99.3	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
12.8	99.3	GSM142740	DH001_ATH1_A7-MPG1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
12.5	99.3	GSM128676	Underwood_1-29_DC3000-10e8-7h_Rep2_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
11.7	99.3	GSM142853	MG001_ATH1_A6-Torres-2N6	GSE6176	Impact of Type III effectors on plant defense responses
11.7	99.3	GSM128660	Underwood_1-13_Cor-5x10e7-10h_Rep1_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
11.6	99.3	E-MEXP-285-raw-cel-440782725
11.3	99.3	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
10.9	99.2	GSM128684	Underwood_1-37_E.coli-0157-H7-10e8-7h_Rep3_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
10.7	99.2	GSM128687	Underwood_1-40_E.coli-TUV86-2-fliC-10e8-7h_Rep3_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
10.6	99.2	GSM128685	Underwood_1-38_E.coli-TUV86-2-fliC-10e8-7h_Rep1_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
10.5	99.2	GSM239253	CaMV::DME pollen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
10.5	99.2	GSM239251	Columbia glabrous (C24) wild type pollen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
10.4	99.2	GSM244448	Arabidopsis wild-type_6 h_ Xanthomonas inoculated_biological rep1_exp1	GSE9674	Expression data from Arabidopsis plants misexpressing AtMYB30 after Xanthomonas inoculation at early timepoints
9.8	99.1	E-MEXP-285-raw-cel-440782791
9.7	99.1	GSM131637	ATGE_73_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.4	99.1	GSM131638	ATGE_73_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.4	99.1	GSM142849	MG001_ATH1_A2-Torres-1N3	GSE6176	Impact of Type III effectors on plant defense responses
9.4	99.1	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
9.2	99.1	E-MEXP-1094-raw-cel-1379507273
9.0	99.1	GSM142850	MG001_ATH1_A3-Torres-1N6	GSE6176	Impact of Type III effectors on plant defense responses
9.0	99.1	GSM142851	MG001_ATH1_A4-Torres-2N1	GSE6176	Impact of Type III effectors on plant defense responses
8.6	99.0	GSM131636	ATGE_73_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.019 1 GO:0045454 Any process that maintains the redox environment of a cell or compartment within a cell.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.019	1	GO:0045454	Any process that maintains the redox environment of a cell or compartment within a cell.

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

Back to the KAGIANA project homepage

Gene ID	At1g78815
Gene name	LSH7 (LIGHT SENSITIVE HYPOCOTYLS 7)
Module size	5 genes
NF	0.62
%ile	83.1

Co-expression analysis

Gene ID At1g78815 Gene name LSH7 (LIGHT SENSITIVE HYPOCOTYLS 7) Module size 5 genes NF 0.62 %ile 83.1

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 AmiGO0.0191GO:0045454Any process that maintains the redox environment of a cell or compartment within a cell.

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 At1g78815

Gene name LSH7 (LIGHT SENSITIVE HYPOCOTYLS 7)

Module size 5 genes

NF 0.62

%ile 83.1

: 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
0.019 1 GO:0045454 Any process that maintains the redox environment of a cell or compartment within a cell.

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