CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At4g00390

Gene name transcription regulator

Module size 5 genes

NF 0.37

%ile 50.6

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
0.44 57.2 1.00 At4g00390 828200 transcription regulator F:transcription regulator activity;P:unknown;C:nucleolus;OMBFPVA O.I. H.G. S.X.
0.40 50.8 0.62 At2g28680 817417 cupin family protein F:nutrient reservoir activity;P:biological_process unknown;C:cellular_component unknown;PMO O.I. H.G. S.X.
0.36 43.6 0.50 At3g10100 820171 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.35 41.6 0.72 At1g31400 840030 meprin and TRAF homology domain-containing protein / MATH domain-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POF O.I. H.G. S.X.
0.33 38.1 0.56 At3g24250 822012 glycine-rich protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BMPOFVA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.44	57.2	1.00	At4g00390	828200	transcription regulator	F:transcription regulator activity;P:unknown;C:nucleolus;OMBFPVA	O.I.	H.G.	S.X.
0.40	50.8	0.62	At2g28680	817417	cupin family protein	F:nutrient reservoir activity;P:biological_process unknown;C:cellular_component unknown;PMO	O.I.	H.G.	S.X.
0.36	43.6	0.50	At3g10100	820171	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.35	41.6	0.72	At1g31400	840030	meprin and TRAF homology domain-containing protein / MATH domain-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POF	O.I.	H.G.	S.X.
0.33	38.1	0.56	At3g24250	822012	glycine-rich protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BMPOFVA	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
131.1 99.9 GSM284391 Arabidopsis GPE3 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
102.5 99.9 GSM142904 WW002_ATH1_A1-willa-CON-REP2 GSE6181 Assembly of the cell wall pectic matrix.
91.8 99.9 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
75.6 99.9 GSM142902 WW001_ATH1_A1-WILLA-CON GSE6181 Assembly of the cell wall pectic matrix.
73.5 99.9 GSM284390 Arabidopsis GPE2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
50.4 99.8 GSM133775 Lindsey_1-27_torpedo-meristem_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
48.7 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.6 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.3 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
43.9 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.6 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
42.7 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.0 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.8 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
41.6 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.3 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.6 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.8 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.4 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
38.1 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
35.7 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.6 99.7 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
34.5 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.1 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
28.0 99.7 E-ATMX-1-raw-cel-1112746095
17.0 99.5 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
13.8 99.4 GSM173447 oxt6 mutant, biological rep3 GSE7211 A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana
11.9 99.3 GSM176880 AWP_Control_2 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
11.8 99.3 GSM67086 Arabidopsis_Stigma02 GSE3056 Arabidopsis Pollination Study
11.7 99.3 GSM184914 Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
11.6 99.3 GSM173446 oxt6 mutant, biological rep2 GSE7211 A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana
11.6 99.3 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.5 99.2 GSM184913 Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
10.3 99.2 GSM290758 root - 01% oxygen - 48h - A GSE11558 transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
10.0 99.2 E-MEXP-807-raw-cel-1173272977
9.7 99.1 GSM131603 ATGE_41_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
9.7 99.1 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
9.6 99.1 Millenaar_A2_ETH_Rep1_ATH1
9.5 99.1 GSM90297 Transgenic LEC2GR Seedling 4h Dex 2 GSE3959 RNA changes induced by LEAFY COTYLEDON2 activity in Arabidopsis seedlings
9.3 99.1 GSM133966 Fukuda_1-11_10A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.3 99.1 GSM291024 root - 08% oxygen - 48h - A GSE11558 transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
9.3 99.1 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.2 99.1 E-MEXP-807-raw-cel-1173273005
9.1 99.1 GSM67087 Arabidopsis_Stigma03 GSE3056 Arabidopsis Pollination Study
8.9 99.0 GSM133967 Fukuda_1-12_10B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
8.8 99.0 GSM142905 WW002_ATH1_A1-willa-CON-REP3 GSE6181 Assembly of the cell wall pectic matrix.
8.7 99.0 GSM291119 root - 21% oxygen - 48h - A GSE11558 transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
8.7 99.0 GSM131275 AtGen_6-1511_Cold(4°C)-Shoots-12.0h_Rep1 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
8.6 99.0 GSM131606 ATGE_42_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
131.1	99.9	GSM284391	Arabidopsis GPE3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
102.5	99.9	GSM142904	WW002_ATH1_A1-willa-CON-REP2	GSE6181	Assembly of the cell wall pectic matrix.
91.8	99.9	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
75.6	99.9	GSM142902	WW001_ATH1_A1-WILLA-CON	GSE6181	Assembly of the cell wall pectic matrix.
73.5	99.9	GSM284390	Arabidopsis GPE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
50.4	99.8	GSM133775	Lindsey_1-27_torpedo-meristem_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
48.7	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.6	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.3	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
43.9	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.6	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
42.7	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.0	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.8	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
41.6	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.3	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.6	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.8	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.4	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
38.1	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.7	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.6	99.7	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
34.5	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.1	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
28.0	99.7	E-ATMX-1-raw-cel-1112746095
17.0	99.5	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
13.8	99.4	GSM173447	oxt6 mutant, biological rep3	GSE7211	A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana
11.9	99.3	GSM176880	AWP_Control_2	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
11.8	99.3	GSM67086	Arabidopsis_Stigma02	GSE3056	Arabidopsis Pollination Study
11.7	99.3	GSM184914	Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
11.6	99.3	GSM173446	oxt6 mutant, biological rep2	GSE7211	A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana
11.6	99.3	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.5	99.2	GSM184913	Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
10.3	99.2	GSM290758	root - 01% oxygen - 48h - A	GSE11558	transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
10.0	99.2	E-MEXP-807-raw-cel-1173272977
9.7	99.1	GSM131603	ATGE_41_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.7	99.1	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
9.6	99.1	Millenaar_A2_ETH_Rep1_ATH1
9.5	99.1	GSM90297	Transgenic LEC2GR Seedling 4h Dex 2	GSE3959	RNA changes induced by LEAFY COTYLEDON2 activity in Arabidopsis seedlings
9.3	99.1	GSM133966	Fukuda_1-11_10A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.3	99.1	GSM291024	root - 08% oxygen - 48h - A	GSE11558	transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
9.3	99.1	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.2	99.1	E-MEXP-807-raw-cel-1173273005
9.1	99.1	GSM67087	Arabidopsis_Stigma03	GSE3056	Arabidopsis Pollination Study
8.9	99.0	GSM133967	Fukuda_1-12_10B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
8.8	99.0	GSM142905	WW002_ATH1_A1-willa-CON-REP3	GSE6181	Assembly of the cell wall pectic matrix.
8.7	99.0	GSM291119	root - 21% oxygen - 48h - A	GSE11558	transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
8.7	99.0	GSM131275	AtGen_6-1511_Cold(4°C)-Shoots-12.0h_Rep1	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
8.6	99.0	GSM131606	ATGE_42_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO

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	At4g00390
Gene name	transcription regulator
Module size	5 genes
NF	0.37
%ile	50.6

Co-expression analysis

Gene ID At4g00390 Gene name transcription regulator Module size 5 genes NF 0.37 %ile 50.6

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 AmiGO

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 At4g00390

Gene name transcription regulator

Module size 5 genes

NF 0.37

%ile 50.6

: 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

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