CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g63450

Gene name CYP94B1

Module size 5 genes

NF 0.09

%ile 5.8

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
0.14 6.8 1.00 At5g63450 836464 CYP94B1 member of CYP94B O.I. H.G. S.X.
0.44 57.2 0.56 At3g48520 824011 CYP94B3 member of CYP94B O.I. H.G. S.X.
0.40 50.8 0.57 At1g43160 840915 RAP2.6 (related to AP2 6) encodes a member of the ERF (ethylene response factor) subfamily B-4 of ERF/AP2 transcription factor family (RAP2.6). The protein contains one AP2 domain. There are 7 members in this subfamily. O.I. H.G. S.X.
0.04 0.9 0.58 At5g13220 831162 JAZ10 (JASMONATE-ZIM-DOMAIN PROTEIN 10) Plants overexpressing At5g13220.3, but not At5g13220.1 showed enhanced insensitivity to MeJa. O.I. H.G. S.X.
0.03 0.6 0.55 At1g02400 839508 GA2OX6 (GIBBERELLIN 2-OXIDASE 6) Encodes a gibberellin 2-oxidase. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.14	6.8	1.00	At5g63450	836464	CYP94B1	member of CYP94B	O.I.	H.G.	S.X.
0.44	57.2	0.56	At3g48520	824011	CYP94B3	member of CYP94B	O.I.	H.G.	S.X.
0.40	50.8	0.57	At1g43160	840915	RAP2.6 (related to AP2 6)	encodes a member of the ERF (ethylene response factor) subfamily B-4 of ERF/AP2 transcription factor family (RAP2.6). The protein contains one AP2 domain. There are 7 members in this subfamily.	O.I.	H.G.	S.X.
0.04	0.9	0.58	At5g13220	831162	JAZ10 (JASMONATE-ZIM-DOMAIN PROTEIN 10)	Plants overexpressing At5g13220.3, but not At5g13220.1 showed enhanced insensitivity to MeJa.	O.I.	H.G.	S.X.
0.03	0.6	0.55	At1g02400	839508	GA2OX6 (GIBBERELLIN 2-OXIDASE 6)	Encodes a gibberellin 2-oxidase.	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
266.4 100.0 GSM133962 Fukuda_1-7_6A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
189.6 100.0 GSM133963 Fukuda_1-8_6B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
149.5 99.9 E-MEXP-67-raw-cel-323396457
129.2 99.9 E-MEXP-67-raw-cel-323396336
94.6 99.9 GSM133965 Fukuda_1-10_8B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
90.3 99.9 GSM133964 Fukuda_1-9_8A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
50.6 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
41.9 99.8 GSM131267 AtGen_6-1311_Cold(4°C)-Shoots-3.0h_Rep1 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
37.4 99.7 GSM133966 Fukuda_1-11_10A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
34.1 99.7 GSM311289 Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
33.6 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.0 99.7 GSM184918 Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
31.6 99.7 GSM311290 Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 2 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
25.8 99.7 GSM133967 Fukuda_1-12_10B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
25.7 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.7 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.8 99.6 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.1 99.6 GSM131268 AtGen_6-1312_Cold(4°C)-Shoots-3.0h_Rep2 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
23.7 99.6 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
22.7 99.6 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.0 99.6 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
20.6 99.6 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.5 99.6 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.7 99.6 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
19.1 99.6 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.6 99.5 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
18.1 99.5 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.2 99.5 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.6 99.5 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.2 99.5 GSM142879 GW001_ATH1_A24-Warre-03f GSE6177 The effects of the sfr2, sfr3 and sfr6 mutations on lyotropic stress responses
15.8 99.5 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
15.7 99.5 GSM184910 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
14.5 99.4 GSM74899 Wildtype_6H Cold_Rep2 GSE3326 ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome
14.3 99.4 GSM74897 Wildtype_3H Cold_Rep2 GSE3326 ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome
12.1 99.3 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
12.1 99.3 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.0 99.3 GSM311288 Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 2 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
11.8 99.3 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.7 99.3 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.7 99.3 GSM311287 Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
11.6 99.3 GSM133961 Fukuda_1-6_4B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
11.5 99.3 GSM128713 Thorlby_1-2_3h-post-freeze_REP3_ATH1 GSE5524 Gene Expression During Recovery from Freezing
11.4 99.3 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.4 99.3 GSM142878 GW001_ATH1_A23-Warre-03f GSE6177 The effects of the sfr2, sfr3 and sfr6 mutations on lyotropic stress responses
10.9 99.2 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.1 99.2 GSM74896 Wildtype_3H Cold_Rep1 GSE3326 ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome
8.8 99.0 GSM74898 Wildtype_6H Cold_Rep1 GSE3326 ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
266.4	100.0	GSM133962	Fukuda_1-7_6A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
189.6	100.0	GSM133963	Fukuda_1-8_6B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
149.5	99.9	E-MEXP-67-raw-cel-323396457
129.2	99.9	E-MEXP-67-raw-cel-323396336
94.6	99.9	GSM133965	Fukuda_1-10_8B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
90.3	99.9	GSM133964	Fukuda_1-9_8A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
50.6	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
41.9	99.8	GSM131267	AtGen_6-1311_Cold(4°C)-Shoots-3.0h_Rep1	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
37.4	99.7	GSM133966	Fukuda_1-11_10A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
34.1	99.7	GSM311289	Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
33.6	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.0	99.7	GSM184918	Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
31.6	99.7	GSM311290	Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
25.8	99.7	GSM133967	Fukuda_1-12_10B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
25.7	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.7	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.8	99.6	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.1	99.6	GSM131268	AtGen_6-1312_Cold(4°C)-Shoots-3.0h_Rep2	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
23.7	99.6	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
22.7	99.6	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.0	99.6	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
20.6	99.6	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.5	99.6	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.7	99.6	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
19.1	99.6	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.6	99.5	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
18.1	99.5	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.2	99.5	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.6	99.5	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.2	99.5	GSM142879	GW001_ATH1_A24-Warre-03f	GSE6177	The effects of the sfr2, sfr3 and sfr6 mutations on lyotropic stress responses
15.8	99.5	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
15.7	99.5	GSM184910	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
14.5	99.4	GSM74899	Wildtype_6H Cold_Rep2	GSE3326	ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome
14.3	99.4	GSM74897	Wildtype_3H Cold_Rep2	GSE3326	ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome
12.1	99.3	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
12.1	99.3	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.0	99.3	GSM311288	Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
11.8	99.3	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.7	99.3	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.7	99.3	GSM311287	Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
11.6	99.3	GSM133961	Fukuda_1-6_4B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
11.5	99.3	GSM128713	Thorlby_1-2_3h-post-freeze_REP3_ATH1	GSE5524	Gene Expression During Recovery from Freezing
11.4	99.3	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.4	99.3	GSM142878	GW001_ATH1_A23-Warre-03f	GSE6177	The effects of the sfr2, sfr3 and sfr6 mutations on lyotropic stress responses
10.9	99.2	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.1	99.2	GSM74896	Wildtype_3H Cold_Rep1	GSE3326	ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome
8.8	99.0	GSM74898	Wildtype_6H Cold_Rep1	GSE3326	ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.200 1 GO:0045487 The chemical reactions and pathways resulting in the breakdown of gibberellin. Gibberellins are a class of highly modified terpenes that function as plant growth regulators.
0.053 1 GO:0009639 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 red or far red light stimulus. Red light is electromagnetic radiation of wavelength of 580-700nm. Far red light is electromagnetic radiation of wavelength 700-800nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.
0.030 2 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
0.200	1	GO:0045487	The chemical reactions and pathways resulting in the breakdown of gibberellin. Gibberellins are a class of highly modified terpenes that function as plant growth regulators.
0.053	1	GO:0009639	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 red or far red light stimulus. Red light is electromagnetic radiation of wavelength of 580-700nm. Far red light is electromagnetic radiation of wavelength 700-800nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.
0.030	2	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

Back to the KAGIANA project homepage

Gene ID	At5g63450
Gene name	CYP94B1
Module size	5 genes
NF	0.09
%ile	5.8

Co-expression analysis

Gene ID At5g63450 Gene name CYP94B1 Module size 5 genes NF 0.09 %ile 5.8

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

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 At5g63450

Gene name CYP94B1

Module size 5 genes

NF 0.09

%ile 5.8

: 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

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