CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g16470

Gene name JR1

Module size 5 genes

NF 0.33

%ile 44.0

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
0.25 22.6 1.00 At3g16470 820895 JR1 JA-responsive gene O.I. H.G. S.X.
0.50 65.3 0.78 At1g52410 841671 TSA1 (TSK-ASSOCIATING PROTEIN 1) Contains a novel calcium-binding repeat sequence. Binds TSK in vitro. Localizes to small cytoplasmic vesicles in interphase cells. In cells synchronized for cell division, TSA1 and TSK relocalize to ends of spindle microtubules that are ahead of separating chromatids during metaphase and anaphase of mitosis. May be involved in mitosis together with TSK. Expressed preferentially in the flower and shoot apex. Can form multimers. O.I. H.G. S.X.
0.40 50.8 0.74 At1g52400 841670 BGLU18 (BETA GLUCOSIDASE 18) encodes a member of glycosyl hydrolase family 1, located in inducible ER bodies which were formed after wounding, required in inducible ER body formation O.I. H.G. S.X.
0.29 30.3 0.75 At2g34490 818012 CYP710A2 (cytochrome P450, family 710, subfamily A, polypeptide 2) Encodes a protein with C22-sterol desaturase activity. The enzyme was shown to catalyze the conversion of both 24-epi-campesterol and β-sitosterol to brassicasterol and stigmasterol, respectively, in the presence of NADPH. O.I. H.G. S.X.
0.25 22.6 0.75 At1g31710 840058 copper amine oxidase, putative F:amine oxidase activity, quinone binding, copper ion binding;P:cellular amine metabolic process;C:endomembrane system;FBMOPA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.25	22.6	1.00	At3g16470	820895	JR1	JA-responsive gene	O.I.	H.G.	S.X.
0.50	65.3	0.78	At1g52410	841671	TSA1 (TSK-ASSOCIATING PROTEIN 1)	Contains a novel calcium-binding repeat sequence. Binds TSK in vitro. Localizes to small cytoplasmic vesicles in interphase cells. In cells synchronized for cell division, TSA1 and TSK relocalize to ends of spindle microtubules that are ahead of separating chromatids during metaphase and anaphase of mitosis. May be involved in mitosis together with TSK. Expressed preferentially in the flower and shoot apex. Can form multimers.	O.I.	H.G.	S.X.
0.40	50.8	0.74	At1g52400	841670	BGLU18 (BETA GLUCOSIDASE 18)	encodes a member of glycosyl hydrolase family 1, located in inducible ER bodies which were formed after wounding, required in inducible ER body formation	O.I.	H.G.	S.X.
0.29	30.3	0.75	At2g34490	818012	CYP710A2 (cytochrome P450, family 710, subfamily A, polypeptide 2)	Encodes a protein with C22-sterol desaturase activity. The enzyme was shown to catalyze the conversion of both 24-epi-campesterol and β-sitosterol to brassicasterol and stigmasterol, respectively, in the presence of NADPH.	O.I.	H.G.	S.X.
0.25	22.6	0.75	At1g31710	840058	copper amine oxidase, putative	F:amine oxidase activity, quinone binding, copper ion binding;P:cellular amine metabolic process;C:endomembrane system;FBMOPA	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
152.6 99.9 E-MEXP-807-raw-cel-1173273252
151.5 99.9 GSM133758 Lindsey_1-11_heart-stage-root_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
127.8 99.9 E-MEXP-807-raw-cel-1173273170
126.9 99.9 GSM133775 Lindsey_1-27_torpedo-meristem_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
97.0 99.9 E-MEXP-807-raw-cel-1173273144
93.9 99.9 E-MEXP-807-raw-cel-1173273060
81.4 99.9 E-MEXP-807-raw-cel-1173273116
71.8 99.9 E-MEXP-807-raw-cel-1173273223
64.0 99.8 E-MEXP-807-raw-cel-1173273196
57.0 99.8 E-MEXP-807-raw-cel-1173273088
32.1 99.7 GSM133755 Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
25.1 99.6 GSM184897 Arabidopsis, root cells, cortex, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
22.4 99.6 GSM131321 AtGen_6-3421_Saltstress-Roots-6.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
18.8 99.5 GSM252665 Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep3 GSE9996 Organ regeneration in plants is independent of stem cell niche activity
17.8 99.5 GSM142631 MC002_ATH1_A3.3-dubos-6kx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
17.4 99.5 GSM142624 MC002_ATH1_A1.2-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
14.1 99.4 E-MEXP-546-raw-cel-863289532
12.5 99.3 GSM142625 MC002_ATH1_A1.3-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
12.2 99.3 GSM142642 MC002_ATH1_A7.2-dubos-wLh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
12.0 99.3 GSM133774 Lindsey_1-26_torpedo-meristem_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.7 99.3 GSM142643 MC002_ATH1_A7.3-dubos-wLh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.5 99.3 GSM142630 MC002_ATH1_A3.2-dubos-6kx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.1 99.2 GSM284388 Arabidopsis GMPE1 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
11.1 99.2 GSM311275 Laser capture microdissected (LCM) micropylar endosperm at the pre-globular stage, biological replicate 1 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
10.7 99.2 E-MEXP-546-raw-cel-863289476
10.4 99.2 GSM284384 Arabidopsis GEP5 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
10.1 99.2 GSM142636 MC002_ATH1_A5.2-dubos-5kx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.8 99.1 GSM284389 Arabidopsis GMPE2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
9.7 99.1 GSM142623 MC002_ATH1_A1.1-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.2 99.1 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
9.1 99.1 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.0 99.1 GSM284387 Arabidopsis GSUS4b GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
8.9 99.0 GSM284386 Arabidopsis GSUS3 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
8.9 99.0 E-MEXP-546-raw-cel-863289424
8.6 99.0 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.6 99.0 GSM133968 Birnbaum_1-19_LRC-1_Rep1_ATH1 GSE5749 A gene expression map of the Arabidopsis root

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
152.6	99.9	E-MEXP-807-raw-cel-1173273252
151.5	99.9	GSM133758	Lindsey_1-11_heart-stage-root_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
127.8	99.9	E-MEXP-807-raw-cel-1173273170
126.9	99.9	GSM133775	Lindsey_1-27_torpedo-meristem_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
97.0	99.9	E-MEXP-807-raw-cel-1173273144
93.9	99.9	E-MEXP-807-raw-cel-1173273060
81.4	99.9	E-MEXP-807-raw-cel-1173273116
71.8	99.9	E-MEXP-807-raw-cel-1173273223
64.0	99.8	E-MEXP-807-raw-cel-1173273196
57.0	99.8	E-MEXP-807-raw-cel-1173273088
32.1	99.7	GSM133755	Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
25.1	99.6	GSM184897	Arabidopsis, root cells, cortex, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
22.4	99.6	GSM131321	AtGen_6-3421_Saltstress-Roots-6.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
18.8	99.5	GSM252665	Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep3	GSE9996	Organ regeneration in plants is independent of stem cell niche activity
17.8	99.5	GSM142631	MC002_ATH1_A3.3-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
17.4	99.5	GSM142624	MC002_ATH1_A1.2-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
14.1	99.4	E-MEXP-546-raw-cel-863289532
12.5	99.3	GSM142625	MC002_ATH1_A1.3-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
12.2	99.3	GSM142642	MC002_ATH1_A7.2-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
12.0	99.3	GSM133774	Lindsey_1-26_torpedo-meristem_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.7	99.3	GSM142643	MC002_ATH1_A7.3-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.5	99.3	GSM142630	MC002_ATH1_A3.2-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.1	99.2	GSM284388	Arabidopsis GMPE1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
11.1	99.2	GSM311275	Laser capture microdissected (LCM) micropylar endosperm at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
10.7	99.2	E-MEXP-546-raw-cel-863289476
10.4	99.2	GSM284384	Arabidopsis GEP5	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
10.1	99.2	GSM142636	MC002_ATH1_A5.2-dubos-5kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.8	99.1	GSM284389	Arabidopsis GMPE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
9.7	99.1	GSM142623	MC002_ATH1_A1.1-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.2	99.1	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
9.1	99.1	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.0	99.1	GSM284387	Arabidopsis GSUS4b	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
8.9	99.0	GSM284386	Arabidopsis GSUS3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
8.9	99.0	E-MEXP-546-raw-cel-863289424
8.6	99.0	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.6	99.0	GSM133968	Birnbaum_1-19_LRC-1_Rep1_ATH1	GSE5749	A gene expression map of the Arabidopsis root

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.133 1 GO:0009308 The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group, as carried out by individual cells. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
0.046 2 GO:0050832 Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
0.016 1 GO:0009753 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 jasmonic acid stimulus.

SF	Genes	GO ID	Process Name
0.133	1	GO:0009308	The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group, as carried out by individual cells. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
0.046	2	GO:0050832	Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
0.016	1	GO:0009753	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 jasmonic acid stimulus.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.065 1 00100 Steroid biosynthesis
0.010 1 01062 Biosynthesis of terpenoids and steroids

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.065	1	00100	Steroid biosynthesis
0.010	1	01062	Biosynthesis of terpenoids and steroids

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	At3g16470
Gene name	JR1
Module size	5 genes
NF	0.33
%ile	44.0

Co-expression analysis

Gene ID At3g16470 Gene name JR1 Module size 5 genes NF 0.33 %ile 44.0

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 KEGG0.065100100Steroid biosynthesis0.010101062Biosynthesis of terpenoids and steroids

Inter-species module comparison

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

Gene ID At3g16470

Gene name JR1

Module size 5 genes

NF 0.33

%ile 44.0

: 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
0.065 1 00100 Steroid biosynthesis
0.010 1 01062 Biosynthesis of terpenoids and steroids

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