CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g50300

Gene name transferase family protein

Module size 5 genes

NF 0.29

%ile 34.2

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
0.22 17.5 1.00 At3g50300 824192 transferase family protein F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFO O.I. H.G. S.X.
0.67 81.6 0.77 At2g40160 818607 - F:unknown;P:biological_process unknown;C:endomembrane system;P O.I. H.G. S.X.
0.38 46.7 0.70 At5g26310 832700 UGT72E3 UGT72E3 is an UDPG:coniferyl alcohol glucosyltransferase which glucosylates sinapyl- and coniferyl alcohol as well as sinapic acid. The enzyme is thought to be involved in lignin- and phenylpropanoid metabolism. A knockdown mutant line (72E3KD) was obtained using RNAi silencing. No reduction in coniferyl alcohol 4-O-glucoside and sinapyl alcohol 4-O-glucoside was detected in this line compared to wildtype, in contrast with the knockdown line constructed for UGT72E2 displayed a twofold reduction in the these phenylpropanoid 4-O-glucosides. O.I. H.G. S.X.
0.33 38.1 0.72 At4g17280 827442 - F:unknown;P:multicellular organismal development;C:membrane;P O.I. H.G. S.X.
0.18 11.4 0.71 At4g20140 827760 GSO1 (GASSHO1) Encodes GASSHO1 (GSO1), a putative leucine-rich repeat transmembrane-type receptor kinase. GSO1 and a homolog GSO2 (At5g44700) are required for the formation of a normal epidermal surface during embryogenesis. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.22	17.5	1.00	At3g50300	824192	transferase family protein	F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFO	O.I.	H.G.	S.X.
0.67	81.6	0.77	At2g40160	818607	-	F:unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	H.G.	S.X.
0.38	46.7	0.70	At5g26310	832700	UGT72E3	UGT72E3 is an UDPG:coniferyl alcohol glucosyltransferase which glucosylates sinapyl- and coniferyl alcohol as well as sinapic acid. The enzyme is thought to be involved in lignin- and phenylpropanoid metabolism. A knockdown mutant line (72E3KD) was obtained using RNAi silencing. No reduction in coniferyl alcohol 4-O-glucoside and sinapyl alcohol 4-O-glucoside was detected in this line compared to wildtype, in contrast with the knockdown line constructed for UGT72E2 displayed a twofold reduction in the these phenylpropanoid 4-O-glucosides.	O.I.	H.G.	S.X.
0.33	38.1	0.72	At4g17280	827442	-	F:unknown;P:multicellular organismal development;C:membrane;P	O.I.	H.G.	S.X.
0.18	11.4	0.71	At4g20140	827760	GSO1 (GASSHO1)	Encodes GASSHO1 (GSO1), a putative leucine-rich repeat transmembrane-type receptor kinase. GSO1 and a homolog GSO2 (At5g44700) are required for the formation of a normal epidermal surface during embryogenesis.	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
237.1 100.0 GSM133775 Lindsey_1-27_torpedo-meristem_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
221.6 100.0 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
98.5 99.9 GSM133774 Lindsey_1-26_torpedo-meristem_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
66.1 99.8 GSM133760 Lindsey_1-12_heart-stage-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
61.2 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.5 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.9 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.0 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.6 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.3 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
45.7 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
44.8 99.8 GSM133769 Lindsey_1-21_torpedo-basal_Rep6_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
42.9 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
42.2 99.8 GSM133756 Lindsey_1-10_heart-stage-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
38.2 99.8 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
37.2 99.7 GSM133303 RIKEN-NAKABAYASHI1A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
36.6 99.7 GSM133768 Lindsey_1-20_torpedo-basal_Rep5_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
35.1 99.7 GSM133772 Lindsey_1-24_torpedo-apical_Rep6_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
34.9 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.8 99.7 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
32.9 99.7 GSM133763 Lindsey_1-15_torpedo-cotyledon_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
30.5 99.7 GSM133755 Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
29.7 99.7 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
28.5 99.7 GSM133117 RIKEN-YAMAUCHI1A GSE5687 AtGenExpress: Different temperature treatment of seeds
24.2 99.6 GSM133767 Lindsey_1-19_torpedo-basal_Rep4_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
23.4 99.6 GSM133770 Lindsey_1-22_torpedo-apical_Rep4_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
19.7 99.6 GSM133771 Lindsey_1-23_torpedo-apical_Rep5_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.8 99.5 GSM133778 Lindsey_1-2_globular-apical_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.8 99.5 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.2 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
14.4 99.4 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.5 99.4 GSM133776 Lindsey_1-1_globular-apical_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.0 99.4 GSM157324 Hammond_3-17_Potassium-starved-root_Rep3_ATH1 GSE6825 Differential gene expression patterns in potassium-starved and Caesium-treated plants
12.2 99.3 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
11.2 99.2 GSM133779 Lindsey_1-5_globular-basal_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.3 99.2 GSM133118 RIKEN-YAMAUCHI1B GSE5687 AtGenExpress: Different temperature treatment of seeds
9.5 99.1 GSM133957 Fukuda_1-2_0B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.5 99.1 GSM142596 DB001_ATH1_A6-Brown-cal GSE6148 The trans-differentiation of cultured Arabidopsis cells
9.3 99.1 GSM142594 DB001_ATH1_A4-Brown-cal GSE6148 The trans-differentiation of cultured Arabidopsis cells
8.9 99.0 GSM157327 Hammond_3-11_Potassium-starved-root_Rep2_ATH1 GSE6825 Differential gene expression patterns in potassium-starved and Caesium-treated plants
8.8 99.0 E-MEXP-509-raw-cel-829148808
8.6 99.0 GSM142592 DB001_ATH1_A2-Brown-cal GSE6148 The trans-differentiation of cultured Arabidopsis cells

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
237.1	100.0	GSM133775	Lindsey_1-27_torpedo-meristem_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
221.6	100.0	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
98.5	99.9	GSM133774	Lindsey_1-26_torpedo-meristem_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
66.1	99.8	GSM133760	Lindsey_1-12_heart-stage-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
61.2	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.5	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.9	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.0	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.6	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.3	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
45.7	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
44.8	99.8	GSM133769	Lindsey_1-21_torpedo-basal_Rep6_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
42.9	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
42.2	99.8	GSM133756	Lindsey_1-10_heart-stage-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
38.2	99.8	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
37.2	99.7	GSM133303	RIKEN-NAKABAYASHI1A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
36.6	99.7	GSM133768	Lindsey_1-20_torpedo-basal_Rep5_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
35.1	99.7	GSM133772	Lindsey_1-24_torpedo-apical_Rep6_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
34.9	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.8	99.7	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
32.9	99.7	GSM133763	Lindsey_1-15_torpedo-cotyledon_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
30.5	99.7	GSM133755	Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
29.7	99.7	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
28.5	99.7	GSM133117	RIKEN-YAMAUCHI1A	GSE5687	AtGenExpress: Different temperature treatment of seeds
24.2	99.6	GSM133767	Lindsey_1-19_torpedo-basal_Rep4_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
23.4	99.6	GSM133770	Lindsey_1-22_torpedo-apical_Rep4_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
19.7	99.6	GSM133771	Lindsey_1-23_torpedo-apical_Rep5_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.8	99.5	GSM133778	Lindsey_1-2_globular-apical_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.8	99.5	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.2	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
14.4	99.4	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.5	99.4	GSM133776	Lindsey_1-1_globular-apical_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.0	99.4	GSM157324	Hammond_3-17_Potassium-starved-root_Rep3_ATH1	GSE6825	Differential gene expression patterns in potassium-starved and Caesium-treated plants
12.2	99.3	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
11.2	99.2	GSM133779	Lindsey_1-5_globular-basal_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.3	99.2	GSM133118	RIKEN-YAMAUCHI1B	GSE5687	AtGenExpress: Different temperature treatment of seeds
9.5	99.1	GSM133957	Fukuda_1-2_0B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.5	99.1	GSM142596	DB001_ATH1_A6-Brown-cal	GSE6148	The trans-differentiation of cultured Arabidopsis cells
9.3	99.1	GSM142594	DB001_ATH1_A4-Brown-cal	GSE6148	The trans-differentiation of cultured Arabidopsis cells
8.9	99.0	GSM157327	Hammond_3-11_Potassium-starved-root_Rep2_ATH1	GSE6825	Differential gene expression patterns in potassium-starved and Caesium-treated plants
8.8	99.0	E-MEXP-509-raw-cel-829148808
8.6	99.0	GSM142592	DB001_ATH1_A2-Brown-cal	GSE6148	The trans-differentiation of cultured Arabidopsis cells

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.286 1 GO:0008544 The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of a plant or animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
0.039 1 GO:0009790 The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
0.015 1 GO:0007169 The series of molecular signals generated as a consequence of a transmembrane receptor tyrosine kinase binding to its physiological ligand.

SF	Genes	GO ID	Process Name
0.286	1	GO:0008544	The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of a plant or animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
0.039	1	GO:0009790	The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
0.015	1	GO:0007169	The series of molecular signals generated as a consequence of a transmembrane receptor tyrosine kinase binding to its physiological ligand.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.019 1 00940 Phenylpropanoid biosynthesis

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.019	1	00940	Phenylpropanoid biosynthesis

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	At3g50300
Gene name	transferase family protein
Module size	5 genes
NF	0.29
%ile	34.2

Co-expression analysis

Gene ID At3g50300 Gene name transferase family protein Module size 5 genes NF 0.29 %ile 34.2

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 KEGG0.019100940Phenylpropanoid biosynthesis

Inter-species module comparison

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

Gene ID At3g50300

Gene name transferase family protein

Module size 5 genes

NF 0.29

%ile 34.2

: 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
0.019 1 00940 Phenylpropanoid biosynthesis

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