CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g64780

Gene name ATAMT1

Module size 5 genes

NF 0.27

%ile 30.5

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 At1g64780 842786 ATAMT1 encodes an ammonium transporter protein believed to act as a high affinity transporter. It is expressed in the root, primarily in endodermal and cortical cells, and contributes to ammonium uptake in the root. O.I. H.G. S.X.
0.60 75.7 0.65 At2g27420 817287 cysteine proteinase, putative F:cysteine-type peptidase activity, cysteine-type endopeptidase activity;P:proteolysis;C:endomembrane system;MOPBVAF O.I. H.G. S.X.
0.33 38.1 0.60 At5g24120 832477 SIGE (SIGMA FACTOR E) Encodes a specialized sigma factor that functions in regulation of plastid genes and is responsible for the light-dependent transcription at the psbD LRP. Activation of SIG5 is dependent upon blue light and mediated by cryptochromes. O.I. H.G. S.X.
0.29 30.3 0.63 At3g56290 824796 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. H.G. S.X.
0.16 8.8 0.63 At1g32900 840184 starch synthase, putative F:transferase activity, transferring glycosyl groups;P:biosynthetic process, glucan biosynthetic process;C:chloroplast;PBOAFM 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	At1g64780	842786	ATAMT1	encodes an ammonium transporter protein believed to act as a high affinity transporter. It is expressed in the root, primarily in endodermal and cortical cells, and contributes to ammonium uptake in the root.	O.I.	H.G.	S.X.
0.60	75.7	0.65	At2g27420	817287	cysteine proteinase, putative	F:cysteine-type peptidase activity, cysteine-type endopeptidase activity;P:proteolysis;C:endomembrane system;MOPBVAF	O.I.	H.G.	S.X.
0.33	38.1	0.60	At5g24120	832477	SIGE (SIGMA FACTOR E)	Encodes a specialized sigma factor that functions in regulation of plastid genes and is responsible for the light-dependent transcription at the psbD LRP. Activation of SIG5 is dependent upon blue light and mediated by cryptochromes.	O.I.	H.G.	S.X.
0.29	30.3	0.63	At3g56290	824796	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	H.G.	S.X.
0.16	8.8	0.63	At1g32900	840184	starch synthase, putative	F:transferase activity, transferring glycosyl groups;P:biosynthetic process, glucan biosynthetic process;C:chloroplast;PBOAFM	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
97.7 99.9 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
94.8 99.9 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
81.6 99.9 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
81.1 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
74.2 99.9 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
70.1 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
63.2 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.6 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
62.0 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
58.3 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.9 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.5 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.4 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.2 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.2 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.7 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.6 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.2 99.8 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
29.9 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.7 99.6 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
16.4 99.5 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
16.3 99.5 GSM133958 Fukuda_1-3_2A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
16.1 99.5 GSM133959 Fukuda_1-4_2B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
13.4 99.4 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
13.3 99.4 GSM133966 Fukuda_1-11_10A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
11.7 99.3 GSM133967 Fukuda_1-12_10B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
11.6 99.3 GSM133964 Fukuda_1-9_8A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
10.2 99.2 GSM284384 Arabidopsis GEP5 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
9.7 99.1 GSM133965 Fukuda_1-10_8B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.4 99.1 GSM133811 Diamond_A-4-Diamo-fum_SLD GSE5735 Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
8.9 99.0 GSM133948 Murray_2-4_T6-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies
8.7 99.0 E-ATMX-13-raw-cel-1556149935
8.6 99.0 E-ATMX-13-raw-cel-1556149727

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
97.7	99.9	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
94.8	99.9	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
81.6	99.9	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
81.1	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
74.2	99.9	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
70.1	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
63.2	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.6	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
62.0	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
58.3	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.9	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.5	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.4	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.2	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.2	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.7	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.6	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.2	99.8	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
29.9	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.7	99.6	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
16.4	99.5	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
16.3	99.5	GSM133958	Fukuda_1-3_2A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
16.1	99.5	GSM133959	Fukuda_1-4_2B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
13.4	99.4	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
13.3	99.4	GSM133966	Fukuda_1-11_10A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
11.7	99.3	GSM133967	Fukuda_1-12_10B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
11.6	99.3	GSM133964	Fukuda_1-9_8A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
10.2	99.2	GSM284384	Arabidopsis GEP5	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
9.7	99.1	GSM133965	Fukuda_1-10_8B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.4	99.1	GSM133811	Diamond_A-4-Diamo-fum_SLD	GSE5735	Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
8.9	99.0	GSM133948	Murray_2-4_T6-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies
8.7	99.0	E-ATMX-13-raw-cel-1556149935
8.6	99.0	E-ATMX-13-raw-cel-1556149727

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.333 1 GO:0015843 The directed movement of methylammonium into, out of, within or between cells.
0.286 1 GO:0009250 The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
0.200 1 GO:0015696 The directed movement of ammonium into, out of, within or between cells. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals.

SF	Genes	GO ID	Process Name
0.333	1	GO:0015843	The directed movement of methylammonium into, out of, within or between cells.
0.286	1	GO:0009250	The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
0.200	1	GO:0015696	The directed movement of ammonium into, out of, within or between cells. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals.

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

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Gene ID	At1g64780
Gene name	ATAMT1
Module size	5 genes
NF	0.27
%ile	30.5

Co-expression analysis

Gene ID At1g64780 Gene name ATAMT1 Module size 5 genes NF 0.27 %ile 30.5

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 At1g64780

Gene name ATAMT1

Module size 5 genes

NF 0.27

%ile 30.5

: 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