CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g02760

Gene name ATP binding / aminoacyl-tRNA ligase/ histidine-tRNA ligase/ nucleotide binding

Module size 6 genes

NF 0.62

%ile 83.4

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
0.73 85.5 1.00 At3g02760 820930 ATP binding / aminoacyl-tRNA ligase/ histidine-tRNA ligase/ nucleotide binding F:histidine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:histidyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:chloroplast, cytoplasm;OBMFAP O.I. H.G. S.X.
0.67 81.6 0.94 At3g19650 821502 cyclin-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBV O.I. H.G. S.X.
0.61 76.7 0.91 At1g15200 838086 protein-protein interaction regulator family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVA O.I. H.G. S.X.
0.61 76.7 0.90 At1g74250 843765 DNAJ heat shock N-terminal domain-containing protein F:heat shock protein binding, zinc ion binding, nucleic acid binding;P:protein folding;C:intracellular;MOBFPVA O.I. H.G. S.X.
0.59 74.7 0.90 At2g39260 818511 RNA binding / binding / protein binding F:protein binding, RNA binding, binding;P:translation, RNA metabolic process;C:cellular_component unknown;MOFBPVA O.I. H.G. S.X.
0.57 73.8 0.91 At3g50690 824233 leucine-rich repeat family protein F:protein binding;P:biological_process unknown;C:cellular_component unknown;MOFBPVA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.73	85.5	1.00	At3g02760	820930	ATP binding / aminoacyl-tRNA ligase/ histidine-tRNA ligase/ nucleotide binding	F:histidine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:histidyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:chloroplast, cytoplasm;OBMFAP	O.I.	H.G.	S.X.
0.67	81.6	0.94	At3g19650	821502	cyclin-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBV	O.I.	H.G.	S.X.
0.61	76.7	0.91	At1g15200	838086	protein-protein interaction regulator family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVA	O.I.	H.G.	S.X.
0.61	76.7	0.90	At1g74250	843765	DNAJ heat shock N-terminal domain-containing protein	F:heat shock protein binding, zinc ion binding, nucleic acid binding;P:protein folding;C:intracellular;MOBFPVA	O.I.	H.G.	S.X.
0.59	74.7	0.90	At2g39260	818511	RNA binding / binding / protein binding	F:protein binding, RNA binding, binding;P:translation, RNA metabolic process;C:cellular_component unknown;MOFBPVA	O.I.	H.G.	S.X.
0.57	73.8	0.91	At3g50690	824233	leucine-rich repeat family protein	F:protein binding;P:biological_process unknown;C:cellular_component unknown;MOFBPVA	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
57.4 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
56.2 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
54.2 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
54.0 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.7 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.8 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
50.1 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.7 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.3 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
46.0 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
45.8 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.5 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.5 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
43.7 99.8 E-MEXP-807-raw-cel-1173273252
43.5 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.7 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.3 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
39.5 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
38.5 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.9 99.7 E-MEXP-807-raw-cel-1173273144
32.6 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
27.2 99.7 E-MEXP-1474-raw-cel-1593932705
24.3 99.6 E-MEXP-1474-raw-cel-1593932609
22.3 99.6 GSM75510 Col-0 6h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
22.2 99.6 E-MEXP-1474-raw-cel-1593932513
19.5 99.6 GSM75514 Col-0 6h NAA replicate 2 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
16.4 99.5 E-MEXP-807-raw-cel-1173273196
15.8 99.5 E-MEXP-1474-raw-cel-1593932673
15.1 99.4 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
13.8 99.4 E-MEXP-807-raw-cel-1173273170
13.0 99.4 E-MEXP-1474-raw-cel-1593932737
11.9 99.3 GSM282693 arf2_brz_1 GSE11216 Brassinazole treatment of arf2 and wild-type dark-grown seedlings
11.2 99.2 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.7 99.2 GSM75509 Col-0 2h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
10.4 99.2 E-MEXP-1474-raw-cel-1593932481
10.4 99.2 E-MEXP-807-raw-cel-1173273116
10.2 99.2 GSM282703 arf2_brz_2 GSE11216 Brassinazole treatment of arf2 and wild-type dark-grown seedlings
10.0 99.2 GSM311277 Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 1 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
9.9 99.1 E-MEXP-1474-raw-cel-1593932641
9.7 99.1 GSM270814 Arabidopsis cell culture, 4 h_control_rep1 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
9.5 99.1 E-MEXP-1474-raw-cel-1593932769
9.4 99.1 GSM311278 Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
9.3 99.1 E-MEXP-1474-raw-cel-1593932897
8.9 99.0 E-MEXP-1474-raw-cel-1593932545
8.9 99.0 GSM311295 Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
8.8 99.0 GSM282698 Col_BRZ_rep2 GSE11216 Brassinazole treatment of arf2 and wild-type dark-grown seedlings
8.7 99.0 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
57.4	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
56.2	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
54.2	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
54.0	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.7	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.8	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
50.1	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.7	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.3	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
46.0	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
45.8	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.5	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.5	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
43.7	99.8	E-MEXP-807-raw-cel-1173273252
43.5	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.7	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.3	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
39.5	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
38.5	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.9	99.7	E-MEXP-807-raw-cel-1173273144
32.6	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
27.2	99.7	E-MEXP-1474-raw-cel-1593932705
24.3	99.6	E-MEXP-1474-raw-cel-1593932609
22.3	99.6	GSM75510	Col-0 6h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
22.2	99.6	E-MEXP-1474-raw-cel-1593932513
19.5	99.6	GSM75514	Col-0 6h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
16.4	99.5	E-MEXP-807-raw-cel-1173273196
15.8	99.5	E-MEXP-1474-raw-cel-1593932673
15.1	99.4	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
13.8	99.4	E-MEXP-807-raw-cel-1173273170
13.0	99.4	E-MEXP-1474-raw-cel-1593932737
11.9	99.3	GSM282693	arf2_brz_1	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
11.2	99.2	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.7	99.2	GSM75509	Col-0 2h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
10.4	99.2	E-MEXP-1474-raw-cel-1593932481
10.4	99.2	E-MEXP-807-raw-cel-1173273116
10.2	99.2	GSM282703	arf2_brz_2	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
10.0	99.2	GSM311277	Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
9.9	99.1	E-MEXP-1474-raw-cel-1593932641
9.7	99.1	GSM270814	Arabidopsis cell culture, 4 h_control_rep1	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
9.5	99.1	E-MEXP-1474-raw-cel-1593932769
9.4	99.1	GSM311278	Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
9.3	99.1	E-MEXP-1474-raw-cel-1593932897
8.9	99.0	E-MEXP-1474-raw-cel-1593932545
8.9	99.0	GSM311295	Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
8.8	99.0	GSM282698	Col_BRZ_rep2	GSE11216	Brassinazole treatment of arf2 and wild-type dark-grown seedlings
8.7	99.0	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.222 1 GO:0006427 The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
0.087 1 GO:0016070 The chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
0.042 1 GO:0006418 The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.

SF	Genes	GO ID	Process Name
0.222	1	GO:0006427	The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
0.087	1	GO:0016070	The chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
0.042	1	GO:0006418	The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.038 1 00970 Aminoacyl-tRNA biosynthesis

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.038	1	00970	Aminoacyl-tRNA 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	At3g02760
Gene name	ATP binding / aminoacyl-tRNA ligase/ histidine-tRNA ligase/ nucleotide binding
Module size	6 genes
NF	0.62
%ile	83.4

Co-expression analysis

Gene ID At3g02760 Gene name ATP binding / aminoacyl-tRNA ligase/ histidine-tRNA ligase/ nucleotide binding Module size 6 genes NF 0.62 %ile 83.4

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 KEGG0.038100970Aminoacyl-tRNA 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 At3g02760

Gene name ATP binding / aminoacyl-tRNA ligase/ histidine-tRNA ligase/ nucleotide binding

Module size 6 genes

NF 0.62

%ile 83.4

: 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
0.038 1 00970 Aminoacyl-tRNA 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