CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g13670

Gene name protein kinase family protein

Module size 7 genes

NF 0.56

%ile 77.1

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
0.31 33.8 1.00 At3g13670 820572 protein kinase family protein F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:unknown;MBOPFVA O.I. H.G. S.X.
0.67 81.6 0.94 At1g33980 840295 Smg-4/UPF3 family protein Involved in mRNA surveillance, detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD) O.I. H.G. S.X.
0.67 81.6 0.95 At2g25760 817118 protein kinase family protein F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:unknown;MBOPFVA O.I. H.G. S.X.
0.67 81.6 0.94 At5g51340 835208 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOB O.I. H.G. S.X.
0.57 73.8 0.95 At3g22170 821781 FHY3 (FAR-RED ELONGATED HYPOCOTYLS 3) A component of the PHYA signaling network, mediates the FR-HIR response to far-red light in concert with FAR1. O.I. H.G. S.X.
0.55 70.6 0.94 At1g54490 841891 XRN4 (EXORIBONUCLEASE 4) Involved in the ethylene response. XRN4 does not appear to regulate ethylene signaling via an RNA-INDUCED SILENCING COMPLEX-based RNA silencing mechanism but acts by independent means. Endogenous suppressor of posttranscriptional gene silencing. O.I. H.G. S.X.
0.50 65.3 0.94 At5g06120 830499 Ran-binding protein, putative F:protein transporter activity, binding;P:intracellular protein transport, protein import into nucleus, docking;C:nucleus, nuclear pore, cytoplasm;MOP O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.31	33.8	1.00	At3g13670	820572	protein kinase family protein	F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:unknown;MBOPFVA	O.I.	H.G.	S.X.
0.67	81.6	0.94	At1g33980	840295	Smg-4/UPF3 family protein	Involved in mRNA surveillance, detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD)	O.I.	H.G.	S.X.
0.67	81.6	0.95	At2g25760	817118	protein kinase family protein	F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:unknown;MBOPFVA	O.I.	H.G.	S.X.
0.67	81.6	0.94	At5g51340	835208	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOB	O.I.	H.G.	S.X.
0.57	73.8	0.95	At3g22170	821781	FHY3 (FAR-RED ELONGATED HYPOCOTYLS 3)	A component of the PHYA signaling network, mediates the FR-HIR response to far-red light in concert with FAR1.	O.I.	H.G.	S.X.
0.55	70.6	0.94	At1g54490	841891	XRN4 (EXORIBONUCLEASE 4)	Involved in the ethylene response. XRN4 does not appear to regulate ethylene signaling via an RNA-INDUCED SILENCING COMPLEX-based RNA silencing mechanism but acts by independent means. Endogenous suppressor of posttranscriptional gene silencing.	O.I.	H.G.	S.X.
0.50	65.3	0.94	At5g06120	830499	Ran-binding protein, putative	F:protein transporter activity, binding;P:intracellular protein transport, protein import into nucleus, docking;C:nucleus, nuclear pore, cytoplasm;MOP	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
103.3 99.9 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
84.4 99.9 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
75.3 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
71.5 99.9 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
71.0 99.9 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.7 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
68.6 99.9 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
67.0 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
66.9 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
62.7 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
62.1 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
61.6 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
61.6 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
58.4 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
58.3 99.8 E-MEXP-711-raw-cel-1563002902
53.5 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.9 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.9 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.3 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.7 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.8 99.8 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
39.1 99.8 E-ATMX-27-raw-cel-1441080540
36.2 99.7 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
22.3 99.6 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
21.9 99.6 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
20.7 99.6 E-ATMX-27-raw-cel-1441080508
19.1 99.6 GSM131539 ATGE_25_C GSE5630 AtGenExpress: Developmental series (leaves)
19.0 99.5 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.4 99.5 E-ATMX-25-raw-cel-1441077482
17.1 99.5 E-ATMX-25-raw-cel-1441077500
16.6 99.5 E-MEXP-509-raw-cel-829148808
16.0 99.5 GSM205185 protoplast_KIN10_rep2 GSE8257 Identification of KIN10-target genes in Arabidopsis mesophyll cells
16.0 99.5 E-MEXP-475-raw-cel-680982521
14.9 99.4 GSM128661 Underwood_1-14_Cor-5x10e7-10h_Rep2_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
14.2 99.4 GSM133731 Buchanan-Wollaston_A-3-bwoll-C0S_SLD GSE5727 The effects of mutants in stress response pathways on gene expression during senescence
14.1 99.4 GSM131538 ATGE_25_B GSE5630 AtGenExpress: Developmental series (leaves)
14.1 99.4 E-ATMX-25-raw-cel-1441077517
14.0 99.4 GSM133736 Buchanan-Wollaston_A-8-bwoll-Ei2_SLD GSE5727 The effects of mutants in stress response pathways on gene expression during senescence
13.9 99.4 GSM176880 AWP_Control_2 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
13.5 99.4 GSM131605 ATGE_41_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
13.5 99.4 GSM131537 ATGE_25_A GSE5630 AtGenExpress: Developmental series (leaves)
13.1 99.4 E-ATMX-27-raw-cel-1441080524
12.3 99.3 E-MEXP-509-raw-cel-829148842
11.9 99.3 E-MEXP-509-raw-cel-829148666
11.3 99.3 GSM133734 Buchanan-Wollaston_A-6-bwoll-NG2_SLD GSE5727 The effects of mutants in stress response pathways on gene expression during senescence
11.3 99.3 GSM268245 dor-drought-1, biological rep 1 GSE10643 Transcription profiling of Arabidopsis dor mutant and wild-type plants in response to drought stress.
11.1 99.2 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
10.9 99.2 GSM131303 AtGen_6-2611_Osmoticstress-Shoots-24.0h_Rep1 GSE5622 AtGenExpress: Stress Treatments (Osmotic stress)
10.9 99.2 GSM133733 Buchanan-Wollaston_A-5-bwoll-NG1_SLD GSE5727 The effects of mutants in stress response pathways on gene expression during senescence
10.8 99.2 GSM269827 C2 leaf-drought-rep2 GSE10670 Global expression profiling of wild type and transgenic Arabidopsis plants in response to water stress
10.8 99.2 GSM131604 ATGE_41_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
10.6 99.2 GSM189112 HSP90_Reduced_RNAi-A3_Biological_Replicate_2_Technical_Replicate_1 GSE7796 Phenotypic Diversity and Altered Environmental Plasticity in Arabidopsis thaliana with Reduced HSP90 Levels
10.4 99.2 GSM131603 ATGE_41_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
9.6 99.1 E-MEXP-509-raw-cel-829148877
9.5 99.1 GSM133819 Yang_1-4_old-pod_Rep2_ATH1 GSE5736 To identify changes in gene expression during silique senescence in Arabidopsis thaliana
9.2 99.1 E-MEXP-739-raw-cel-1099467321
9.1 99.1 Cornah_1-10_A2-irv_Rep3_ATH1
9.0 99.1 GSM133735 Buchanan-Wollaston_A-7-bwoll-Ei1_SLD GSE5727 The effects of mutants in stress response pathways on gene expression during senescence
8.8 99.0 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.6 99.0 E-ATMX-32-raw-cel-1562974409

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
103.3	99.9	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
84.4	99.9	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
75.3	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
71.5	99.9	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
71.0	99.9	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.7	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
68.6	99.9	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
67.0	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
66.9	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
62.7	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
62.1	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
61.6	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
61.6	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
58.4	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
58.3	99.8	E-MEXP-711-raw-cel-1563002902
53.5	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.9	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.9	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.3	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.7	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.8	99.8	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
39.1	99.8	E-ATMX-27-raw-cel-1441080540
36.2	99.7	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
22.3	99.6	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
21.9	99.6	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
20.7	99.6	E-ATMX-27-raw-cel-1441080508
19.1	99.6	GSM131539	ATGE_25_C	GSE5630	AtGenExpress: Developmental series (leaves)
19.0	99.5	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.4	99.5	E-ATMX-25-raw-cel-1441077482
17.1	99.5	E-ATMX-25-raw-cel-1441077500
16.6	99.5	E-MEXP-509-raw-cel-829148808
16.0	99.5	GSM205185	protoplast_KIN10_rep2	GSE8257	Identification of KIN10-target genes in Arabidopsis mesophyll cells
16.0	99.5	E-MEXP-475-raw-cel-680982521
14.9	99.4	GSM128661	Underwood_1-14_Cor-5x10e7-10h_Rep2_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
14.2	99.4	GSM133731	Buchanan-Wollaston_A-3-bwoll-C0S_SLD	GSE5727	The effects of mutants in stress response pathways on gene expression during senescence
14.1	99.4	GSM131538	ATGE_25_B	GSE5630	AtGenExpress: Developmental series (leaves)
14.1	99.4	E-ATMX-25-raw-cel-1441077517
14.0	99.4	GSM133736	Buchanan-Wollaston_A-8-bwoll-Ei2_SLD	GSE5727	The effects of mutants in stress response pathways on gene expression during senescence
13.9	99.4	GSM176880	AWP_Control_2	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
13.5	99.4	GSM131605	ATGE_41_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
13.5	99.4	GSM131537	ATGE_25_A	GSE5630	AtGenExpress: Developmental series (leaves)
13.1	99.4	E-ATMX-27-raw-cel-1441080524
12.3	99.3	E-MEXP-509-raw-cel-829148842
11.9	99.3	E-MEXP-509-raw-cel-829148666
11.3	99.3	GSM133734	Buchanan-Wollaston_A-6-bwoll-NG2_SLD	GSE5727	The effects of mutants in stress response pathways on gene expression during senescence
11.3	99.3	GSM268245	dor-drought-1, biological rep 1	GSE10643	Transcription profiling of Arabidopsis dor mutant and wild-type plants in response to drought stress.
11.1	99.2	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
10.9	99.2	GSM131303	AtGen_6-2611_Osmoticstress-Shoots-24.0h_Rep1	GSE5622	AtGenExpress: Stress Treatments (Osmotic stress)
10.9	99.2	GSM133733	Buchanan-Wollaston_A-5-bwoll-NG1_SLD	GSE5727	The effects of mutants in stress response pathways on gene expression during senescence
10.8	99.2	GSM269827	C2 leaf-drought-rep2	GSE10670	Global expression profiling of wild type and transgenic Arabidopsis plants in response to water stress
10.8	99.2	GSM131604	ATGE_41_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
10.6	99.2	GSM189112	HSP90_Reduced_RNAi-A3_Biological_Replicate_2_Technical_Replicate_1	GSE7796	Phenotypic Diversity and Altered Environmental Plasticity in Arabidopsis thaliana with Reduced HSP90 Levels
10.4	99.2	GSM131603	ATGE_41_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.6	99.1	E-MEXP-509-raw-cel-829148877
9.5	99.1	GSM133819	Yang_1-4_old-pod_Rep2_ATH1	GSE5736	To identify changes in gene expression during silique senescence in Arabidopsis thaliana
9.2	99.1	E-MEXP-739-raw-cel-1099467321
9.1	99.1	Cornah_1-10_A2-irv_Rep3_ATH1
9.0	99.1	GSM133735	Buchanan-Wollaston_A-7-bwoll-Ei1_SLD	GSE5727	The effects of mutants in stress response pathways on gene expression during senescence
8.8	99.0	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.6	99.0	E-ATMX-32-raw-cel-1562974409

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.250 1 GO:0000291 The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 5'-cap or the 3'-poly(A) tail.
0.200 1 GO:0000184 The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
0.200 1 GO:0009961 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 1-aminocyclopropane-1-carboxylic acid stimulus.

SF	Genes	GO ID	Process Name
0.250	1	GO:0000291	The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 5'-cap or the 3'-poly(A) tail.
0.200	1	GO:0000184	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
0.200	1	GO:0009961	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 1-aminocyclopropane-1-carboxylic acid stimulus.

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	At3g13670
Gene name	protein kinase family protein
Module size	7 genes
NF	0.56
%ile	77.1

Co-expression analysis

Gene ID At3g13670 Gene name protein kinase family protein Module size 7 genes NF 0.56 %ile 77.1

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 At3g13670

Gene name protein kinase family protein

Module size 7 genes

NF 0.56

%ile 77.1

: 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