CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g54490

Gene name XRN4 (EXORIBONUCLEASE 4)

Module size 14 genes

NF 0.52

%ile 73.5

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
1.00 100.0 1.00 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.
0.80 89.8 0.96 At3g06670 819852 binding F:binding;P:biological_process unknown;C:cellular_component unknown;MOFPBV O.I. H.G. S.X.
0.72 84.8 0.96 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 0.95 At5g22760 832339 PHD finger family protein F:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:unknown;MPFO O.I. H.G. S.X.
0.63 78.1 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.
0.57 73.8 0.95 At1g09730 837501 Ulp1 protease family protein F:cysteine-type peptidase activity;P:proteolysis;C:cellular_component unknown;MOFPBVA O.I. H.G. S.X.
0.52 67.4 0.95 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.
0.49 63.5 0.95 At2g46560 819268 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:unknown;C:CUL4 RING ubiquitin ligase complex;BFMOP O.I. H.G. S.X.
0.46 59.8 0.94 At4g05420 825890 DDB1A (DAMAGED DNA BINDING PROTEIN 1A) Structurally similar to damaged DNA binding proteins.DDB1a is part of a 350 KDa nuclear localized DET1 protein complex. This complex may physically interact with histone tails and while bound to chromatin- repress transcription of genes involved in photomorphogenesis. O.I. H.G. S.X.
0.43 55.3 0.95 At1g50200 841442 ALATS (ALANYL-TRNA SYNTHETASE) F:alanine-tRNA ligase activity, ligase activity, forming aminoacyl-tRNA and related compounds, nucleotide binding, nucleic acid binding, ATP binding;P:alanyl-tRNA aminoacylation, response to cadmium ion;C:mitochondrion, chloroplast;OBMAFP O.I. H.G. S.X.
0.42 53.9 0.95 At2g27900 817335 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO O.I. H.G. S.X.
0.38 46.7 0.95 At1g02080 839244 transcriptional regulator-related F:transcription regulator activity;P:unknown;C:membrane;MOFBP O.I. H.G. S.X.
0.36 43.6 0.95 At5g28850 833004 calcium-binding EF hand family protein F:calcium ion binding;P:biological_process unknown;C:endomembrane system;MOPF O.I. H.G. S.X.
0.26 24.4 0.95 At3g05090 819671 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFOBPAV O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
1.00	100.0	1.00	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.
0.80	89.8	0.96	At3g06670	819852	binding	F:binding;P:biological_process unknown;C:cellular_component unknown;MOFPBV	O.I.	H.G.	S.X.
0.72	84.8	0.96	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	0.95	At5g22760	832339	PHD finger family protein	F:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:unknown;MPFO	O.I.	H.G.	S.X.
0.63	78.1	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.
0.57	73.8	0.95	At1g09730	837501	Ulp1 protease family protein	F:cysteine-type peptidase activity;P:proteolysis;C:cellular_component unknown;MOFPBVA	O.I.	H.G.	S.X.
0.52	67.4	0.95	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.
0.49	63.5	0.95	At2g46560	819268	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:unknown;C:CUL4 RING ubiquitin ligase complex;BFMOP	O.I.	H.G.	S.X.
0.46	59.8	0.94	At4g05420	825890	DDB1A (DAMAGED DNA BINDING PROTEIN 1A)	Structurally similar to damaged DNA binding proteins.DDB1a is part of a 350 KDa nuclear localized DET1 protein complex. This complex may physically interact with histone tails and while bound to chromatin- repress transcription of genes involved in photomorphogenesis.	O.I.	H.G.	S.X.
0.43	55.3	0.95	At1g50200	841442	ALATS (ALANYL-TRNA SYNTHETASE)	F:alanine-tRNA ligase activity, ligase activity, forming aminoacyl-tRNA and related compounds, nucleotide binding, nucleic acid binding, ATP binding;P:alanyl-tRNA aminoacylation, response to cadmium ion;C:mitochondrion, chloroplast;OBMAFP	O.I.	H.G.	S.X.
0.42	53.9	0.95	At2g27900	817335	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO	O.I.	H.G.	S.X.
0.38	46.7	0.95	At1g02080	839244	transcriptional regulator-related	F:transcription regulator activity;P:unknown;C:membrane;MOFBP	O.I.	H.G.	S.X.
0.36	43.6	0.95	At5g28850	833004	calcium-binding EF hand family protein	F:calcium ion binding;P:biological_process unknown;C:endomembrane system;MOPF	O.I.	H.G.	S.X.
0.26	24.4	0.95	At3g05090	819671	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFOBPAV	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
56.7 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.5 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
55.3 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
54.7 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
53.4 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
52.0 99.8 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
51.8 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.6 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.2 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.0 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
46.2 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
44.9 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.4 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
40.1 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.5 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.4 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.9 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.9 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.6 99.7 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
30.5 99.7 E-MEXP-711-raw-cel-1563002902
28.1 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.3 99.6 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
18.4 99.5 E-ATMX-27-raw-cel-1441080540
15.5 99.5 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
11.2 99.2 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.6 99.2 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.5 99.1 E-ATMX-27-raw-cel-1441080508
9.3 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

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
56.7	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.5	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
55.3	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
54.7	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
53.4	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
52.0	99.8	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
51.8	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.6	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.2	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.0	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
46.2	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
44.9	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.4	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
40.1	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.5	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.4	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.9	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.9	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.6	99.7	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
30.5	99.7	E-MEXP-711-raw-cel-1563002902
28.1	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.3	99.6	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
18.4	99.5	E-ATMX-27-raw-cel-1441080540
15.5	99.5	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
11.2	99.2	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.6	99.2	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.5	99.1	E-ATMX-27-raw-cel-1441080508
9.3	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

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.133 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.
0.118 1 GO:0006419 The process of coupling alanine to alanyl-tRNA, catalyzed by alanyl-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.
0.118 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
0.133	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.
0.118	1	GO:0006419	The process of coupling alanine to alanyl-tRNA, catalyzed by alanyl-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.
0.118	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
0.033 1 00970 Aminoacyl-tRNA biosynthesis
0.032 1 03018 RNA degradation
0.031 1 03420 Nucleotide excision repair

SF	Genes	KEGG ID	Pathway name
0.033	1	00970	Aminoacyl-tRNA biosynthesis
0.032	1	03018	RNA degradation
0.031	1	03420	Nucleotide excision repair

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

Back to the KAGIANA project homepage

Gene ID	At1g54490
Gene name	XRN4 (EXORIBONUCLEASE 4)
Module size	14 genes
NF	0.52
%ile	73.5

Co-expression analysis

Gene ID At1g54490 Gene name XRN4 (EXORIBONUCLEASE 4) Module size 14 genes NF 0.52 %ile 73.5

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 KEGG0.033100970Aminoacyl-tRNA biosynthesis0.032103018RNA degradation0.031103420Nucleotide excision repair

Inter-species module comparison

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

Gene ID At1g54490

Gene name XRN4 (EXORIBONUCLEASE 4)

Module size 14 genes

NF 0.52

%ile 73.5

: 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
0.033 1 00970 Aminoacyl-tRNA biosynthesis
0.032 1 03018 RNA degradation
0.031 1 03420 Nucleotide excision repair

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