CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Ta.20649.1.S1_x_at

Gene name
Homology with Arabidopsis Similar to At1g68020: ATTPS6 (HF=7e-11)

Module size 6 genes

NF 0.23

%ile 38.0

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. Ev AGI code Arabidopsis gene name O.I. H.G. S.X. Other DB
0.46 66.8 0.90 Ta.20649.1.S1_x_at BU100263 - - 7e-11 At1g68020 ATTPS6 O.I. H.G. S.X.
0.50 72.4 0.89 Ta.3840.1.S1_at CD919677 - - 4e-5 At5g21170 5'-AMP-activated protein kinase beta-2 subunit, putative O.I. H.G. S.X.
0.32 44.4 0.88 Ta.20649.1.S1_a_at BU100263 - - 7e-11 At1g68020 ATTPS6 O.I. H.G. S.X.
0.17 19.8 0.90 Ta.28185.1.S1_at AL820475 - - 2e-4 At3g46900 COPT2 O.I. H.G. S.X.
0.16 18.2 0.89 Ta.1275.1.S1_at CA619292 - - 1e+1 At2g36100 integral membrane family protein O.I. H.G. S.X.
0.11 12.4 0.89 TaAffx.20065.1.S1_at CK207580 - - 2e-1 At3g45970 ATEXLA1 (ARABIDOPSIS THALIANA EXPANSIN-LIKE A1) O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	Ev	AGI code	Arabidopsis gene name	O.I.	H.G.	S.X.
0.46	66.8	0.90	Ta.20649.1.S1_x_at	BU100263	-	-	7e-11	At1g68020	ATTPS6	O.I.	H.G.	S.X.
0.50	72.4	0.89	Ta.3840.1.S1_at	CD919677	-	-	4e-5	At5g21170	5'-AMP-activated protein kinase beta-2 subunit, putative	O.I.	H.G.	S.X.
0.32	44.4	0.88	Ta.20649.1.S1_a_at	BU100263	-	-	7e-11	At1g68020	ATTPS6	O.I.	H.G.	S.X.
0.17	19.8	0.90	Ta.28185.1.S1_at	AL820475	-	-	2e-4	At3g46900	COPT2	O.I.	H.G.	S.X.
0.16	18.2	0.89	Ta.1275.1.S1_at	CA619292	-	-	1e+1	At2g36100	integral membrane family protein	O.I.	H.G.	S.X.
0.11	12.4	0.89	TaAffx.20065.1.S1_at	CK207580	-	-	2e-1	At3g45970	ATEXLA1 (ARABIDOPSIS THALIANA EXPANSIN-LIKE A1)	O.I.	H.G.	S.X.

Click More genes

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
10.4 99.2 GSM314287 tissue type: 22 DAP endosperm - rep1 GSE12508 Transcription patterns during wheat development
9.7 99.1 GSM298062 Crown tissue of Harnesk at 5 weeks post germination, biological rep 2 GSE11774 Expression data from cold treated wheat cultivars
9.5 99.1 GSM314289 tissue type: 22 DAP endosperm - rep3 GSE12508 Transcription patterns during wheat development
7.8 98.7 GSM314288 tissue type: 22 DAP endosperm - rep2 GSE12508 Transcription patterns during wheat development
6.4 98.2 GSM250898 TcLr1_3dpi_inoculated_rep3 GSE9915 Transcript profiling of Lr1- and Lr34-mediated leaf rust resistance in wheat
5.8 97.9 GSM314261 tissue type: seedling, root - rep2 GSE12508 Transcription patterns during wheat development
5.7 97.9 GSM298061 Crown tissue of Harnesk at 5 weeks post germination, biological rep 1 GSE11774 Expression data from cold treated wheat cultivars
4.9 97.3 GSM250900 TcLr34_3dpi_inoculated_rep3 GSE9915 Transcript profiling of Lr1- and Lr34-mediated leaf rust resistance in wheat
4.6 97.0 GSM298063 Crown tissue of Harnesk at 9 weeks post germination, biological rep 1 GSE11774 Expression data from cold treated wheat cultivars
4.6 97.0 GSM298094 Crown tissue of Solstice at 9 weeks post germination GSE11774 Expression data from cold treated wheat cultivars

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
10.4	99.2	GSM314287	tissue type: 22 DAP endosperm - rep1	GSE12508	Transcription patterns during wheat development
9.7	99.1	GSM298062	Crown tissue of Harnesk at 5 weeks post germination, biological rep 2	GSE11774	Expression data from cold treated wheat cultivars
9.5	99.1	GSM314289	tissue type: 22 DAP endosperm - rep3	GSE12508	Transcription patterns during wheat development
7.8	98.7	GSM314288	tissue type: 22 DAP endosperm - rep2	GSE12508	Transcription patterns during wheat development
6.4	98.2	GSM250898	TcLr1_3dpi_inoculated_rep3	GSE9915	Transcript profiling of Lr1- and Lr34-mediated leaf rust resistance in wheat
5.8	97.9	GSM314261	tissue type: seedling, root - rep2	GSE12508	Transcription patterns during wheat development
5.7	97.9	GSM298061	Crown tissue of Harnesk at 5 weeks post germination, biological rep 1	GSE11774	Expression data from cold treated wheat cultivars
4.9	97.3	GSM250900	TcLr34_3dpi_inoculated_rep3	GSE9915	Transcript profiling of Lr1- and Lr34-mediated leaf rust resistance in wheat
4.6	97.0	GSM298063	Crown tissue of Harnesk at 9 weeks post germination, biological rep 1	GSE11774	Expression data from cold treated wheat cultivars
4.6	97.0	GSM298094	Crown tissue of Solstice at 9 weeks post germination	GSE11774	Expression data from cold treated wheat cultivars

Inter-species module comparison

A co-expression module including the Arabidopsis gene, At1g68020, orthologous to the query gene, Ta.20649.1.S1_x_at

VF %ile Gene ID Repr. ID Gene Name Func. O.I. H.G. S.X. Other DB
1.00 100.0 At1g68020 843130 ATTPS6 Encodes an enzyme putatively involved in trehalose biosynthesis. The protein has a trehalose synthase (TPS)-like domain and a trehalose phosphatase (TPP)-like domain. It can complement a yeast mutant lacking both of these activities suggesting that this is a bifunctional enzyme. O.I. H.G. S.X.
0.35 41.6 At2g32710 817831 KRP4 Kip-related protein (KRP) gene, encodes CDK (cyclin-dependent kinase) inhibitor (CKI). A member of seven KRP genes found in Arabidopsis thaliana. Negative regulator of cell division. Expressed in actively dividing cells. O.I. H.G. S.X.
0.29 30.3 At1g13190 837877 RNA recognition motif (RRM)-containing protein F:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:unknown;MBOPFVA O.I. H.G. S.X.
0.29 30.3 At3g61600 825333 ATPOB1 POZ/BTB containing-protein AtPOB1 O.I. H.G. S.X.
0.26 24.4 At1g08680 837390 ZIGA4 (ARF GAP-like zinc finger-containing protein ZiGA4) A member of ARF GAP domain (AGD), A thaliana has 15 members, grouped into four classes. AGD14 belongs to the class 4, together with AGD15. O.I. H.G. S.X.
0.25 22.6 At2g18915 816408 LKP2 (LOV KELCH PROTEIN 2) encodes a member of F-box proteins that includes two other proteins in Arabidopsis (ZTL and FKF1). These proteins contain a unique structure containing a PAS domain at their N-terminus, an F-box motif, and 6 kelch repeats at their C-terminus. Overexpression results in arrhythmic phenotypes for a number of circadian clock outputs in both constant light and constant darkness, long hypocotyls under multiple fluences of both red and blue light, and a loss of photoperiodic control of flowering time. Although this the expression of this gene itself is not regulated by circadian clock, it physically interacts with Dof transcription factors that are transcriptionally regulated by circadian rhythm. LKP2 interacts with Di19, CO/COL family proteins. O.I. H.G. S.X.
0.24 20.7 At1g18030 838383 protein phosphatase 2C, putative / PP2C, putative F:protein serine/threonine phosphatase activity, catalytic activity;P:biological_process unknown;C:cellular_component unknown;PMOFBVA O.I. H.G. S.X.
0.23 19.3 At5g40740 834074 unknown protein F:unknown;P:biological_process unknown;C:unknown;OBFMP O.I. H.G. S.X.
0.22 17.5 At1g16710 838242 HAC12 (histone acetyltransferase of the CBP family 12) Encodes an enzyme with histone acetyltransferase activity that can use both H3 and H4 histones as substrates. No single prior lysine acetylation is sufficient to block HAC12 acetylation of the H3 or H4 peptides, suggesting that HAC12 can acetylate any of several lysines present in the peptides. O.I. H.G. S.X.
0.22 17.5 At4g24800 828582 MA3 domain-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOF O.I. H.G. S.X.
0.22 17.5 At5g13570 831201 DCP2 (DECAPPING 2) Encodes DCP2 with mRNA decapping activity. DCP2 forms a mRNA decapping complex with DCP1 (At1g08370) and VCS (VARICOSE) (At3g13300). Recombinant DCP2 is enzymatically active in vitro, generating from capped mRNAs m7GDP, and 5�-phosphorylated mRNAs. DCP1, DCP2 and VCS colocalize in cytoplasmic loci, which are putative Arabidopsis mRNA processing bodies. Null mutants of DCP1, DCP2, and VCS accumulate capped mRNAs with a reduced degradation rate. These mutants also share a similar lethal phenotype at the seedling cotyledon stage, with disorganized veins, swollen root hairs, and altered epidermal cell morphology. The protein was shown by immunoprecipitation not to interact with DCP1. O.I. H.G. S.X.
0.22 17.5 At4g11110 826712 SPA2 (SPA1-RELATED 2) Encodes a member of the SPA (suppressor of phyA-105) protein family (SPA1-SPA4). SPA proteins contain an N-terminal serine/threonine kinase-like motif followed by a coiled-coil structure and a C-terminal WD-repeat domain. SPA proteins function redundantly in suppressing photomorphogenesis in dark- and light-grown seedlings. SPA2 primarily regulates seedling development in darkness and has little function in light-grown seedlings or adult plants. O.I. H.G. S.X.
0.21 15.8 At3g04740 819634 SWP (STRUWWELPETER) encodes a protein with similarities to subunits of the Mediator complex, required for RNA polymerase II recruitment at target promoters in response to specific activators. Lines carrying loss of function mutations in the gene have reduced cell numbers in aerial organs. On the other hand, lines overexpressing the gene have increased number of small cells in clusters, suggesting cell division is more unsynchronized in the overexpressors. O.I. H.G. S.X.
0.21 15.8 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.
0.20 14.4 At5g63200 836441 tetratricopeptide repeat (TPR)-containing protein F:binding;P:biological_process unknown;C:cellular_component unknown;OBMAFP O.I. H.G. S.X.
0.19 12.7 At5g19330 832053 armadillo/beta-catenin repeat family protein / BTB/POZ domain-containing protein F:protein binding, binding;P:unknown;C:plasma membrane;MPOFVBA O.I. H.G. S.X.
0.17 10.2 At1g27510 839642 - F:unknown;P:response to singlet oxygen;C:thylakoid membrane;PMOFB O.I. H.G. S.X.
0.17 10.2 At4g00450 827954 CRP (CRYPTIC PRECOCIOUS) A genetic locus involved in flowering time. The mutant enhances the expression of the flowering time (FT) gene. A knockout mutant of this gene showed late-flowering phenotype. O.I. H.G. S.X.
0.17 10.2 At3g06670 819852 binding F:binding;P:biological_process unknown;C:cellular_component unknown;MOFPBV O.I. H.G. S.X.
0.17 10.2 At4g09580 826542 - F:unknown;P:biological_process unknown;C:endoplasmic reticulum;BOMPFA O.I. H.G. S.X.
0.16 8.8 At1g04950 839370 TAF6 (TBP-ASSOCIATED FACTOR 6) Encodes one of two Arabidopsis proteins with significant similarity to the histone fold TBP-associated factor TAF6. Mutants are embryo lethal and transmission of the mutant allele through the male gametophyte is significantly reduced. This is due to reduced pollen tube growth of the mutant. O.I. H.G. S.X.
0.15 7.8 At2g32450 817806 calcium-binding EF hand family protein F:binding, zinc ion binding, calcium ion binding;P:unknown;C:plasma membrane;BOMAPF O.I. H.G. S.X.
0.13 5.8 At5g02250 830864 EMB2730 (EMBRYO DEFECTIVE 2730) Encodes a exoribonuclease involved in rRNA processing in mitochondria and chloroplasts.Loss of function mutations are pale green and require supplementation with sucrose for germination and early development. Plants are pale green due to defects in chloroplast biogenesis. O.I. H.G. S.X.
0.12 4.9 At4g15475 827219 F-box family protein (FBL4) F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:unknown;MPOFBV O.I. H.G. S.X.
0.11 4.1 At3g17750 821043 protein kinase family protein F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cytosol, plasma membrane;MOPFBVA O.I. H.G. S.X.
0.11 4.1 At2g21240 816663 BPC4 (BASIC PENTACYSTEINE 4) F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;PMB O.I. H.G. S.X.

VF	%ile	Gene ID	Repr. ID	Gene Name	Func.	O.I.	H.G.	S.X.
1.00	100.0	At1g68020	843130	ATTPS6	Encodes an enzyme putatively involved in trehalose biosynthesis. The protein has a trehalose synthase (TPS)-like domain and a trehalose phosphatase (TPP)-like domain. It can complement a yeast mutant lacking both of these activities suggesting that this is a bifunctional enzyme.	O.I.	H.G.	S.X.
0.35	41.6	At2g32710	817831	KRP4	Kip-related protein (KRP) gene, encodes CDK (cyclin-dependent kinase) inhibitor (CKI). A member of seven KRP genes found in Arabidopsis thaliana. Negative regulator of cell division. Expressed in actively dividing cells.	O.I.	H.G.	S.X.
0.29	30.3	At1g13190	837877	RNA recognition motif (RRM)-containing protein	F:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:unknown;MBOPFVA	O.I.	H.G.	S.X.
0.29	30.3	At3g61600	825333	ATPOB1	POZ/BTB containing-protein AtPOB1	O.I.	H.G.	S.X.
0.26	24.4	At1g08680	837390	ZIGA4 (ARF GAP-like zinc finger-containing protein ZiGA4)	A member of ARF GAP domain (AGD), A thaliana has 15 members, grouped into four classes. AGD14 belongs to the class 4, together with AGD15.	O.I.	H.G.	S.X.
0.25	22.6	At2g18915	816408	LKP2 (LOV KELCH PROTEIN 2)	encodes a member of F-box proteins that includes two other proteins in Arabidopsis (ZTL and FKF1). These proteins contain a unique structure containing a PAS domain at their N-terminus, an F-box motif, and 6 kelch repeats at their C-terminus. Overexpression results in arrhythmic phenotypes for a number of circadian clock outputs in both constant light and constant darkness, long hypocotyls under multiple fluences of both red and blue light, and a loss of photoperiodic control of flowering time. Although this the expression of this gene itself is not regulated by circadian clock, it physically interacts with Dof transcription factors that are transcriptionally regulated by circadian rhythm. LKP2 interacts with Di19, CO/COL family proteins.	O.I.	H.G.	S.X.
0.24	20.7	At1g18030	838383	protein phosphatase 2C, putative / PP2C, putative	F:protein serine/threonine phosphatase activity, catalytic activity;P:biological_process unknown;C:cellular_component unknown;PMOFBVA	O.I.	H.G.	S.X.
0.23	19.3	At5g40740	834074	unknown protein	F:unknown;P:biological_process unknown;C:unknown;OBFMP	O.I.	H.G.	S.X.
0.22	17.5	At1g16710	838242	HAC12 (histone acetyltransferase of the CBP family 12)	Encodes an enzyme with histone acetyltransferase activity that can use both H3 and H4 histones as substrates. No single prior lysine acetylation is sufficient to block HAC12 acetylation of the H3 or H4 peptides, suggesting that HAC12 can acetylate any of several lysines present in the peptides.	O.I.	H.G.	S.X.
0.22	17.5	At4g24800	828582	MA3 domain-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOF	O.I.	H.G.	S.X.
0.22	17.5	At5g13570	831201	DCP2 (DECAPPING 2)	Encodes DCP2 with mRNA decapping activity. DCP2 forms a mRNA decapping complex with DCP1 (At1g08370) and VCS (VARICOSE) (At3g13300). Recombinant DCP2 is enzymatically active in vitro, generating from capped mRNAs m7GDP, and 5�-phosphorylated mRNAs. DCP1, DCP2 and VCS colocalize in cytoplasmic loci, which are putative Arabidopsis mRNA processing bodies. Null mutants of DCP1, DCP2, and VCS accumulate capped mRNAs with a reduced degradation rate. These mutants also share a similar lethal phenotype at the seedling cotyledon stage, with disorganized veins, swollen root hairs, and altered epidermal cell morphology. The protein was shown by immunoprecipitation not to interact with DCP1.	O.I.	H.G.	S.X.
0.22	17.5	At4g11110	826712	SPA2 (SPA1-RELATED 2)	Encodes a member of the SPA (suppressor of phyA-105) protein family (SPA1-SPA4). SPA proteins contain an N-terminal serine/threonine kinase-like motif followed by a coiled-coil structure and a C-terminal WD-repeat domain. SPA proteins function redundantly in suppressing photomorphogenesis in dark- and light-grown seedlings. SPA2 primarily regulates seedling development in darkness and has little function in light-grown seedlings or adult plants.	O.I.	H.G.	S.X.
0.21	15.8	At3g04740	819634	SWP (STRUWWELPETER)	encodes a protein with similarities to subunits of the Mediator complex, required for RNA polymerase II recruitment at target promoters in response to specific activators. Lines carrying loss of function mutations in the gene have reduced cell numbers in aerial organs. On the other hand, lines overexpressing the gene have increased number of small cells in clusters, suggesting cell division is more unsynchronized in the overexpressors.	O.I.	H.G.	S.X.
0.21	15.8	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.
0.20	14.4	At5g63200	836441	tetratricopeptide repeat (TPR)-containing protein	F:binding;P:biological_process unknown;C:cellular_component unknown;OBMAFP	O.I.	H.G.	S.X.
0.19	12.7	At5g19330	832053	armadillo/beta-catenin repeat family protein / BTB/POZ domain-containing protein	F:protein binding, binding;P:unknown;C:plasma membrane;MPOFVBA	O.I.	H.G.	S.X.
0.17	10.2	At1g27510	839642	-	F:unknown;P:response to singlet oxygen;C:thylakoid membrane;PMOFB	O.I.	H.G.	S.X.
0.17	10.2	At4g00450	827954	CRP (CRYPTIC PRECOCIOUS)	A genetic locus involved in flowering time. The mutant enhances the expression of the flowering time (FT) gene. A knockout mutant of this gene showed late-flowering phenotype.	O.I.	H.G.	S.X.
0.17	10.2	At3g06670	819852	binding	F:binding;P:biological_process unknown;C:cellular_component unknown;MOFPBV	O.I.	H.G.	S.X.
0.17	10.2	At4g09580	826542	-	F:unknown;P:biological_process unknown;C:endoplasmic reticulum;BOMPFA	O.I.	H.G.	S.X.
0.16	8.8	At1g04950	839370	TAF6 (TBP-ASSOCIATED FACTOR 6)	Encodes one of two Arabidopsis proteins with significant similarity to the histone fold TBP-associated factor TAF6. Mutants are embryo lethal and transmission of the mutant allele through the male gametophyte is significantly reduced. This is due to reduced pollen tube growth of the mutant.	O.I.	H.G.	S.X.
0.15	7.8	At2g32450	817806	calcium-binding EF hand family protein	F:binding, zinc ion binding, calcium ion binding;P:unknown;C:plasma membrane;BOMAPF	O.I.	H.G.	S.X.
0.13	5.8	At5g02250	830864	EMB2730 (EMBRYO DEFECTIVE 2730)	Encodes a exoribonuclease involved in rRNA processing in mitochondria and chloroplasts.Loss of function mutations are pale green and require supplementation with sucrose for germination and early development. Plants are pale green due to defects in chloroplast biogenesis.	O.I.	H.G.	S.X.
0.12	4.9	At4g15475	827219	F-box family protein (FBL4)	F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:unknown;MPOFBV	O.I.	H.G.	S.X.
0.11	4.1	At3g17750	821043	protein kinase family protein	F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cytosol, plasma membrane;MOPFBVA	O.I.	H.G.	S.X.
0.11	4.1	At2g21240	816663	BPC4 (BASIC PENTACYSTEINE 4)	F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;PMB	O.I.	H.G.	S.X.

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

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Gene ID	Ta.20649.1.S1_x_at
Gene name
Homology with Arabidopsis	Similar to At1g68020: ATTPS6 (HF=7e-11)
Module size	6 genes
NF	0.23
%ile	38.0

Co-expression analysis

Gene ID Ta.20649.1.S1_x_at Gene name Homology with ArabidopsisSimilar to At1g68020: ATTPS6 (HF=7e-11) Module size 6 genes NF 0.23 %ile 38.0

Co-expressed genes

Click More genes

Specific experiments for the module

Inter-species module comparison

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

Gene ID Ta.20649.1.S1_x_at

Gene name
Homology with Arabidopsis Similar to At1g68020: ATTPS6 (HF=7e-11)

Module size 6 genes

NF 0.23

%ile 38.0

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