CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Contig20974_at

Gene name
Homology with Arabidopsis Similar to At3g14650: CYP72A11 (HF=7e-6)

Module size 7 genes

NF 0.41

%ile 56.2

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
0.44 58.9 0.96 Contig20974_at Contig20974 - - 7e-6 At3g14650 CYP72A11 O.I. H.G. S.X.
0.55 72.0 0.97 Contig14904_at Contig14904 - - 2e+0 At2g28330 unknown protein O.I. H.G. S.X.
0.46 61.0 0.96 Contig16886_at Contig16886 - - 5e+0 At5g60460 sec61beta family protein O.I. H.G. S.X.
0.39 50.5 0.96 Contig9392_at Contig9392 - - 5e+0 At5g62780 DNAJ heat shock N-terminal domain-containing protein O.I. H.G. S.X.
0.33 42.6 0.96 Contig21935_at Contig21935 - - 1e+0 At3g49700 ACS9 (1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 9) O.I. H.G. S.X.
0.32 40.3 0.96 Contig9752_at Contig9752 - - 3e+0 At2g11651 unknown protein O.I. H.G. S.X.
0.29 35.5 0.96 Contig13215_at Contig13215 - - 3e-10 At5g49720 ATGH9A1 (ARABIDOPSIS THALIANA GLYCOSYL HYDROLASE 9A1) 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.
0.44	58.9	0.96	Contig20974_at	Contig20974	-	-	7e-6	At3g14650	CYP72A11	O.I.	H.G.	S.X.
0.55	72.0	0.97	Contig14904_at	Contig14904	-	-	2e+0	At2g28330	unknown protein	O.I.	H.G.	S.X.
0.46	61.0	0.96	Contig16886_at	Contig16886	-	-	5e+0	At5g60460	sec61beta family protein	O.I.	H.G.	S.X.
0.39	50.5	0.96	Contig9392_at	Contig9392	-	-	5e+0	At5g62780	DNAJ heat shock N-terminal domain-containing protein	O.I.	H.G.	S.X.
0.33	42.6	0.96	Contig21935_at	Contig21935	-	-	1e+0	At3g49700	ACS9 (1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 9)	O.I.	H.G.	S.X.
0.32	40.3	0.96	Contig9752_at	Contig9752	-	-	3e+0	At2g11651	unknown protein	O.I.	H.G.	S.X.
0.29	35.5	0.96	Contig13215_at	Contig13215	-	-	3e-10	At5g49720	ATGH9A1 (ARABIDOPSIS THALIANA GLYCOSYL HYDROLASE 9A1)	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
10.9 99.2 GSM372981 genotype: 11542 - pathogen isolates: 5874 - time: 16 - rep2 GSE14930 Comparison of wild-type and cell death mutant of barley plants containing Mla6 powdery mildew resistance gene
5.1 97.3 GSM238435 Embryo 24 h; Seed germination; Rep 2 GSE9365 Expression data from barley maturing and germinating grains
4.8 97.0 GSM373002 genotype: 11542 - pathogen isolates: K1 - time: 20 - rep2 GSE14930 Comparison of wild-type and cell death mutant of barley plants containing Mla6 powdery mildew resistance gene
3.8 95.7 GSM372987 genotype: 11542 - pathogen isolates: 5874 - time: 24 - rep2 GSE14930 Comparison of wild-type and cell death mutant of barley plants containing Mla6 powdery mildew resistance gene
3.6 95.3 GSM382234 Root_Hg3 GSE15295 Mercury toxicity in barley roots
3.4 94.8 GSM372982 genotype: 11542 - pathogen isolates: 5874 - time: 16 - rep3 GSE14930 Comparison of wild-type and cell death mutant of barley plants containing Mla6 powdery mildew resistance gene
3.2 94.3 GSM146359 Golden Promise Root Control, biological rep 3 GSE6325 Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise
3.1 94.1 GSM146368 Maythorpe Root Salt, biological rep 3 GSE6325 Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise
3.0 93.8 GSM372984 genotype: 11542 - pathogen isolates: 5874 - time: 20 - rep2 GSE14930 Comparison of wild-type and cell death mutant of barley plants containing Mla6 powdery mildew resistance gene
2.9 93.4 GSM431546 pathogen isolates: Mock - rep1 GSE17238 Response of barley roots during the host interaction with the plasmodiophorid virus vector Polymyxa graminis

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
10.9	99.2	GSM372981	genotype: 11542 - pathogen isolates: 5874 - time: 16 - rep2	GSE14930	Comparison of wild-type and cell death mutant of barley plants containing Mla6 powdery mildew resistance gene
5.1	97.3	GSM238435	Embryo 24 h; Seed germination; Rep 2	GSE9365	Expression data from barley maturing and germinating grains
4.8	97.0	GSM373002	genotype: 11542 - pathogen isolates: K1 - time: 20 - rep2	GSE14930	Comparison of wild-type and cell death mutant of barley plants containing Mla6 powdery mildew resistance gene
3.8	95.7	GSM372987	genotype: 11542 - pathogen isolates: 5874 - time: 24 - rep2	GSE14930	Comparison of wild-type and cell death mutant of barley plants containing Mla6 powdery mildew resistance gene
3.6	95.3	GSM382234	Root_Hg3	GSE15295	Mercury toxicity in barley roots
3.4	94.8	GSM372982	genotype: 11542 - pathogen isolates: 5874 - time: 16 - rep3	GSE14930	Comparison of wild-type and cell death mutant of barley plants containing Mla6 powdery mildew resistance gene
3.2	94.3	GSM146359	Golden Promise Root Control, biological rep 3	GSE6325	Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise
3.1	94.1	GSM146368	Maythorpe Root Salt, biological rep 3	GSE6325	Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise
3.0	93.8	GSM372984	genotype: 11542 - pathogen isolates: 5874 - time: 20 - rep2	GSE14930	Comparison of wild-type and cell death mutant of barley plants containing Mla6 powdery mildew resistance gene
2.9	93.4	GSM431546	pathogen isolates: Mock - rep1	GSE17238	Response of barley roots during the host interaction with the plasmodiophorid virus vector Polymyxa graminis

Inter-species module comparison

A co-expression module including the Arabidopsis gene, At3g14650, orthologous to the query gene, Contig20974_at

VF %ile Gene ID Repr. ID Gene Name Func. O.I. H.G. S.X. Other DB
1.00 100.0 At3g14650 820693 CYP72A11 putative cytochrome P450 O.I. H.G. S.X.
0.49 63.5 At4g02260 828096 RSH1 (RELA-SPOT HOMOLOG 1) F:catalytic activity;P:response to wounding;C:chloroplast;BOPMAFV O.I. H.G. S.X.
0.49 63.5 At5g42310 834236 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:unknown;C:chloroplast;POMFBA O.I. H.G. S.X.
0.46 59.8 At1g23400 838948 CAF2 Promotes the splicing of chloroplast group II introns. O.I. H.G. S.X.
0.46 59.8 At4g01800 827922 preprotein translocase secA subunit, putative F:protein binding, ATP binding;P:intracellular protein transport, protein targeting, protein import;C:chloroplast stroma, chloroplast, chloroplast envelope;OBPMA O.I. H.G. S.X.
0.46 59.8 At5g50920 835165 CLPC1 Encodes a protein that is similar to ATP-dependent Clp protease ATP-binding subunit / ClpC. Involved in protein import into the chloroplast. May provide ATP source that drives the TIC (Translocon at the Inner envelope membrane of Chloroplasts) translocation machinery. O.I. H.G. S.X.
0.44 57.2 At5g42390 834245 metalloendopeptidase F:metalloendopeptidase activity, zinc ion binding, catalytic activity, metal ion binding;P:proteolysis;C:mitochondrion, chloroplast stroma, chloroplast;BOMFPAV O.I. H.G. S.X.
0.41 52.4 At4g30993 829225 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. H.G. S.X.
0.41 52.4 At2g24820 817019 TIC55 (TRANSLOCON AT THE INNER ENVELOPE MEMBRANE OF CHLOROPLASTS 55) F:electron carrier activity, oxidoreductase activity, 2 iron, 2 sulfur cluster binding;P:oxidation reduction;C:chloroplast, chloroplast envelope;BOPMFA O.I. H.G. S.X.
0.39 48.4 At5g60600 836181 HDS (4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE SYNTHASE) Encodes a chloroplast-localized hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase (HDS), catalyzes the formation of HMBPP from 2-C-methyl-D-erythrytol 2,4-cyclodiphosphate (MEcPP). The HDS enzyme controls the penultimate steps of the biosynthesis of IPP and dimethylallyl diphosphate (DMAPP) via the MEP pathway and may serve as a metabolic control point for SA-mediated disease resistance. In the light, the electrons required for the reaction catalyzed by HDS are directly provided by the electron flow from photosynthesis via ferredoxin. In the dark however, the enzyme requires an electron shuttle: ferredoxin-NADP⁺ reductase. O.I. H.G. S.X.
0.39 48.4 At3g10970 820268 haloacid dehalogenase-like hydrolase family protein F:hydrolase activity, catalytic activity;P:metabolic process;C:chloroplast;BOPAMF O.I. H.G. S.X.
0.36 43.6 At1g36320 840539 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;PO O.I. H.G. S.X.
0.33 38.1 At5g03900 831927 - F:molecular_function unknown;P:biological_process unknown;C:chloroplast envelope;BPO O.I. H.G. S.X.
0.31 33.8 At3g10230 820185 LYC (LYCOPENE CYCLASE) Encodes a protein with lycopene β-cyclase activity. This enzyme uses the linear, symmetrical lycopene as substrate. However, unlike the ε-cyclase which adds only one ring, the β-cyclase introduces a ring at both ends of lycopene to form the bicyclic β-carotene. O.I. H.G. S.X.
0.28 30.3 At1g22850 838890 - F:unknown;P:biological_process unknown;C:chloroplast;BOMPFA O.I. H.G. S.X.
0.28 30.3 At5g52440 835320 HCF106 HCF106; nuclear gene for chloroplast. Thylakoid membrane delta pH translocation pathway component protein; related to Escherichia coli TatA and TatB O.I. H.G. S.X.
0.26 24.4 At5g14260 831276 SET domain-containing protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMFO O.I. H.G. S.X.
0.22 17.5 At5g57930 835904 APO2 (ACCUMULATION OF PHOTOSYSTEM ONE 2) ACCUMULATION OF PHOTOSYSTEM ONE 2 O.I. H.G. S.X.
0.22 17.5 At4g35760 829729 - F:unknown;P:unknown;C:chloroplast;OBP O.I. H.G. S.X.
0.21 15.8 At1g08540 837376 SIG2 (RNA POLYMERASE SIGMA SUBUNIT 2) Enodes a subunit of chloroplast RNA polymerase, confers the ability to recognize promoter sequences on the core enzyme. SIG1 is induced by red and blue light. O.I. H.G. S.X.
0.20 14.4 At2g30950 817646 VAR2 (VARIEGATED 2) Metalloprotease that functions in thylakoid membrane biogenesis. Involved in the repair of PSII following damaged incurred during photoinhibition. Forms a complex with VAR1. Mutants show a variegated phenotype, which decreases during development. Transcript and protein levels increase with light intensity. O.I. H.G. S.X.
0.17 10.2 At2g28800 817429 ALB3 (ALBINO 3) member of Chloroplast membrane protein ALBINO3 family O.I. H.G. S.X.
0.16 8.8 At5g53580 835440 aldo/keto reductase family protein F:oxidoreductase activity, aldo-keto reductase activity;P:oxidation reduction;C:chloroplast;BOMFPA O.I. H.G. S.X.
0.13 5.8 At1g32060 840098 PRK (PHOSPHORIBULOKINASE) F:protein binding, phosphoribulokinase activity, ATP binding;P:response to cold, defense response to bacterium, peptidyl-cysteine S-nitrosylation, biosynthetic process;C:in 8 components;BPOMFAV O.I. H.G. S.X.
0.13 5.8 At1g71500 843491 Rieske (2Fe-2S) domain-containing protein F:electron carrier activity, oxidoreductase activity, 2 iron, 2 sulfur cluster binding;P:oxidation reduction;C:chloroplast thylakoid membrane, chloroplast, chloroplast envelope;BPO 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	At3g14650	820693	CYP72A11	putative cytochrome P450	O.I.	H.G.	S.X.
0.49	63.5	At4g02260	828096	RSH1 (RELA-SPOT HOMOLOG 1)	F:catalytic activity;P:response to wounding;C:chloroplast;BOPMAFV	O.I.	H.G.	S.X.
0.49	63.5	At5g42310	834236	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:unknown;C:chloroplast;POMFBA	O.I.	H.G.	S.X.
0.46	59.8	At1g23400	838948	CAF2	Promotes the splicing of chloroplast group II introns.	O.I.	H.G.	S.X.
0.46	59.8	At4g01800	827922	preprotein translocase secA subunit, putative	F:protein binding, ATP binding;P:intracellular protein transport, protein targeting, protein import;C:chloroplast stroma, chloroplast, chloroplast envelope;OBPMA	O.I.	H.G.	S.X.
0.46	59.8	At5g50920	835165	CLPC1	Encodes a protein that is similar to ATP-dependent Clp protease ATP-binding subunit / ClpC. Involved in protein import into the chloroplast. May provide ATP source that drives the TIC (Translocon at the Inner envelope membrane of Chloroplasts) translocation machinery.	O.I.	H.G.	S.X.
0.44	57.2	At5g42390	834245	metalloendopeptidase	F:metalloendopeptidase activity, zinc ion binding, catalytic activity, metal ion binding;P:proteolysis;C:mitochondrion, chloroplast stroma, chloroplast;BOMFPAV	O.I.	H.G.	S.X.
0.41	52.4	At4g30993	829225	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	H.G.	S.X.
0.41	52.4	At2g24820	817019	TIC55 (TRANSLOCON AT THE INNER ENVELOPE MEMBRANE OF CHLOROPLASTS 55)	F:electron carrier activity, oxidoreductase activity, 2 iron, 2 sulfur cluster binding;P:oxidation reduction;C:chloroplast, chloroplast envelope;BOPMFA	O.I.	H.G.	S.X.
0.39	48.4	At5g60600	836181	HDS (4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE SYNTHASE)	Encodes a chloroplast-localized hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase (HDS), catalyzes the formation of HMBPP from 2-C-methyl-D-erythrytol 2,4-cyclodiphosphate (MEcPP). The HDS enzyme controls the penultimate steps of the biosynthesis of IPP and dimethylallyl diphosphate (DMAPP) via the MEP pathway and may serve as a metabolic control point for SA-mediated disease resistance. In the light, the electrons required for the reaction catalyzed by HDS are directly provided by the electron flow from photosynthesis via ferredoxin. In the dark however, the enzyme requires an electron shuttle: ferredoxin-NADP⁺ reductase.	O.I.	H.G.	S.X.
0.39	48.4	At3g10970	820268	haloacid dehalogenase-like hydrolase family protein	F:hydrolase activity, catalytic activity;P:metabolic process;C:chloroplast;BOPAMF	O.I.	H.G.	S.X.
0.36	43.6	At1g36320	840539	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;PO	O.I.	H.G.	S.X.
0.33	38.1	At5g03900	831927	-	F:molecular_function unknown;P:biological_process unknown;C:chloroplast envelope;BPO	O.I.	H.G.	S.X.
0.31	33.8	At3g10230	820185	LYC (LYCOPENE CYCLASE)	Encodes a protein with lycopene β-cyclase activity. This enzyme uses the linear, symmetrical lycopene as substrate. However, unlike the ε-cyclase which adds only one ring, the β-cyclase introduces a ring at both ends of lycopene to form the bicyclic β-carotene.	O.I.	H.G.	S.X.
0.28	30.3	At1g22850	838890	-	F:unknown;P:biological_process unknown;C:chloroplast;BOMPFA	O.I.	H.G.	S.X.
0.28	30.3	At5g52440	835320	HCF106	HCF106; nuclear gene for chloroplast. Thylakoid membrane delta pH translocation pathway component protein; related to Escherichia coli TatA and TatB	O.I.	H.G.	S.X.
0.26	24.4	At5g14260	831276	SET domain-containing protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMFO	O.I.	H.G.	S.X.
0.22	17.5	At5g57930	835904	APO2 (ACCUMULATION OF PHOTOSYSTEM ONE 2)	ACCUMULATION OF PHOTOSYSTEM ONE 2	O.I.	H.G.	S.X.
0.22	17.5	At4g35760	829729	-	F:unknown;P:unknown;C:chloroplast;OBP	O.I.	H.G.	S.X.
0.21	15.8	At1g08540	837376	SIG2 (RNA POLYMERASE SIGMA SUBUNIT 2)	Enodes a subunit of chloroplast RNA polymerase, confers the ability to recognize promoter sequences on the core enzyme. SIG1 is induced by red and blue light.	O.I.	H.G.	S.X.
0.20	14.4	At2g30950	817646	VAR2 (VARIEGATED 2)	Metalloprotease that functions in thylakoid membrane biogenesis. Involved in the repair of PSII following damaged incurred during photoinhibition. Forms a complex with VAR1. Mutants show a variegated phenotype, which decreases during development. Transcript and protein levels increase with light intensity.	O.I.	H.G.	S.X.
0.17	10.2	At2g28800	817429	ALB3 (ALBINO 3)	member of Chloroplast membrane protein ALBINO3 family	O.I.	H.G.	S.X.
0.16	8.8	At5g53580	835440	aldo/keto reductase family protein	F:oxidoreductase activity, aldo-keto reductase activity;P:oxidation reduction;C:chloroplast;BOMFPA	O.I.	H.G.	S.X.
0.13	5.8	At1g32060	840098	PRK (PHOSPHORIBULOKINASE)	F:protein binding, phosphoribulokinase activity, ATP binding;P:response to cold, defense response to bacterium, peptidyl-cysteine S-nitrosylation, biosynthetic process;C:in 8 components;BPOMFAV	O.I.	H.G.	S.X.
0.13	5.8	At1g71500	843491	Rieske (2Fe-2S) domain-containing protein	F:electron carrier activity, oxidoreductase activity, 2 iron, 2 sulfur cluster binding;P:oxidation reduction;C:chloroplast thylakoid membrane, chloroplast, chloroplast envelope;BPO	O.I.	H.G.	S.X.

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

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Gene ID	Contig20974_at
Gene name
Homology with Arabidopsis	Similar to At3g14650: CYP72A11 (HF=7e-6)
Module size	7 genes
NF	0.41
%ile	56.2

Co-expression analysis

Gene ID Contig20974_at Gene name Homology with ArabidopsisSimilar to At3g14650: CYP72A11 (HF=7e-6) Module size 7 genes NF 0.41 %ile 56.2

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_maxOryza_sativaPopulus_trichocarpaTriticum_aestivumVitis_viniferaZea_mays

Gene ID Contig20974_at

Gene name
Homology with Arabidopsis Similar to At3g14650: CYP72A11 (HF=7e-6)

Module size 7 genes

NF 0.41

%ile 56.2

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