CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Os11g0140400

Gene name
Homology with Arabidopsis Similar to At3g57330: ACA11 (autoinhibited Ca2+-ATPase 11) (HF=2e-24)

Module size 6 genes

NF 0.23

%ile 22.4

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
0.59 78.0 0.89 Os11g0140400 9640.m00336 - Calcium-translocating P-type ATPase, PMCA-typefamily protein 2e-24 At3g57330 ACA11 (autoinhibited Ca2+-ATPase 11) O.I. H.G. S.X.
0.55 73.7 0.89 Os01g0236300 AK102521.1 - Auxin response factor 18 2e-2 At4g23980 ARF9 (AUXIN RESPONSE FACTOR 9) O.I. H.G. S.X.
0.50 68.0 0.90 Os06g0222400 AK063886.1 - Hypothetical protein 2e-3 At5g46780 VQ motif-containing protein O.I. H.G. S.X.
0.19 15.1 0.90 Os01g0897600 CA762923 - Glycoside hydrolase, family 1 protein 2e-7 At5g36890 BGLU42 (BETA GLUCOSIDASE 42) O.I. H.G. S.X.
0.18 13.7 0.90 Os05g0120700 AK062874.1 - Cation transporting ATPase, C-terminal domaincontaining protein 2e-23 At1g07810 ECA1 (ER-TYPE CA2+-ATPASE 1) O.I. H.G. S.X.
0.07 3.7 0.89 Os01g0864700 AU172991 - Protein kinase domain containing protein 3e-51 At3g44200 NEK6 ("NIMA (NEVER IN MITOSIS, GENE A)-RELATED 6") 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.
0.59	78.0	0.89	Os11g0140400	9640.m00336	-	Calcium-translocating P-type ATPase, PMCA-typefamily protein	2e-24	At3g57330	ACA11 (autoinhibited Ca2+-ATPase 11)	O.I.	H.G.	S.X.
0.55	73.7	0.89	Os01g0236300	AK102521.1	-	Auxin response factor 18	2e-2	At4g23980	ARF9 (AUXIN RESPONSE FACTOR 9)	O.I.	H.G.	S.X.
0.50	68.0	0.90	Os06g0222400	AK063886.1	-	Hypothetical protein	2e-3	At5g46780	VQ motif-containing protein	O.I.	H.G.	S.X.
0.19	15.1	0.90	Os01g0897600	CA762923	-	Glycoside hydrolase, family 1 protein	2e-7	At5g36890	BGLU42 (BETA GLUCOSIDASE 42)	O.I.	H.G.	S.X.
0.18	13.7	0.90	Os05g0120700	AK062874.1	-	Cation transporting ATPase, C-terminal domaincontaining protein	2e-23	At1g07810	ECA1 (ER-TYPE CA2+-ATPASE 1)	O.I.	H.G.	S.X.
0.07	3.7	0.89	Os01g0864700	AU172991	-	Protein kinase domain containing protein	3e-51	At3g44200	NEK6 ("NIMA (NEVER IN MITOSIS, GENE A)-RELATED 6")	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
19.5 99.1 GSM422672 Drought GSE16865 Heterologous microarrays for the study of drought stress in Musa
10.4 98.1 GSM377070 Genomic DNA - 45 day old leaf sample - mutant d1 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
10.0 98.0 GSM377071 Genomic DNA - 45 day old leaf sample - mutant d256 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
9.3 97.9 GSM377075 Genomic DNA - 45 day old leaf sample - mutant g650 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
9.2 97.9 GSM377084 Genomic DNA - 45 day old leaf sample - mutant f1856 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
9.2 97.9 GSM377076 Genomic DNA - 45 day old leaf sample - mutant g6485 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.9 97.8 GSM422676 Control GSE16865 Heterologous microarrays for the study of drought stress in Musa
8.7 97.8 GSM377073 Genomic DNA - 45 day old leaf sample - mutant d2943 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.2 97.7 GSM377080 Genomic DNA - 45 day old leaf sample - mutant g6728 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.1 97.7 GSM377077 Genomic DNA - 45 day old leaf sample - mutant g6489 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
19.5	99.1	GSM422672	Drought	GSE16865	Heterologous microarrays for the study of drought stress in Musa
10.4	98.1	GSM377070	Genomic DNA - 45 day old leaf sample - mutant d1	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
10.0	98.0	GSM377071	Genomic DNA - 45 day old leaf sample - mutant d256	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
9.3	97.9	GSM377075	Genomic DNA - 45 day old leaf sample - mutant g650	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
9.2	97.9	GSM377084	Genomic DNA - 45 day old leaf sample - mutant f1856	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
9.2	97.9	GSM377076	Genomic DNA - 45 day old leaf sample - mutant g6485	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.9	97.8	GSM422676	Control	GSE16865	Heterologous microarrays for the study of drought stress in Musa
8.7	97.8	GSM377073	Genomic DNA - 45 day old leaf sample - mutant d2943	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.2	97.7	GSM377080	Genomic DNA - 45 day old leaf sample - mutant g6728	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.1	97.7	GSM377077	Genomic DNA - 45 day old leaf sample - mutant g6489	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO

Inter-species module comparison

A co-expression module including the Arabidopsis gene, At3g57330, orthologous to the query gene, Os11g0140400

VF %ile Gene ID Repr. ID Gene Name Func. O.I. H.G. S.X. Other DB
0.60 75.7 At3g57330 824900 ACA11 (autoinhibited Ca2+-ATPase 11) F:calmodulin binding, calcium-transporting ATPase activity;P:cation transport, calcium ion transport, metabolic process, ATP biosynthetic process;C:chloroplast, plasma membrane, vacuole;BMOFPAV O.I. H.G. S.X.
0.46 59.8 At4g33300 829466 ADR1-L1 (ADR1-like 1) F:protein binding, ATP binding;P:defense response, apoptosis;C:apoplast;PMBOFA O.I. H.G. S.X.
0.42 53.9 At5g04720 830350 ADR1-L2 (ADR1-like 2) F:protein binding, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:defense response, apoptosis;C:unknown;PMBOFA O.I. H.G. S.X.
0.40 50.8 At4g23470 828446 hydroxyproline-rich glycoprotein family protein F:unknown;P:unknown;C:unknown;MOPFBVA O.I. H.G. S.X.
0.39 48.4 At4g17070 827415 peptidyl-prolyl cis-trans isomerase F:peptidyl-prolyl cis-trans isomerase activity;P:response to oxidative stress;C:unknown;PBMO O.I. H.G. S.X.
0.34 39.8 At3g28450 822474 leucine-rich repeat transmembrane protein kinase, putative F:protein serine/threonine kinase activity, kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:chloroplast, plasma membrane, membrane;PMOBFVA O.I. H.G. S.X.
0.34 39.8 At2g22300 816762 SR1 (SIGNAL RESPONSIVE 1) Encodes a putative CAM binding transcription factor. Loss of function mutations show enhanced resistance to fungal and bacterial pathogens suggesting that CAMTA functions to suppress defense responses. O.I. H.G. S.X.
0.31 33.8 At4g33430 829480 BAK1 (BRI1-ASSOCIATED RECEPTOR KINASE) Leu-rich receptor Serine/threonine protein kinase. Component of BR signaling that interacts with BRI1 in vitro and in vivo to form a heterodimer. Brassinolide-dependent association of BRI1 and BAK1 in vivo. Phosphorylation of both BRI1 and BAK1 on Thr residues was BR dependent. Although BAK1 and BRI1 alone localize in the plasma membrane, when BAK1 and BRI1 are coexpressed, the heterodimer BAK1/BRI1 they form is localized in the endosome. O.I. H.G. S.X.
0.27 26.2 At3g12740 820456 ALIS1 (ALA-INTERACTING SUBUNIT 1) Physically interacts with ALA3, and is required for the phospholipid translocase activity of ALA3. O.I. H.G. S.X.
0.24 20.7 At4g37640 829918 ACA2 (CALCIUM ATPASE 2) Encodes a calmodulin-regulated Ca(2+)-pump located in the endoplasmic reticulum. Belongs to plant 2B ATPase's with an N-terminal autoinhibitor. O.I. H.G. S.X.
0.23 19.3 At1g11310 837673 MLO2 (MILDEW RESISTANCE LOCUS O 2) A member of a large family of seven-transmembrane domain proteins specific to plants, homologs of the barley mildew resistance locus o (MLO) protein. The Arabidopsis genome contains 15 genes encoding MLO proteins, with localization in plasma membrane. Phylogenetic analysis revealed four clades of closely-related AtMLO genes. ATMLO2 belongs to the clade IV, with AtMLO3, AtMLO6 and AtMLO12. The gene is expressed during early seedling growth, in roots, in vascular system of cotyledons and young leaves,and in fruit abscission zone; it was not expressed in anthers and pollen, as shown by GUS activity patterns. The expression of several phylogenetically closely-related AtMLO genes showed similar or overlapping tissue specificity and analogous responsiveness to external stimuli, suggesting functional redundancy, co-function, or antagonistic function(s). mlo resistance in A. thaliana does not involve the signaling molecules ethylene, jasmonic acid or salicylic acid, but requires a syntaxin, glycosyl hydrolase and ABC transporter. O.I. H.G. S.X.
0.22 17.5 At1g31130 839998 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBOA O.I. H.G. S.X.
0.20 14.4 At1g64280 842733 NPR1 (NONEXPRESSER OF PR GENES 1) This gene is a key regulator of the salicylic acid (SA)-mediated systemic acquired resistance (SAR) pathway. It is similar to the transcription factor inhibitor I kappa B, and contains ankyrin repeats. It confers resistance to the pathogens Pseudomonas syringae and Peronospora parasitica in a dosage-dependent fashion. Although transgenic Arabidopsis plants overexpressing NPR1 acquire enhanced sensitivity to SA and (benzothiadiazole) BTH, they display no obvious detrimental morphological changes and do not have elevated pathogenesis-related gene expression until activated by inducers or pathogens. O.I. H.G. S.X.
0.18 11.4 At1g07630 837276 PLL5 Encodes a protein phosphatase 2C like gene, similar to POL. Involved in leaf development. Knockout mutants have abnormally shaped leaves. O.I. H.G. S.X.
0.17 10.2 At3g57280 824895 unknown protein F:unknown;P:biological_process unknown;C:chloroplast, chloroplast inner membrane, chloroplast envelope;PMO O.I. H.G. S.X.
0.17 10.2 At2g20900 816624 diacylglycerol kinase, putative F:diacylglycerol kinase activity;P:activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway;C:cellular_component unknown;MPO O.I. H.G. S.X.
0.17 10.2 At2g21120 816647 unknown protein F:unknown;P:biological_process unknown;C:unknown;MFPBO O.I. H.G. S.X.
0.14 6.8 At4g29900 829112 ACA10 (AUTOINHIBITED CA(2+)-ATPASE 10) one of the type IIB calcium pump isoforms. encodes an autoinhibited Ca(2+)-ATPase that contains an N-terminal calmodulin binding autoinhibitory domain. O.I. H.G. S.X.
0.13 5.8 At1g02170 839561 AMC1 (METACASPASE 1) Metacaspase AtMCP1b. Arginine/lysine-specific cysteine protease activity. Induces apoptosis in yeast. Contains Pfam profile PF00656: ICE-like protease (caspase) p20 domain O.I. H.G. S.X.
0.12 4.9 At1g07240 837235 UGT71C5 (UDP-GLUCOSYL TRANSFERASE 71C5) F:quercetin 3-O-glucosyltransferase activity, UDP-glycosyltransferase activity, transferase activity, transferring glycosyl groups;P:metabolic process;C:cellular_component unknown;PMBOVF O.I. H.G. S.X.
0.10 3.4 At1g61140 842407 EDA16 (embryo sac development arrest 16) F:in 6 functions;P:embryo sac development;C:unknown;MBFOPVA O.I. H.G. S.X.

VF	%ile	Gene ID	Repr. ID	Gene Name	Func.	O.I.	H.G.	S.X.
0.60	75.7	At3g57330	824900	ACA11 (autoinhibited Ca2+-ATPase 11)	F:calmodulin binding, calcium-transporting ATPase activity;P:cation transport, calcium ion transport, metabolic process, ATP biosynthetic process;C:chloroplast, plasma membrane, vacuole;BMOFPAV	O.I.	H.G.	S.X.
0.46	59.8	At4g33300	829466	ADR1-L1 (ADR1-like 1)	F:protein binding, ATP binding;P:defense response, apoptosis;C:apoplast;PMBOFA	O.I.	H.G.	S.X.
0.42	53.9	At5g04720	830350	ADR1-L2 (ADR1-like 2)	F:protein binding, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:defense response, apoptosis;C:unknown;PMBOFA	O.I.	H.G.	S.X.
0.40	50.8	At4g23470	828446	hydroxyproline-rich glycoprotein family protein	F:unknown;P:unknown;C:unknown;MOPFBVA	O.I.	H.G.	S.X.
0.39	48.4	At4g17070	827415	peptidyl-prolyl cis-trans isomerase	F:peptidyl-prolyl cis-trans isomerase activity;P:response to oxidative stress;C:unknown;PBMO	O.I.	H.G.	S.X.
0.34	39.8	At3g28450	822474	leucine-rich repeat transmembrane protein kinase, putative	F:protein serine/threonine kinase activity, kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:chloroplast, plasma membrane, membrane;PMOBFVA	O.I.	H.G.	S.X.
0.34	39.8	At2g22300	816762	SR1 (SIGNAL RESPONSIVE 1)	Encodes a putative CAM binding transcription factor. Loss of function mutations show enhanced resistance to fungal and bacterial pathogens suggesting that CAMTA functions to suppress defense responses.	O.I.	H.G.	S.X.
0.31	33.8	At4g33430	829480	BAK1 (BRI1-ASSOCIATED RECEPTOR KINASE)	Leu-rich receptor Serine/threonine protein kinase. Component of BR signaling that interacts with BRI1 in vitro and in vivo to form a heterodimer. Brassinolide-dependent association of BRI1 and BAK1 in vivo. Phosphorylation of both BRI1 and BAK1 on Thr residues was BR dependent. Although BAK1 and BRI1 alone localize in the plasma membrane, when BAK1 and BRI1 are coexpressed, the heterodimer BAK1/BRI1 they form is localized in the endosome.	O.I.	H.G.	S.X.
0.27	26.2	At3g12740	820456	ALIS1 (ALA-INTERACTING SUBUNIT 1)	Physically interacts with ALA3, and is required for the phospholipid translocase activity of ALA3.	O.I.	H.G.	S.X.
0.24	20.7	At4g37640	829918	ACA2 (CALCIUM ATPASE 2)	Encodes a calmodulin-regulated Ca(2+)-pump located in the endoplasmic reticulum. Belongs to plant 2B ATPase's with an N-terminal autoinhibitor.	O.I.	H.G.	S.X.
0.23	19.3	At1g11310	837673	MLO2 (MILDEW RESISTANCE LOCUS O 2)	A member of a large family of seven-transmembrane domain proteins specific to plants, homologs of the barley mildew resistance locus o (MLO) protein. The Arabidopsis genome contains 15 genes encoding MLO proteins, with localization in plasma membrane. Phylogenetic analysis revealed four clades of closely-related AtMLO genes. ATMLO2 belongs to the clade IV, with AtMLO3, AtMLO6 and AtMLO12. The gene is expressed during early seedling growth, in roots, in vascular system of cotyledons and young leaves,and in fruit abscission zone; it was not expressed in anthers and pollen, as shown by GUS activity patterns. The expression of several phylogenetically closely-related AtMLO genes showed similar or overlapping tissue specificity and analogous responsiveness to external stimuli, suggesting functional redundancy, co-function, or antagonistic function(s). mlo resistance in A. thaliana does not involve the signaling molecules ethylene, jasmonic acid or salicylic acid, but requires a syntaxin, glycosyl hydrolase and ABC transporter.	O.I.	H.G.	S.X.
0.22	17.5	At1g31130	839998	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBOA	O.I.	H.G.	S.X.
0.20	14.4	At1g64280	842733	NPR1 (NONEXPRESSER OF PR GENES 1)	This gene is a key regulator of the salicylic acid (SA)-mediated systemic acquired resistance (SAR) pathway. It is similar to the transcription factor inhibitor I kappa B, and contains ankyrin repeats. It confers resistance to the pathogens Pseudomonas syringae and Peronospora parasitica in a dosage-dependent fashion. Although transgenic Arabidopsis plants overexpressing NPR1 acquire enhanced sensitivity to SA and (benzothiadiazole) BTH, they display no obvious detrimental morphological changes and do not have elevated pathogenesis-related gene expression until activated by inducers or pathogens.	O.I.	H.G.	S.X.
0.18	11.4	At1g07630	837276	PLL5	Encodes a protein phosphatase 2C like gene, similar to POL. Involved in leaf development. Knockout mutants have abnormally shaped leaves.	O.I.	H.G.	S.X.
0.17	10.2	At3g57280	824895	unknown protein	F:unknown;P:biological_process unknown;C:chloroplast, chloroplast inner membrane, chloroplast envelope;PMO	O.I.	H.G.	S.X.
0.17	10.2	At2g20900	816624	diacylglycerol kinase, putative	F:diacylglycerol kinase activity;P:activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway;C:cellular_component unknown;MPO	O.I.	H.G.	S.X.
0.17	10.2	At2g21120	816647	unknown protein	F:unknown;P:biological_process unknown;C:unknown;MFPBO	O.I.	H.G.	S.X.
0.14	6.8	At4g29900	829112	ACA10 (AUTOINHIBITED CA(2+)-ATPASE 10)	one of the type IIB calcium pump isoforms. encodes an autoinhibited Ca(2+)-ATPase that contains an N-terminal calmodulin binding autoinhibitory domain.	O.I.	H.G.	S.X.
0.13	5.8	At1g02170	839561	AMC1 (METACASPASE 1)	Metacaspase AtMCP1b. Arginine/lysine-specific cysteine protease activity. Induces apoptosis in yeast. Contains Pfam profile PF00656: ICE-like protease (caspase) p20 domain	O.I.	H.G.	S.X.
0.12	4.9	At1g07240	837235	UGT71C5 (UDP-GLUCOSYL TRANSFERASE 71C5)	F:quercetin 3-O-glucosyltransferase activity, UDP-glycosyltransferase activity, transferase activity, transferring glycosyl groups;P:metabolic process;C:cellular_component unknown;PMBOVF	O.I.	H.G.	S.X.
0.10	3.4	At1g61140	842407	EDA16 (embryo sac development arrest 16)	F:in 6 functions;P:embryo sac development;C:unknown;MBFOPVA	O.I.	H.G.	S.X.

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

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Gene ID	Os11g0140400
Gene name
Homology with Arabidopsis	Similar to At3g57330: ACA11 (autoinhibited Ca2+-ATPase 11) (HF=2e-24)
Module size	6 genes
NF	0.23
%ile	22.4

Co-expression analysis

Gene ID Os11g0140400 Gene name Homology with ArabidopsisSimilar to At3g57330: ACA11 (autoinhibited Ca2+-ATPase 11) (HF=2e-24) Module size 6 genes NF 0.23 %ile 22.4

Co-expressed genes

Click More genes

Specific experiments for the module

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO

Inter-species module comparison

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

Gene ID Os11g0140400

Gene name
Homology with Arabidopsis Similar to At3g57330: ACA11 (autoinhibited Ca2+-ATPase 11) (HF=2e-24)

Module size 6 genes

NF 0.23

%ile 22.4

SF Genes GO ID Process Name Link to AmiGO

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