CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Os09g0462300

Gene name
Homology with Arabidopsis Similar to At5g16200: 50S ribosomal protein-related (HF=3e+0)

Module size 6 genes

NF 0.28

%ile 28.2

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
0.80 94.6 0.96 Os09g0462300 9637.m02532 - Esterase/lipase/thioesterase domain containingprotein 3e+0 At5g16200 50S ribosomal protein-related O.I. H.G. S.X.
0.55 73.7 0.96 Os07g0216100 AK107820.1 - Hypothetical protein 9e-2 At5g66490 unknown protein O.I. H.G. S.X.
0.29 31.1 0.96 Os09g0433500 9637.m02294 - Glycosyl transferase, family 31 protein 5e-1 At3g29300 unknown protein O.I. H.G. S.X.
0.26 25.6 0.96 Os01g0176700 AK109808.1 - Myb, DNA-binding domain containing protein 1e-12 At2g03500 myb family transcription factor O.I. H.G. S.X.
0.22 19.4 0.96 Os02g0602600 9630.m03753 - RNA-binding region RNP-1 (RNA recognition motif)domain containing protein 3e+0 At5g24316 proline-rich family protein O.I. H.G. S.X.
0.11 6.5 0.96 Os03g0118100 AK072029.1 - Conserved hypothetical protein 2e-1 At4g15460 glycine-rich protein 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.
0.80	94.6	0.96	Os09g0462300	9637.m02532	-	Esterase/lipase/thioesterase domain containingprotein	3e+0	At5g16200	50S ribosomal protein-related	O.I.	H.G.	S.X.
0.55	73.7	0.96	Os07g0216100	AK107820.1	-	Hypothetical protein	9e-2	At5g66490	unknown protein	O.I.	H.G.	S.X.
0.29	31.1	0.96	Os09g0433500	9637.m02294	-	Glycosyl transferase, family 31 protein	5e-1	At3g29300	unknown protein	O.I.	H.G.	S.X.
0.26	25.6	0.96	Os01g0176700	AK109808.1	-	Myb, DNA-binding domain containing protein	1e-12	At2g03500	myb family transcription factor	O.I.	H.G.	S.X.
0.22	19.4	0.96	Os02g0602600	9630.m03753	-	RNA-binding region RNP-1 (RNA recognition motif)domain containing protein	3e+0	At5g24316	proline-rich family protein	O.I.	H.G.	S.X.
0.11	6.5	0.96	Os03g0118100	AK072029.1	-	Conserved hypothetical protein	2e-1	At4g15460	glycine-rich protein	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
27.4 99.6 GSM422672 Drought GSE16865 Heterologous microarrays for the study of drought stress in Musa
13.5 98.5 GSM422674 Musa_DNA_RICE GSE16865 Heterologous microarrays for the study of drought stress in Musa
11.9 98.3 GSM377081 Genomic DNA - 45 day old leaf sample - mutant g7534 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
11.7 98.2 GSM377076 Genomic DNA - 45 day old leaf sample - mutant g6485 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
11.0 98.2 GSM377078 Genomic DNA - 45 day old leaf sample - mutant g6603 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
10.1 98.0 GSM195218 stigma 1, biological rep1 GSE7951 Genome-wide gene expression profiling of rice stigma
10.0 98.0 GSM195219 stigma 2, biological rep 2 GSE7951 Genome-wide gene expression profiling of rice stigma
9.7 98.0 GSM377080 Genomic DNA - 45 day old leaf sample - mutant g6728 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
9.7 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
9.5 97.9 GSM377070 Genomic DNA - 45 day old leaf sample - mutant d1 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
27.4	99.6	GSM422672	Drought	GSE16865	Heterologous microarrays for the study of drought stress in Musa
13.5	98.5	GSM422674	Musa_DNA_RICE	GSE16865	Heterologous microarrays for the study of drought stress in Musa
11.9	98.3	GSM377081	Genomic DNA - 45 day old leaf sample - mutant g7534	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
11.7	98.2	GSM377076	Genomic DNA - 45 day old leaf sample - mutant g6485	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
11.0	98.2	GSM377078	Genomic DNA - 45 day old leaf sample - mutant g6603	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
10.1	98.0	GSM195218	stigma 1, biological rep1	GSE7951	Genome-wide gene expression profiling of rice stigma
10.0	98.0	GSM195219	stigma 2, biological rep 2	GSE7951	Genome-wide gene expression profiling of rice stigma
9.7	98.0	GSM377080	Genomic DNA - 45 day old leaf sample - mutant g6728	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
9.7	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
9.5	97.9	GSM377070	Genomic DNA - 45 day old leaf sample - mutant d1	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, At5g16200, orthologous to the query gene, Os09g0462300

VF %ile Gene ID Repr. ID Gene Name Func. O.I. H.G. S.X. Other DB
0.69 82.9 At5g16200 831478 50S ribosomal protein-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.60 75.7 At4g37260 829880 MYB73 (MYB DOMAIN PROTEIN 73) Member of the R2R3 factor gene family. O.I. H.G. S.X.
0.50 65.3 At1g51700 841595 ADOF1 Encodes dof zinc finger protein (adof1). O.I. H.G. S.X.
0.50 65.3 At1g70740 843411 protein kinase family protein F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVA O.I. H.G. S.X.
0.50 65.3 At5g24590 832530 - - O.I. H.G. S.X.
0.44 57.2 At1g19770 838565 ATPUP14 Member of a family of proteins related to PUP1, a purine transporter. May be involved in the transport of purine and purine derivatives such as cytokinins, across the plasma membrane. O.I. H.G. S.X.
0.43 55.3 At1g27770 839670 ACA1 (AUTO-INHIBITED CA2+-ATPASE 1) Encodes a chloroplast envelope Ca2+-ATPase with an N-terminal autoinhibitor. O.I. H.G. S.X.
0.40 50.8 At3g50060 824168 MYB77 Encodes a member of the R2R3 transcription factor gene family. Expressed in response to potassium deprivation and auxin. Involved in lateral root development. Interacts with ARF7 and regulates the expression of some auxin responsive genes. O.I. H.G. S.X.
0.38 46.7 At5g62570 836377 calmodulin-binding protein F:calmodulin binding;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.38 46.7 At3g15210 820752 ERF4 (ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 4) Encodes a member of the ERF (ethylene response factor) subfamily B-1 of ERF/AP2 transcription factor family (ATERF-4). The protein contains one AP2 domain. Acts as a negative regulator of JA-responsive defense gene expression and resistance to the necrotrophic fungal pathogen Fusarium oxysporum and antagonizes JA inhibition of root elongation. O.I. H.G. S.X.
0.36 43.6 At4g01090 827898 extra-large G-protein-related F:unknown;P:unknown;C:unknown;MPFOBV O.I. H.G. S.X.
0.36 43.6 At1g18740 838456 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;PA O.I. H.G. S.X.
0.35 41.6 At5g58430 835956 ATEXO70B1 (exocyst subunit EXO70 family protein B1) A member of EXO70 gene family, putative exocyst subunits, conserved in land plants. Arabidopsis thaliana contains 23 putative EXO70 genes, which can be classified into eight clusters on the phylogenetic tree. O.I. H.G. S.X.
0.35 41.6 At1g74450 843786 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. H.G. S.X.
0.35 41.6 At1g11050 837646 protein kinase family protein F:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVA O.I. H.G. S.X.
0.34 39.8 At1g67470 843068 protein kinase family protein F:protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;PMOBFVA O.I. H.G. S.X.
0.33 38.1 At4g27280 828836 calcium-binding EF hand family protein F:calcium ion binding;P:biological_process unknown;C:unknown;MPOF O.I. H.G. S.X.
0.32 35.7 At5g66210 836753 CPK28 member of Calcium Dependent Protein Kinase O.I. H.G. S.X.
0.32 35.7 At3g46600 823813 scarecrow transcription factor family protein F:transcription factor activity;P:response to chitin, regulation of transcription;C:cellular_component unknown;PBM O.I. H.G. S.X.
0.31 33.8 At3g46620 823815 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:response to chitin;C:unknown;PMOFVB O.I. H.G. S.X.
0.30 32.1 At2g26190 817159 calmodulin-binding family protein F:calmodulin binding;P:N-terminal protein myristoylation;C:unknown;PFOB O.I. H.G. S.X.
0.29 30.3 At5g67300 836865 MYBR1 (MYB DOMAIN PROTEIN R1) Member of the R2R3 factor MYB gene family involved in mediating plant responses to a variety of abiotic stimiuli. O.I. H.G. S.X.
0.28 30.3 At1g75230 843860 HhH-GPD base excision DNA repair family protein F:catalytic activity;P:DNA repair, base-excision repair;C:nucleus;OBFPAM O.I. H.G. S.X.
0.27 26.2 At3g56880 824855 VQ motif-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PF O.I. H.G. S.X.
0.25 22.6 At3g45640 823706 ATMPK3 (ARABIDOPSIS THALIANA MITOGEN-ACTIVATED PROTEIN KINASE 3) Encodes a mitogen-activated kinase whose mRNA levels increase in response to touch, cold, salinity stress and chitin oligomers.Also functions in ovule development. Heterozygous MPK3 mutants in a homozygous MPK6 background are female sterile due to defects in integument development. MPK3 can be dephosphorylated by MKP2 in vitro. O.I. H.G. S.X.
0.25 22.6 At5g46470 834690 disease resistance protein (TIR-NBS-LRR class), putative F:transmembrane receptor activity, protein binding, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:signal transduction, defense response, apoptosis, innate immune response;C:intrinsic to membrane;PMBOFAV O.I. H.G. S.X.
0.24 20.7 At1g09070 837428 SRC2 (SOYBEAN GENE REGULATED BY COLD-2) SRC2 specifically binds the peptide PIEPPPHH, and moves from ER to a vacuole fraction where it gets internalized. Involved in Protein Storage Vacuole targeting. O.I. H.G. S.X.
0.22 17.5 At2g47060 819320 serine/threonine protein kinase, putative F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:unknown;MPOBFVA O.I. H.G. S.X.
0.20 14.4 At1g29340 839808 PUB17 (PLANT U-BOX 17) Encodes a protein containing a UND, a U-box, and an ARM domain. This protein has E3 ubiquitin ligase activity. It is required for cell death and full resistance specified by Arabidopsis RPM1 and RPS4 resistance proteins against Pseudomonas syringae pv tomato. O.I. H.G. S.X.
0.17 10.2 At3g26980 822315 MUB4 (MEMBRANE-ANCHORED UBIQUITIN-FOLD PROTEIN 4 PRECURSOR) F:molecular_function unknown;P:protein modification process;C:cellular_component unknown;PF O.I. H.G. S.X.

VF	%ile	Gene ID	Repr. ID	Gene Name	Func.	O.I.	H.G.	S.X.
0.69	82.9	At5g16200	831478	50S ribosomal protein-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.60	75.7	At4g37260	829880	MYB73 (MYB DOMAIN PROTEIN 73)	Member of the R2R3 factor gene family.	O.I.	H.G.	S.X.
0.50	65.3	At1g51700	841595	ADOF1	Encodes dof zinc finger protein (adof1).	O.I.	H.G.	S.X.
0.50	65.3	At1g70740	843411	protein kinase family protein	F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVA	O.I.	H.G.	S.X.
0.50	65.3	At5g24590	832530	-	-	O.I.	H.G.	S.X.
0.44	57.2	At1g19770	838565	ATPUP14	Member of a family of proteins related to PUP1, a purine transporter. May be involved in the transport of purine and purine derivatives such as cytokinins, across the plasma membrane.	O.I.	H.G.	S.X.
0.43	55.3	At1g27770	839670	ACA1 (AUTO-INHIBITED CA2+-ATPASE 1)	Encodes a chloroplast envelope Ca2+-ATPase with an N-terminal autoinhibitor.	O.I.	H.G.	S.X.
0.40	50.8	At3g50060	824168	MYB77	Encodes a member of the R2R3 transcription factor gene family. Expressed in response to potassium deprivation and auxin. Involved in lateral root development. Interacts with ARF7 and regulates the expression of some auxin responsive genes.	O.I.	H.G.	S.X.
0.38	46.7	At5g62570	836377	calmodulin-binding protein	F:calmodulin binding;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.38	46.7	At3g15210	820752	ERF4 (ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 4)	Encodes a member of the ERF (ethylene response factor) subfamily B-1 of ERF/AP2 transcription factor family (ATERF-4). The protein contains one AP2 domain. Acts as a negative regulator of JA-responsive defense gene expression and resistance to the necrotrophic fungal pathogen Fusarium oxysporum and antagonizes JA inhibition of root elongation.	O.I.	H.G.	S.X.
0.36	43.6	At4g01090	827898	extra-large G-protein-related	F:unknown;P:unknown;C:unknown;MPFOBV	O.I.	H.G.	S.X.
0.36	43.6	At1g18740	838456	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;PA	O.I.	H.G.	S.X.
0.35	41.6	At5g58430	835956	ATEXO70B1 (exocyst subunit EXO70 family protein B1)	A member of EXO70 gene family, putative exocyst subunits, conserved in land plants. Arabidopsis thaliana contains 23 putative EXO70 genes, which can be classified into eight clusters on the phylogenetic tree.	O.I.	H.G.	S.X.
0.35	41.6	At1g74450	843786	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	H.G.	S.X.
0.35	41.6	At1g11050	837646	protein kinase family protein	F:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVA	O.I.	H.G.	S.X.
0.34	39.8	At1g67470	843068	protein kinase family protein	F:protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;PMOBFVA	O.I.	H.G.	S.X.
0.33	38.1	At4g27280	828836	calcium-binding EF hand family protein	F:calcium ion binding;P:biological_process unknown;C:unknown;MPOF	O.I.	H.G.	S.X.
0.32	35.7	At5g66210	836753	CPK28	member of Calcium Dependent Protein Kinase	O.I.	H.G.	S.X.
0.32	35.7	At3g46600	823813	scarecrow transcription factor family protein	F:transcription factor activity;P:response to chitin, regulation of transcription;C:cellular_component unknown;PBM	O.I.	H.G.	S.X.
0.31	33.8	At3g46620	823815	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:response to chitin;C:unknown;PMOFVB	O.I.	H.G.	S.X.
0.30	32.1	At2g26190	817159	calmodulin-binding family protein	F:calmodulin binding;P:N-terminal protein myristoylation;C:unknown;PFOB	O.I.	H.G.	S.X.
0.29	30.3	At5g67300	836865	MYBR1 (MYB DOMAIN PROTEIN R1)	Member of the R2R3 factor MYB gene family involved in mediating plant responses to a variety of abiotic stimiuli.	O.I.	H.G.	S.X.
0.28	30.3	At1g75230	843860	HhH-GPD base excision DNA repair family protein	F:catalytic activity;P:DNA repair, base-excision repair;C:nucleus;OBFPAM	O.I.	H.G.	S.X.
0.27	26.2	At3g56880	824855	VQ motif-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PF	O.I.	H.G.	S.X.
0.25	22.6	At3g45640	823706	ATMPK3 (ARABIDOPSIS THALIANA MITOGEN-ACTIVATED PROTEIN KINASE 3)	Encodes a mitogen-activated kinase whose mRNA levels increase in response to touch, cold, salinity stress and chitin oligomers.Also functions in ovule development. Heterozygous MPK3 mutants in a homozygous MPK6 background are female sterile due to defects in integument development. MPK3 can be dephosphorylated by MKP2 in vitro.	O.I.	H.G.	S.X.
0.25	22.6	At5g46470	834690	disease resistance protein (TIR-NBS-LRR class), putative	F:transmembrane receptor activity, protein binding, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:signal transduction, defense response, apoptosis, innate immune response;C:intrinsic to membrane;PMBOFAV	O.I.	H.G.	S.X.
0.24	20.7	At1g09070	837428	SRC2 (SOYBEAN GENE REGULATED BY COLD-2)	SRC2 specifically binds the peptide PIEPPPHH, and moves from ER to a vacuole fraction where it gets internalized. Involved in Protein Storage Vacuole targeting.	O.I.	H.G.	S.X.
0.22	17.5	At2g47060	819320	serine/threonine protein kinase, putative	F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:unknown;MPOBFVA	O.I.	H.G.	S.X.
0.20	14.4	At1g29340	839808	PUB17 (PLANT U-BOX 17)	Encodes a protein containing a UND, a U-box, and an ARM domain. This protein has E3 ubiquitin ligase activity. It is required for cell death and full resistance specified by Arabidopsis RPM1 and RPS4 resistance proteins against Pseudomonas syringae pv tomato.	O.I.	H.G.	S.X.
0.17	10.2	At3g26980	822315	MUB4 (MEMBRANE-ANCHORED UBIQUITIN-FOLD PROTEIN 4 PRECURSOR)	F:molecular_function unknown;P:protein modification process;C:cellular_component unknown;PF	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	Os09g0462300
Gene name
Homology with Arabidopsis	Similar to At5g16200: 50S ribosomal protein-related (HF=3e+0)
Module size	6 genes
NF	0.28
%ile	28.2

Co-expression analysis

Gene ID Os09g0462300 Gene name Homology with ArabidopsisSimilar to At5g16200: 50S ribosomal protein-related (HF=3e+0) Module size 6 genes NF 0.28 %ile 28.2

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 Os09g0462300

Gene name
Homology with Arabidopsis Similar to At5g16200: 50S ribosomal protein-related (HF=3e+0)

Module size 6 genes

NF 0.28

%ile 28.2

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