CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Os12g0169800

Gene name
Homology with Arabidopsis Similar to At4g09570: CPK4 (HF=2e-8)

Module size 37 genes

NF 0.43

%ile 53.5

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
0.87 96.6 0.94 Os12g0169800 9640.m00650 - Calcium-dependent protein kinase SK5 (EC 2.7.1.-)(CDPK) 2e-8 At4g09570 CPK4 O.I. H.G. S.X.
0.58 77.0 0.96 Os12g0617900 AK066418.1 - Serine/threonine protein phosphatase BSL2 (EC3.1.3.16) (BSU1-like protein 2) 5e-109 At2g27210 kelch repeat-containing serine/threonine phosphoesterase family protein O.I. H.G. S.X.
0.55 73.7 0.97 Os02g0101700 AK072570.1 - HECT ubiquitin-protein ligase 3 (KAKTUS protein) 2e-14 At4g38600 KAK (KAKTUS) O.I. H.G. S.X.
0.54 71.9 0.96 Os03g0833300 AK065741.1 - SBP domain containing protein 1e-4 At2g47070 SPL1 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 1) O.I. H.G. S.X.
0.54 71.9 0.96 Os10g0575200 AK066761.1 - Protein psi1 (Protein psi) 1e-30 At2g26890 GRV2 (GRAVITROPISM DEFECTIVE 2) O.I. H.G. S.X.
0.53 71.3 0.96 Os09g0434000 AK062791.1 - FYVE/PHD zinc finger domain containing protein 9e-30 At3g43240 ARID/BRIGHT DNA-binding domain-containing protein O.I. H.G. S.X.
0.53 71.3 0.96 Os07g0632600 AK102629.1 - Heat shock protein DnaJ, N-terminal domaincontaining protein 1e+0 At4g29080 PAP2 (PHYTOCHROME-ASSOCIATED PROTEIN 2) O.I. H.G. S.X.
0.51 68.7 0.96 Os05g0292200 AK065373.1 - Transcription factor IIA large subunit (TFIIA-L1) 3e+0 At4g14315 unknown protein O.I. H.G. S.X.
0.50 68.0 0.97 Os03g0395600 AK063311.1 - Hypothetical protein 4e-1 At1g30260 - O.I. H.G. S.X.
0.48 63.7 0.97 Os09g0281600 AK067020.1 - SWAP/Surp domain containing protein 6e-12 At3g52120 SWAP (Suppressor-of-White-APricot)/surp domain-containing protein / D111/G-patch domain-containing protein O.I. H.G. S.X.
0.48 63.7 0.96 Os02g0550000 CA998950 - Conserved hypothetical protein 7e+0 At5g11360 - O.I. H.G. S.X.
0.46 60.9 0.96 Os03g0366200 AK059466.1 - CaMK1 3e-14 At3g19100 calcium-dependent protein kinase, putative / CDPK, putative O.I. H.G. S.X.
0.46 60.9 0.97 Os04g0440100 AK105415.1 - Nonsense-mediated decay UPF3 domain containingprotein 2e-9 At1g33980 Smg-4/UPF3 family protein O.I. H.G. S.X.
0.45 58.8 0.96 Os11g0148700 AK066721.1 - Zn-finger-like, PHD finger domain containingprotein 7e+0 At5g35210 peptidase M50 family protein / sterol-regulatory element binding protein (SREBP) site 2 protease family protein O.I. H.G. S.X.
0.45 58.8 0.96 Os05g0562400 AK121237.1 - DDT domain containing protein 2e-7 At1g28420 HB-1 (homeobox-1) O.I. H.G. S.X.
0.45 58.8 0.97 Os07g0495900 AK060293.1 - Regulator of nonsense transcripts 1 homolog 1e-6 At5g47010 LBA1 (LOW-LEVEL BETA-AMYLASE 1) O.I. H.G. S.X.
0.44 58.1 0.97 Os12g0102400 AK103750.1 - RNA-binding region RNP-1 (RNA recognition motif)domain containing protein 6e-16 At3g45630 RNA recognition motif (RRM)-containing protein O.I. H.G. S.X.
0.42 53.9 0.96 Os03g0214900 AK100534.1 - Hypothetical protein 1e-1 At5g45860 Bet v I allergen family protein O.I. H.G. S.X.
0.41 52.4 0.96 Os03g0281600 AK070260.1 - Ca2+-ATPase 1e-63 At1g07670 calcium-transporting ATPase O.I. H.G. S.X.
0.41 52.4 0.97 Os03g0213300 AK058608.1 - Hypothetical protein 7e-1 At1g47495 unknown protein O.I. H.G. S.X.
0.40 51.1 0.96 Os08g0474700 AK064878.1 - - 1e-13 At2g21630 transport protein, putative O.I. H.G. S.X.
0.40 51.1 0.97 Os03g0223700 AK068416.1 - ARM repeat fold domain containing protein 2e-49 At2g01690 binding O.I. H.G. S.X.
0.40 51.1 0.97 Os01g0945800 AK072850.1 - RNA-binding region RNP-1 (RNA recognition motif)domain containing protein 2e-17 At4g36960 RNA recognition motif (RRM)-containing protein O.I. H.G. S.X.
0.40 51.1 0.96 Os07g0163800 NM_186432.1 - Ubiquitin-specific protease 12 2e-89 At5g06600 UBP12 (UBIQUITIN-SPECIFIC PROTEASE 12) O.I. H.G. S.X.
0.40 51.1 0.97 Os03g0750800 AK061386.1 - Transcriptional adaptor ADA2b (AT4g16420/dl4235c) 9e-11 At4g16420 ADA2B (HOMOLOG OF YEAST ADA2 2B) O.I. H.G. S.X.
0.39 48.3 0.97 Os04g0195000 AK073992.1 - Vacuolar assembly protein VPS41 homolog 2e-24 At1g08190 vacuolar assembly protein, putative (VPS41) O.I. H.G. S.X.
0.39 48.3 0.96 Os09g0515800 AK066076.1 - RabGAP/TBC domain containing protein 3e-19 At2g30710 RabGAP/TBC domain-containing protein O.I. H.G. S.X.
0.38 46.9 0.96 Os02g0787500 AY224451.1 - The start codon is not identified. 7e-39 At4g32600 zinc finger (C3HC4-type RING finger) family protein O.I. H.G. S.X.
0.35 41.7 0.97 Os05g0126300 CB635555 - Conserved hypothetical protein 1e-2 At3g57740 protein kinase family protein O.I. H.G. S.X.
0.34 40.0 0.96 Os08g0137100 AK111761.1 - Polycomb group protein FIE2(FERTILIZATION-INDEPENDENT ENDOSPERM 2) 1e-24 At3g20740 FIE (FERTILIZATION-INDEPENDENT ENDOSPERM) O.I. H.G. S.X.
0.34 40.0 0.96 Os03g0427900 AU078411 - U box domain containing protein 1e-4 At5g15400 U-box domain-containing protein O.I. H.G. S.X.
0.32 36.3 0.95 Os01g0897800 AK072409.1 - Rad21/Rec8 like protein, N-terminal domaincontaining protein 8e-37 At5g16270 SYN4 (SISTER CHROMATID COHESION 1 PROTEIN 4) O.I. H.G. S.X.
0.32 36.3 0.95 Os10g0182000 AK066368.1 - Alanyl-tRNA synthetase, mitochondrial precursor(EC 6.1.1.7) (Alanine--tRNA ligase) (AlaRS) 3e-23 At1g50200 ALATS (ALANYL-TRNA SYNTHETASE) O.I. H.G. S.X.
0.30 32.7 0.97 Os01g0744300 NM_191171.1 - Casein kinase-like protein 4e-15 At2g25760 protein kinase family protein O.I. H.G. S.X.
0.29 31.1 0.96 Os02g0781800 AK099467.1 - WD40-like domain containing protein 6e-10 At3g54190 - O.I. H.G. S.X.
0.28 31.1 0.96 Os08g0537800 AK059388.1 - The start codon is not identified. 4e-2 At2g37600 60S ribosomal protein L36 (RPL36A) O.I. H.G. S.X.
0.26 25.6 0.95 Os01g0235800 AK058731.1 - KH, type 1 domain containing protein 3e-1 At1g20450 ERD10 (EARLY RESPONSIVE TO DEHYDRATION 10) 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.
0.87	96.6	0.94	Os12g0169800	9640.m00650	-	Calcium-dependent protein kinase SK5 (EC 2.7.1.-)(CDPK)	2e-8	At4g09570	CPK4	O.I.	H.G.	S.X.
0.58	77.0	0.96	Os12g0617900	AK066418.1	-	Serine/threonine protein phosphatase BSL2 (EC3.1.3.16) (BSU1-like protein 2)	5e-109	At2g27210	kelch repeat-containing serine/threonine phosphoesterase family protein	O.I.	H.G.	S.X.
0.55	73.7	0.97	Os02g0101700	AK072570.1	-	HECT ubiquitin-protein ligase 3 (KAKTUS protein)	2e-14	At4g38600	KAK (KAKTUS)	O.I.	H.G.	S.X.
0.54	71.9	0.96	Os03g0833300	AK065741.1	-	SBP domain containing protein	1e-4	At2g47070	SPL1 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 1)	O.I.	H.G.	S.X.
0.54	71.9	0.96	Os10g0575200	AK066761.1	-	Protein psi1 (Protein psi)	1e-30	At2g26890	GRV2 (GRAVITROPISM DEFECTIVE 2)	O.I.	H.G.	S.X.
0.53	71.3	0.96	Os09g0434000	AK062791.1	-	FYVE/PHD zinc finger domain containing protein	9e-30	At3g43240	ARID/BRIGHT DNA-binding domain-containing protein	O.I.	H.G.	S.X.
0.53	71.3	0.96	Os07g0632600	AK102629.1	-	Heat shock protein DnaJ, N-terminal domaincontaining protein	1e+0	At4g29080	PAP2 (PHYTOCHROME-ASSOCIATED PROTEIN 2)	O.I.	H.G.	S.X.
0.51	68.7	0.96	Os05g0292200	AK065373.1	-	Transcription factor IIA large subunit (TFIIA-L1)	3e+0	At4g14315	unknown protein	O.I.	H.G.	S.X.
0.50	68.0	0.97	Os03g0395600	AK063311.1	-	Hypothetical protein	4e-1	At1g30260	-	O.I.	H.G.	S.X.
0.48	63.7	0.97	Os09g0281600	AK067020.1	-	SWAP/Surp domain containing protein	6e-12	At3g52120	SWAP (Suppressor-of-White-APricot)/surp domain-containing protein / D111/G-patch domain-containing protein	O.I.	H.G.	S.X.
0.48	63.7	0.96	Os02g0550000	CA998950	-	Conserved hypothetical protein	7e+0	At5g11360	-	O.I.	H.G.	S.X.
0.46	60.9	0.96	Os03g0366200	AK059466.1	-	CaMK1	3e-14	At3g19100	calcium-dependent protein kinase, putative / CDPK, putative	O.I.	H.G.	S.X.
0.46	60.9	0.97	Os04g0440100	AK105415.1	-	Nonsense-mediated decay UPF3 domain containingprotein	2e-9	At1g33980	Smg-4/UPF3 family protein	O.I.	H.G.	S.X.
0.45	58.8	0.96	Os11g0148700	AK066721.1	-	Zn-finger-like, PHD finger domain containingprotein	7e+0	At5g35210	peptidase M50 family protein / sterol-regulatory element binding protein (SREBP) site 2 protease family protein	O.I.	H.G.	S.X.
0.45	58.8	0.96	Os05g0562400	AK121237.1	-	DDT domain containing protein	2e-7	At1g28420	HB-1 (homeobox-1)	O.I.	H.G.	S.X.
0.45	58.8	0.97	Os07g0495900	AK060293.1	-	Regulator of nonsense transcripts 1 homolog	1e-6	At5g47010	LBA1 (LOW-LEVEL BETA-AMYLASE 1)	O.I.	H.G.	S.X.
0.44	58.1	0.97	Os12g0102400	AK103750.1	-	RNA-binding region RNP-1 (RNA recognition motif)domain containing protein	6e-16	At3g45630	RNA recognition motif (RRM)-containing protein	O.I.	H.G.	S.X.
0.42	53.9	0.96	Os03g0214900	AK100534.1	-	Hypothetical protein	1e-1	At5g45860	Bet v I allergen family protein	O.I.	H.G.	S.X.
0.41	52.4	0.96	Os03g0281600	AK070260.1	-	Ca2+-ATPase	1e-63	At1g07670	calcium-transporting ATPase	O.I.	H.G.	S.X.
0.41	52.4	0.97	Os03g0213300	AK058608.1	-	Hypothetical protein	7e-1	At1g47495	unknown protein	O.I.	H.G.	S.X.
0.40	51.1	0.96	Os08g0474700	AK064878.1	-	-	1e-13	At2g21630	transport protein, putative	O.I.	H.G.	S.X.
0.40	51.1	0.97	Os03g0223700	AK068416.1	-	ARM repeat fold domain containing protein	2e-49	At2g01690	binding	O.I.	H.G.	S.X.
0.40	51.1	0.97	Os01g0945800	AK072850.1	-	RNA-binding region RNP-1 (RNA recognition motif)domain containing protein	2e-17	At4g36960	RNA recognition motif (RRM)-containing protein	O.I.	H.G.	S.X.
0.40	51.1	0.96	Os07g0163800	NM_186432.1	-	Ubiquitin-specific protease 12	2e-89	At5g06600	UBP12 (UBIQUITIN-SPECIFIC PROTEASE 12)	O.I.	H.G.	S.X.
0.40	51.1	0.97	Os03g0750800	AK061386.1	-	Transcriptional adaptor ADA2b (AT4g16420/dl4235c)	9e-11	At4g16420	ADA2B (HOMOLOG OF YEAST ADA2 2B)	O.I.	H.G.	S.X.
0.39	48.3	0.97	Os04g0195000	AK073992.1	-	Vacuolar assembly protein VPS41 homolog	2e-24	At1g08190	vacuolar assembly protein, putative (VPS41)	O.I.	H.G.	S.X.
0.39	48.3	0.96	Os09g0515800	AK066076.1	-	RabGAP/TBC domain containing protein	3e-19	At2g30710	RabGAP/TBC domain-containing protein	O.I.	H.G.	S.X.
0.38	46.9	0.96	Os02g0787500	AY224451.1	-	The start codon is not identified.	7e-39	At4g32600	zinc finger (C3HC4-type RING finger) family protein	O.I.	H.G.	S.X.
0.35	41.7	0.97	Os05g0126300	CB635555	-	Conserved hypothetical protein	1e-2	At3g57740	protein kinase family protein	O.I.	H.G.	S.X.
0.34	40.0	0.96	Os08g0137100	AK111761.1	-	Polycomb group protein FIE2(FERTILIZATION-INDEPENDENT ENDOSPERM 2)	1e-24	At3g20740	FIE (FERTILIZATION-INDEPENDENT ENDOSPERM)	O.I.	H.G.	S.X.
0.34	40.0	0.96	Os03g0427900	AU078411	-	U box domain containing protein	1e-4	At5g15400	U-box domain-containing protein	O.I.	H.G.	S.X.
0.32	36.3	0.95	Os01g0897800	AK072409.1	-	Rad21/Rec8 like protein, N-terminal domaincontaining protein	8e-37	At5g16270	SYN4 (SISTER CHROMATID COHESION 1 PROTEIN 4)	O.I.	H.G.	S.X.
0.32	36.3	0.95	Os10g0182000	AK066368.1	-	Alanyl-tRNA synthetase, mitochondrial precursor(EC 6.1.1.7) (Alanine--tRNA ligase) (AlaRS)	3e-23	At1g50200	ALATS (ALANYL-TRNA SYNTHETASE)	O.I.	H.G.	S.X.
0.30	32.7	0.97	Os01g0744300	NM_191171.1	-	Casein kinase-like protein	4e-15	At2g25760	protein kinase family protein	O.I.	H.G.	S.X.
0.29	31.1	0.96	Os02g0781800	AK099467.1	-	WD40-like domain containing protein	6e-10	At3g54190	-	O.I.	H.G.	S.X.
0.28	31.1	0.96	Os08g0537800	AK059388.1	-	The start codon is not identified.	4e-2	At2g37600	60S ribosomal protein L36 (RPL36A)	O.I.	H.G.	S.X.
0.26	25.6	0.95	Os01g0235800	AK058731.1	-	KH, type 1 domain containing protein	3e-1	At1g20450	ERD10 (EARLY RESPONSIVE TO DEHYDRATION 10)	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
12.6 98.4 GSM422672 Drought GSE16865 Heterologous microarrays for the study of drought stress in Musa
8.8 97.8 GSM377075 Genomic DNA - 45 day old leaf sample - mutant g650 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.4 97.7 GSM377070 Genomic DNA - 45 day old leaf sample - mutant d1 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.2 97.7 GSM377084 Genomic DNA - 45 day old leaf sample - mutant f1856 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.9 97.6 GSM377080 Genomic DNA - 45 day old leaf sample - mutant g6728 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.6 97.5 GSM377085 Genomic DNA - 45 day old leaf sample - mutant f2045 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.4 97.5 GSM377081 Genomic DNA - 45 day old leaf sample - mutant g7534 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.3 97.5 GSM377071 Genomic DNA - 45 day old leaf sample - mutant d256 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.2 97.4 GSM377082 Genomic DNA - 45 day old leaf sample - mutant g9799 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.1 97.4 GSM377073 Genomic DNA - 45 day old leaf sample - mutant d2943 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
12.6	98.4	GSM422672	Drought	GSE16865	Heterologous microarrays for the study of drought stress in Musa
8.8	97.8	GSM377075	Genomic DNA - 45 day old leaf sample - mutant g650	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.4	97.7	GSM377070	Genomic DNA - 45 day old leaf sample - mutant d1	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.2	97.7	GSM377084	Genomic DNA - 45 day old leaf sample - mutant f1856	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.9	97.6	GSM377080	Genomic DNA - 45 day old leaf sample - mutant g6728	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.6	97.5	GSM377085	Genomic DNA - 45 day old leaf sample - mutant f2045	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.4	97.5	GSM377081	Genomic DNA - 45 day old leaf sample - mutant g7534	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.3	97.5	GSM377071	Genomic DNA - 45 day old leaf sample - mutant d256	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.2	97.4	GSM377082	Genomic DNA - 45 day old leaf sample - mutant g9799	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.1	97.4	GSM377073	Genomic DNA - 45 day old leaf sample - mutant d2943	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
0.051 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.
0.049 1 GO:0006816 The directed movement of calcium (Ca) ions into, out of, within or between cells.
0.049 1 GO:0009307 Any process that protect an organism from invading foreign DNA by methylation of self DNA at specific sequences and nucleolytic cleavage of unmethylated foreign DNA.

SF	Genes	GO ID	Process Name
0.051	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.
0.049	1	GO:0006816	The directed movement of calcium (Ca) ions into, out of, within or between cells.
0.049	1	GO:0009307	Any process that protect an organism from invading foreign DNA by methylation of self DNA at specific sequences and nucleolytic cleavage of unmethylated foreign DNA.

Inter-species module comparison

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

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Gene ID	Os12g0169800
Gene name
Homology with Arabidopsis	Similar to At4g09570: CPK4 (HF=2e-8)
Module size	37 genes
NF	0.43
%ile	53.5

Co-expression analysis

Gene ID Os12g0169800 Gene name Homology with ArabidopsisSimilar to At4g09570: CPK4 (HF=2e-8) Module size 37 genes NF 0.43 %ile 53.5

Co-expressed genes

Click More genes

Specific experiments for the module

Biological processes inferred to relate to the module

Inter-species module comparison

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

Gene ID Os12g0169800

Gene name
Homology with Arabidopsis Similar to At4g09570: CPK4 (HF=2e-8)

Module size 37 genes

NF 0.43

%ile 53.5

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