CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Zm.12634.3.A1_a_at

Gene name
Homology with Arabidopsis Similar to At4g16830: nuclear RNA-binding protein (RGGA) (HF=4e+0)

Module size 6 genes

NF 0.59

%ile 78.8

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 76.1 0.96 Zm.12634.3.A1_a_at AI891366 - - 4e+0 At4g16830 nuclear RNA-binding protein (RGGA) O.I. H.G. S.X.
0.67 85.8 0.97 Zm.1322.1.A1_at AI737263 hypothetical protein LOC100279212 - 5e-31 At3g02760 ATP binding / aminoacyl-tRNA ligase/ histidine-tRNA ligase/ nucleotide binding O.I. H.G. S.X.
0.55 71.6 0.97 Zm.4977.1.S1_at AY109232.1 - - 2e-1 At1g58360 AAP1 (AMINO ACID PERMEASE 1) O.I. H.G. S.X.
0.53 69.1 0.97 - - O.I. H.G. S.X.
0.50 65.7 0.98 Zm.2758.1.A1_at AW067110 - - 2e-6 At2g25730 unknown protein O.I. H.G. S.X.
0.48 61.3 0.97 Zm.16861.2.S1_at AW498347 L-ascorbate oxidase - 7e-4 At1g55570 sks12 (SKU5 Similar 12) 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	76.1	0.96	Zm.12634.3.A1_a_at	AI891366	-	-	4e+0	At4g16830	nuclear RNA-binding protein (RGGA)	O.I.	H.G.	S.X.
0.67	85.8	0.97	Zm.1322.1.A1_at	AI737263	hypothetical protein LOC100279212	-	5e-31	At3g02760	ATP binding / aminoacyl-tRNA ligase/ histidine-tRNA ligase/ nucleotide binding	O.I.	H.G.	S.X.
0.55	71.6	0.97	Zm.4977.1.S1_at	AY109232.1	-	-	2e-1	At1g58360	AAP1 (AMINO ACID PERMEASE 1)	O.I.	H.G.	S.X.
0.53	69.1	0.97			-	-				O.I.	H.G.	S.X.
0.50	65.7	0.98	Zm.2758.1.A1_at	AW067110	-	-	2e-6	At2g25730	unknown protein	O.I.	H.G.	S.X.
0.48	61.3	0.97	Zm.16861.2.S1_at	AW498347	L-ascorbate oxidase	-	7e-4	At1g55570	sks12 (SKU5 Similar 12)	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.
0.50	65.7	0.97	Zm.27.1.S1_at	AF041043.1	Helminthosporium carbonum susceptibility1	-	2e+0	At3g59460	-	O.I.	H.G.	S.X.
0.50	65.7	0.97	Zm.5998.1.A1_at	AI666110	-	-	4e-8	At2g03780	translin family protein	O.I.	H.G.	S.X.
0.44	55.7	0.94	Zm.4457.1.A1_at	BG266182	hypothetical protein LOC100194059 /// hypothetical protein LOC100276691	-	1e+0	At1g78790	unknown protein	O.I.	H.G.	S.X.
0.42	51.3	0.93	Zm.5466.1.A1_at	BM500911	-	-	9e-2	At1g20450	ERD10 (EARLY RESPONSIVE TO DEHYDRATION 10)	O.I.	H.G.	S.X.
0.40	48.5	0.96	Zm.4464.1.A1_at	AY109260.1	TRANSPARENT TESTA 1 protein	-	2e+0	At1g34370	STOP1 (sensitive to proton rhizotoxicity 1)	O.I.	H.G.	S.X.
0.36	41.3	0.97	Zm.4316.1.S1_a_at	AI881448	hypothetical protein LOC100273812 /// cleavage and polyadenylation specificity factor 5	-	1e-39	At4g25550	protein binding	O.I.	H.G.	S.X.
0.35	38.9	0.93	Zm.2857.1.A1_at	AW231567	-	-	5e+0	At2g17705	unknown protein	O.I.	H.G.	S.X.
0.35	38.9	0.96	Zm.2957.1.A1_at	CK371564	-	-	5e-12	At1g34370	STOP1 (sensitive to proton rhizotoxicity 1)	O.I.	H.G.	S.X.
0.35	38.9	0.96	ZmAffx.955.1.A1_at	AI833505	-	-	8e-1	At2g47480	unknown protein	O.I.	H.G.	S.X.
0.33	36.0	0.93	ZmAffx.1410.1.S1_at	40794996-85	-	-	4e+0	At2g07674	unknown protein	O.I.	H.G.	S.X.
0.33	36.0	0.94	Zm.4630.2.A1_at	CK347497	hypothetical protein LOC100273246	-	8e-7	At1g12840	DET3 (DE-ETIOLATED 3)	O.I.	H.G.	S.X.
0.33	36.0	0.96	Zm.6398.1.A1_at	CA398579	transposon protein Mutator sub-class	-	3e+0	At2g43660	glycosyl hydrolase family protein 17	O.I.	H.G.	S.X.
0.33	36.0	0.97	Zm.6416.1.S1_at	BQ744568	hypothetical protein LOC100277106	-	3e+0	At5g22880	HTB2	O.I.	H.G.	S.X.
0.33	36.0	0.97	ZmAffx.744.1.S1_at	AI745738	-	-	1e-1	At1g48300	unknown protein	O.I.	H.G.	S.X.
0.31	31.6	0.95	Zm.3591.1.A1_at	AW000408	hypothetical protein LOC100279870	-	1e-30	At5g12040	carbon-nitrogen hydrolase family protein	O.I.	H.G.	S.X.
0.31	31.6	0.97	Zm.5008.1.A1_at	AY108557.1	hypothetical protein LOC100275589	-	2e-29	At5g54870	unknown protein	O.I.	H.G.	S.X.
0.30	29.8	0.94	Zm.6513.2.S1_a_at	CF043636	-	-	2e-15	At2g33430	DAL1 (DIFFERENTIATION AND GREENING-LIKE 1)	O.I.	H.G.	S.X.
0.30	29.8	0.96	Zm.430.1.S1_at	AF099111.1	sigma-like factor2B	-	4e+0	At5g04820	OFP13 (ARABIDOPSIS THALIANA OVATE FAMILY PROTEIN 13)	O.I.	H.G.	S.X.
0.30	29.8	0.97	Zm.2489.1.A1_at	CD447064	mitochondrial chaperonin-60	-	8e-82	At3g23990	HSP60 (HEAT SHOCK PROTEIN 60)	O.I.	H.G.	S.X.
0.29	28.1	0.96	ZmAffx.81.1.A1_at	AI665287	-	-	2e-1	At5g65940	CHY1 (BETA-HYDROXYISOBUTYRYL-COA HYDROLASE 1)	O.I.	H.G.	S.X.
0.29	28.1	0.96	Zm.13103.1.S1_at	CO534624	hypothetical protein LOC100191205	-	2e-4	At5g49710	unknown protein	O.I.	H.G.	S.X.
0.29	28.1	0.97	Zm.157.1.S1_at	AY107763.1	catalase2	-	3e-22	At4g35090	CAT2 (CATALASE 2)	O.I.	H.G.	S.X.
0.29	28.1	0.97	Zm.3623.1.S1_at	BG873827	hypothetical protein LOC100216808	-	7e+0	At5g52440	HCF106	O.I.	H.G.	S.X.
0.28	28.1	0.96	Zm.13707.1.A1_at	BQ547937	rhythmically expressed protein	-	2e-14	At2g41250	haloacid dehalogenase-like hydrolase family protein	O.I.	H.G.	S.X.
0.27	24.6	0.93	ZmAffx.1010.1.S1_at	AI881417	ZF-HD protein dimerisation region containing protein	-	3e+0	At4g16840	unknown protein	O.I.	H.G.	S.X.
0.27	24.6	0.96	Zm.3098.1.A1_at	BM379893	caffeoyl-CoA O-methyltransferase 1	-	7e-10	At4g34050	caffeoyl-CoA 3-O-methyltransferase, putative	O.I.	H.G.	S.X.
0.26	22.7	0.95	Zm.4702.1.A1_at	CA401021	-	-	9e-3	At4g36180	leucine-rich repeat family protein	O.I.	H.G.	S.X.
0.25	21.3	0.95	Zm.4524.1.A1_at	CD971358	-	-	1e+1	At4g00420	double-stranded RNA-binding domain (DsRBD)-containing protein	O.I.	H.G.	S.X.
0.25	21.3	0.95	Zm.12997.2.S1_a_at	BF728194	-	-	6e-10	At3g46740	TOC75-III (TRANSLOCON AT THE OUTER ENVELOPE MEMBRANE OF CHLOROPLASTS 75-III)	O.I.	H.G.	S.X.
0.25	21.3	0.96	Zm.14290.1.S1_at	CD998001	hypothetical protein LOC100278212	-	2e-9	At3g51610	unknown protein	O.I.	H.G.	S.X.

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
5.8 97.2 GSM253279 ZM_8d_SG200_3inf_III GSE10023 Maize gene expression during infection with Ustilago maydis
5.5 97.1 GSM253278 ZM_8d_SG200_3inf_II GSE10023 Maize gene expression during infection with Ustilago maydis
4.5 96.3 GSM320452 protocol: Cot filtration (CF) - genotype: Mo17 maize inbred - rep3 GSE12770 Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
4.5 96.3 GSM320451 protocol: Cot filtration (CF) - genotype: Mo17 maize inbred - rep2 GSE12770 Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
4.3 96.1 GSM320441 protocol: mRNA - genotype: Mo17 maize inbred - rep1 GSE12770 Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
4.2 96.0 GSM320453 protocol: Cot filtration (CF) - genotype: CML69 maize inbred - rep1 GSE12770 Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
4.0 95.8 GSM320449 protocol: Cot filtration (CF) - genotype: B73 maize inbred - rep3 GSE12770 Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
4.0 95.8 GSM253277 ZM_8d_SG200_3inf_I GSE10023 Maize gene expression during infection with Ustilago maydis
3.8 95.5 GSM320450 protocol: Cot filtration (CF) - genotype: Mo17 maize inbred - rep1 GSE12770 Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
3.7 95.4 GSM320455 protocol: Cot filtration (CF) - genotype: CML69 maize inbred - rep3 GSE12770 Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
5.8	97.2	GSM253279	ZM_8d_SG200_3inf_III	GSE10023	Maize gene expression during infection with Ustilago maydis
5.5	97.1	GSM253278	ZM_8d_SG200_3inf_II	GSE10023	Maize gene expression during infection with Ustilago maydis
4.5	96.3	GSM320452	protocol: Cot filtration (CF) - genotype: Mo17 maize inbred - rep3	GSE12770	Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
4.5	96.3	GSM320451	protocol: Cot filtration (CF) - genotype: Mo17 maize inbred - rep2	GSE12770	Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
4.3	96.1	GSM320441	protocol: mRNA - genotype: Mo17 maize inbred - rep1	GSE12770	Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
4.2	96.0	GSM320453	protocol: Cot filtration (CF) - genotype: CML69 maize inbred - rep1	GSE12770	Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
4.0	95.8	GSM320449	protocol: Cot filtration (CF) - genotype: B73 maize inbred - rep3	GSE12770	Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
4.0	95.8	GSM253277	ZM_8d_SG200_3inf_I	GSE10023	Maize gene expression during infection with Ustilago maydis
3.8	95.5	GSM320450	protocol: Cot filtration (CF) - genotype: Mo17 maize inbred - rep1	GSE12770	Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
3.7	95.4	GSM320455	protocol: Cot filtration (CF) - genotype: CML69 maize inbred - rep3	GSE12770	Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes

Inter-species module comparison

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

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Gene ID	Zm.12634.3.A1_a_at
Gene name
Homology with Arabidopsis	Similar to At4g16830: nuclear RNA-binding protein (RGGA) (HF=4e+0)
Module size	6 genes
NF	0.59
%ile	78.8

Co-expression analysis

Gene ID Zm.12634.3.A1_a_at Gene name Homology with ArabidopsisSimilar to At4g16830: nuclear RNA-binding protein (RGGA) (HF=4e+0) Module size 6 genes NF 0.59 %ile 78.8

Co-expressed genes

Specific experiments for the module

Inter-species module comparison

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

Gene ID Zm.12634.3.A1_a_at

Gene name
Homology with Arabidopsis Similar to At4g16830: nuclear RNA-binding protein (RGGA) (HF=4e+0)

Module size 6 genes

NF 0.59

%ile 78.8

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