CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Zm.12746.1.A1_at

Gene name somatic embryogenesis related protein
Homology with Arabidopsis Similar to At2g18530: protein kinase family protein (HF=1e+0)

Module size 6 genes

NF 0.49

%ile 61.4

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
0.50 65.7 0.98 Zm.12746.1.A1_at BU499218 somatic embryogenesis related protein - 1e+0 At2g18530 protein kinase family protein O.I. H.G. S.X.
0.67 85.8 0.99 Zm.16824.1.S1_at CF602732 SAM domain family protein - 5e-1 At3g07170 sterile alpha motif (SAM) domain-containing protein O.I. H.G. S.X.
0.60 77.8 0.99 ZmAffx.587.1.A1_at AI715015 - - 3e+0 At5g35900 LBD35 (LOB DOMAIN-CONTAINING PROTEIN 35) O.I. H.G. S.X.
0.40 48.5 0.99 Zm.18109.1.S1_at AI881274 - - 3e+0 At4g23340 oxidoreductase, 2OG-Fe(II) oxygenase family protein O.I. H.G. S.X.
0.36 41.3 0.99 ZmAffx.743.1.S1_at AI745735 - - 8e-1 At4g28170 unknown protein O.I. H.G. S.X.
0.32 33.4 0.99 Zm.7309.1.S1_at AF384036.1 nucleosome/chromatin assembly factor A - 2e-3 At1g18800 NRP2 (NAP1-RELATED PROTEIN 2) 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	0.98	Zm.12746.1.A1_at	BU499218	somatic embryogenesis related protein	-	1e+0	At2g18530	protein kinase family protein	O.I.	H.G.	S.X.
0.67	85.8	0.99	Zm.16824.1.S1_at	CF602732	SAM domain family protein	-	5e-1	At3g07170	sterile alpha motif (SAM) domain-containing protein	O.I.	H.G.	S.X.
0.60	77.8	0.99	ZmAffx.587.1.A1_at	AI715015	-	-	3e+0	At5g35900	LBD35 (LOB DOMAIN-CONTAINING PROTEIN 35)	O.I.	H.G.	S.X.
0.40	48.5	0.99	Zm.18109.1.S1_at	AI881274	-	-	3e+0	At4g23340	oxidoreductase, 2OG-Fe(II) oxygenase family protein	O.I.	H.G.	S.X.
0.36	41.3	0.99	ZmAffx.743.1.S1_at	AI745735	-	-	8e-1	At4g28170	unknown protein	O.I.	H.G.	S.X.
0.32	33.4	0.99	Zm.7309.1.S1_at	AF384036.1	nucleosome/chromatin assembly factor A	-	2e-3	At1g18800	NRP2 (NAP1-RELATED PROTEIN 2)	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.
0.57	75.1	0.97	Zm.2778.1.S1_at	AW067213	myb family transcription factor-related protein	-	3e-15	At1g79430	APL (ALTERED PHLOEM DEVELOPMENT)	O.I.	H.G.	S.X.
0.50	65.7	0.98	Zm.6183.1.A1_at	AY106169.1	MKI67 FHA domain-interacting nucleolar phosphoprotein-like	-	2e+0	At2g47020	peptide chain release factor, putative	O.I.	H.G.	S.X.
0.50	65.7	0.99	Zm.6555.2.S1_at	CD446565	hypothetical protein LOC100273907	-	1e-31	At3g11710	ATKRS-1 (ARABIDOPSIS THALIANA LYSYL-TRNA SYNTHETASE 1)	O.I.	H.G.	S.X.
0.43	52.8	0.97	Zm.18107.1.S1_at	AY536125.1	meg5 protein	-	3e-1	At5g22190	unknown protein	O.I.	H.G.	S.X.
0.40	48.5	0.98	Zm.14012.1.S1_at	AY108370.1	hypothetical protein LOC100276126	-	9e-2	At4g35750	Rho-GTPase-activating protein-related	O.I.	H.G.	S.X.
0.40	48.5	0.98	Zm.3930.1.S1_at	BQ538158	AMP-binding protein	-	8e-37	At3g05970	LACS6 (long-chain acyl-CoA synthetase 6)	O.I.	H.G.	S.X.
0.38	44.2	0.98	Zm.6828.1.A1_at	AI396546	-	-	2e-1	At1g02710	glycine-rich protein	O.I.	H.G.	S.X.
0.36	41.3	0.98	Zm.2319.2.S1_at	CD444652	hypothetical protein LOC100272537	-	5e+0	At5g65350	histone H3	O.I.	H.G.	S.X.
0.36	41.3	0.99	ZmAffx.754.1.S1_at	AI745921	-	-	2e-1	At1g33960	AIG1 (AVRRPT2-INDUCED GENE 1)	O.I.	H.G.	S.X.
0.33	36.0	0.97	Zm.9568.1.A1_x_at	CD435747	hypothetical protein LOC100191846	-	6e-58	At3g03250	UGP (UDP-glucose pyrophosphorylase)	O.I.	H.G.	S.X.
0.33	36.0	0.98	Zm.206.3.S1_a_at	Y09636.1	40S ribosomal subunit protein S21	-	5e-12	At3g53890	40S ribosomal protein S21 (RPS21B)	O.I.	H.G.	S.X.
0.33	36.0	0.98	Zm.10147.1.A1_at	BM381621	NAC1 transcription factor	-	2e+0	At3g15280	unknown protein	O.I.	H.G.	S.X.
0.33	36.0	0.98	Zm.12383.1.S1_at	BQ578166	-	-	1e-1	At5g12480	CPK7 (calmodulin-domain protein kinase 7)	O.I.	H.G.	S.X.
0.33	36.0	0.98	Zm.18135.1.A1_at	CN845300	-	-	4e+0	Atmg01410	-	O.I.	H.G.	S.X.
0.32	33.4	0.98	Zm.5065.1.S1_s_at	BM318796	Diacylglycerol kinase 1	-	9e+0	At2g39630	glycosyl transferase family 2 protein	O.I.	H.G.	S.X.
0.30	29.8	0.98	Zm.2741.1.A1_at	CB603857	-	-	2e+0	At4g13140	-	O.I.	H.G.	S.X.
0.29	28.1	0.98	Zm.5321.1.A1_at	BG841445	hypothetical protein LOC100191836	-	5e+0	At2g45250	unknown protein	O.I.	H.G.	S.X.
0.29	28.1	0.98	Zm.14524.1.S1_at	AY104558.1	hypothetical protein LOC100272454	-	8e-3	At4g38620	MYB4	O.I.	H.G.	S.X.
0.27	24.6	0.98	Zm.547.1.A1_at	CK827104	glutathione transferase17	-	1e-1	At1g02405	proline-rich family protein	O.I.	H.G.	S.X.
0.27	24.6	0.99	Zm.5230.1.A1_at	CA404914	acyl-desaturase	-	2e-17	At2g43710	SSI2	O.I.	H.G.	S.X.
0.26	22.7	0.98	Zm.5115.1.A1_at	AI600917	hypothetical protein LOC100272658	-	2e-46	At3g20290	ATEHD1 (EPS15 HOMOLOGY DOMAIN 1)	O.I.	H.G.	S.X.
0.26	22.7	0.96	Zm.16575.1.A1_at	CF648732	hypothetical protein LOC100193462	-	8e-5	At3g14270	phosphatidylinositol-4-phosphate 5-kinase family protein	O.I.	H.G.	S.X.
0.25	21.3	0.96	Zm.5882.1.A1_at	AI637237	-	-	2e-1	At1g52880	NAM (NO APICAL MERISTEM)	O.I.	H.G.	S.X.
0.25	21.3	0.97	Zm.7750.2.S1_a_at	AY103542.1	Beta-6 tubulin	-	3e-155	At5g12250	TUB6 (BETA-6 TUBULIN)	O.I.	H.G.	S.X.
0.25	21.3	0.98	ZmAffx.816.1.A1_at	AI770437	-	-	3e+0	At3g12977	DNA binding	O.I.	H.G.	S.X.
0.25	21.3	0.98	Zm.16796.2.A1_x_at	AI734496	-	-	3e+0	At2g23570	MES19 (METHYL ESTERASE 19)	O.I.	H.G.	S.X.
0.25	21.3	0.99	Zm.2012.1.S1_at	AW566063	-	-	8e+0	At5g23220	NIC3 (NICOTINAMIDASE 3)	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
9.2 98.2 GSM320447 protocol: Cot filtration (CF) - genotype: B73 maize inbred - rep1 GSE12770 Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
8.4 98.1 GSM320448 protocol: Cot filtration (CF) - genotype: B73 maize inbred - rep2 GSE12770 Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
6.4 97.5 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
4.1 95.9 GSM202298 B73 immature ear tissue, biological replicate 2 GSE8176 Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data
4.0 95.8 GSM202304 B73 immature ear tissue, biological replicate 3 GSE8176 Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data
3.6 95.2 GSM202292 B73 immature ear tissue, biological replicate 1 GSE8176 Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data
3.5 95.1 GSM202296 B73xMo17 immature ear tissue, biological replicate 1 GSE8176 Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data
3.4 94.9 GSM202302 B73xMo17 immature ear tissue, biological replicate 2 GSE8176 Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data
3.4 94.9 GSM202306 Mo17xB73 immature ear tissue, biological replicate 3 GSE8176 Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data
3.3 94.7 GSM202299 Mo17xB73 immature ear tissue, biological replicate 2 GSE8176 Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
9.2	98.2	GSM320447	protocol: Cot filtration (CF) - genotype: B73 maize inbred - rep1	GSE12770	Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
8.4	98.1	GSM320448	protocol: Cot filtration (CF) - genotype: B73 maize inbred - rep2	GSE12770	Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
6.4	97.5	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
4.1	95.9	GSM202298	B73 immature ear tissue, biological replicate 2	GSE8176	Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data
4.0	95.8	GSM202304	B73 immature ear tissue, biological replicate 3	GSE8176	Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data
3.6	95.2	GSM202292	B73 immature ear tissue, biological replicate 1	GSE8176	Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data
3.5	95.1	GSM202296	B73xMo17 immature ear tissue, biological replicate 1	GSE8176	Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data
3.4	94.9	GSM202302	B73xMo17 immature ear tissue, biological replicate 2	GSE8176	Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data
3.4	94.9	GSM202306	Mo17xB73 immature ear tissue, biological replicate 3	GSE8176	Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data
3.3	94.7	GSM202299	Mo17xB73 immature ear tissue, biological replicate 2	GSE8176	Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data

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

Back to the CoP portal site

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Gene ID	Zm.12746.1.A1_at
Gene name	somatic embryogenesis related protein
Homology with Arabidopsis	Similar to At2g18530: protein kinase family protein (HF=1e+0)
Module size	6 genes
NF	0.49
%ile	61.4

Co-expression analysis

Gene ID Zm.12746.1.A1_at Gene name somatic embryogenesis related protein Homology with ArabidopsisSimilar to At2g18530: protein kinase family protein (HF=1e+0) Module size 6 genes NF 0.49 %ile 61.4

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.12746.1.A1_at

Gene name somatic embryogenesis related protein
Homology with Arabidopsis Similar to At2g18530: protein kinase family protein (HF=1e+0)

Module size 6 genes

NF 0.49

%ile 61.4

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