CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID EBem08_SQ002_D16_s_at

Gene name
Homology with Arabidopsis Similar to At5g60460: sec61beta family protein (HF=2e-4)

Module size 7 genes

NF 0.45

%ile 62.5

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
0.60 77.3 0.96 EBem08_SQ002_D16_s_at EBem08_SQ002_D16 - - 2e-4 At5g60460 sec61beta family protein O.I. H.G. S.X.
0.50 66.9 0.96 Contig4268_s_at Contig4268 - - 3e-49 At5g23250 succinyl-CoA ligase (GDP-forming) alpha-chain, mitochondrial, putative / succinyl-CoA synthetase, alpha chain, putative / SCS-alpha, putative O.I. H.G. S.X.
0.50 66.9 0.97 Contig5696_at Contig5696 - - 7e-3 At5g48335 unknown protein O.I. H.G. S.X.
0.48 63.2 0.96 Contig4366_at Contig4366 - - 5e-16 At5g49810 MMT O.I. H.G. S.X.
0.47 62.2 0.96 Contig3205_at Contig3205 - - 3e-7 At4g14710 acireductone dioxygenase [iron(II)-requiring]/ metal ion binding O.I. H.G. S.X.
0.35 45.1 0.96 Contig2575_s_at Contig2575 - - 2e-1 At4g27540 PRA1.H (PRENYLATED RAB ACCEPTOR 1.H) O.I. H.G. S.X.
0.28 35.5 0.96 Contig3920_at Contig3920 - - 3e-21 At5g01410 RSR4 (REDUCED SUGAR RESPONSE 4) 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.
0.60	77.3	0.96	EBem08_SQ002_D16_s_at	EBem08_SQ002_D16	-	-	2e-4	At5g60460	sec61beta family protein	O.I.	H.G.	S.X.
0.50	66.9	0.96	Contig4268_s_at	Contig4268	-	-	3e-49	At5g23250	succinyl-CoA ligase (GDP-forming) alpha-chain, mitochondrial, putative / succinyl-CoA synthetase, alpha chain, putative / SCS-alpha, putative	O.I.	H.G.	S.X.
0.50	66.9	0.97	Contig5696_at	Contig5696	-	-	7e-3	At5g48335	unknown protein	O.I.	H.G.	S.X.
0.48	63.2	0.96	Contig4366_at	Contig4366	-	-	5e-16	At5g49810	MMT	O.I.	H.G.	S.X.
0.47	62.2	0.96	Contig3205_at	Contig3205	-	-	3e-7	At4g14710	acireductone dioxygenase [iron(II)-requiring]/ metal ion binding	O.I.	H.G.	S.X.
0.35	45.1	0.96	Contig2575_s_at	Contig2575	-	-	2e-1	At4g27540	PRA1.H (PRENYLATED RAB ACCEPTOR 1.H)	O.I.	H.G.	S.X.
0.28	35.5	0.96	Contig3920_at	Contig3920	-	-	3e-21	At5g01410	RSR4 (REDUCED SUGAR RESPONSE 4)	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.
0.63	80.3	0.94	EBpi03_SQ003_P13_s_at	EBpi03_SQ003_P13	-	-	9e-1	At5g42030	ABIL4 (ABL INTERACTOR-LIKE PROTEIN 4)	O.I.	H.G.	S.X.
0.59	75.8	0.93	Contig4077_at	Contig4077	-	-	5e-11	At1g65260	PTAC4 (PLASTID TRANSCRIPTIONALLY ACTIVE4)	O.I.	H.G.	S.X.
0.47	62.2	0.95	Contig2764_s_at	Contig2764	-	-	3e-9	At5g54190	PORA	O.I.	H.G.	S.X.
0.46	61.0	0.95	Contig2909_s_at	Contig2909	-	-	7e-1	At3g18295	unknown protein	O.I.	H.G.	S.X.
0.40	53.1	0.95	HV02E01u_at	HV02E01u	-	-	8e-1	At5g35069	unknown protein	O.I.	H.G.	S.X.
0.40	53.1	0.95	HW09F23V_s_at	HW09F23V	-	-	3e+0	At4g10240	zinc finger (B-box type) family protein	O.I.	H.G.	S.X.
0.40	53.1	0.96	Contig4907_s_at	Contig4907	-	-	5e-4	At1g66340	ETR1 (ETHYLENE RESPONSE 1)	O.I.	H.G.	S.X.
0.40	53.1	0.96	Contig25764_at	Contig25764	-	-	2e-6	At5g19160	unknown protein	O.I.	H.G.	S.X.
0.38	49.5	0.96	Contig8077_at	Contig8077	-	-	7e-9	At5g05710	pleckstrin homology (PH) domain-containing protein	O.I.	H.G.	S.X.
0.36	47.1	0.96	Contig8678_s_at	Contig8678	-	-	3e-17	At1g31230	AK-HSDH I (ASPARTATE KINASE-HOMOSERINE DEHYDROGENASE I)	O.I.	H.G.	S.X.
0.36	47.1	0.96	Contig4660_s_at	Contig4660	-	-	2e-14	At1g61700	DNA-directed RNA polymerase II, putative (RPB10)	O.I.	H.G.	S.X.
0.35	45.1	0.94	Contig7496_at	Contig7496	-	-	1e-1	At3g11200	AL2 (ALFIN-LIKE 2)	O.I.	H.G.	S.X.
0.33	42.6	0.93	Contig19346_at	Contig19346	-	-	1e+0	At5g19870	unknown protein	O.I.	H.G.	S.X.
0.33	42.6	0.94	Contig3195_s_at	Contig3195	-	-	1e+0	At3g22580	protease inhibitor/seed storage/lipid transfer protein (LTP) family protein	O.I.	H.G.	S.X.
0.33	42.6	0.94	S0000800179B07F1_s_at	S0000800179B07F1	-	-	4e-6	At3g10920	MSD1 (MANGANESE SUPEROXIDE DISMUTASE 1)	O.I.	H.G.	S.X.
0.33	42.6	0.95	Contig15025_at	Contig15025	-	-	2e+0	At5g48655	zinc finger (C3HC4-type RING finger) family protein	O.I.	H.G.	S.X.
0.33	42.6	0.96	Contig3102_at	Contig3102	-	-	2e-13	At5g66510	GAMMA CA3 (GAMMA CARBONIC ANHYDRASE 3)	O.I.	H.G.	S.X.
0.33	42.6	0.96	Contig3699_s_at	Contig3699	-	-	1e+0	At2g26060	emb1345 (embryo defective 1345)	O.I.	H.G.	S.X.
0.33	42.6	0.96	Contig3100_at	Contig3100	-	-	1e-5	At4g16830	nuclear RNA-binding protein (RGGA)	O.I.	H.G.	S.X.
0.31	38.6	0.95	Contig6921_at	Contig6921	-	-	7e-22	At5g45130	RHA1 (RAB HOMOLOG 1)	O.I.	H.G.	S.X.
0.31	38.6	0.95	HZ42D16r_at	HZ42D16r	-	-	4e-3	At5g60460	sec61beta family protein	O.I.	H.G.	S.X.
0.28	35.5	0.97	Contig3961_at	Contig3961	-	-	1e+0	At3g29560	unknown protein	O.I.	H.G.	S.X.
0.25	28.9	0.95	Contig9437_at	Contig9437	-	-	2e+0	At2g46330	AGP16 (ARABINOGALACTAN PROTEIN 16)	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
8.5 98.8 GSM238428 Embryo 16DAF; Seed development; Rep 1 GSE9365 Expression data from barley maturing and germinating grains
8.4 98.8 GSM238430 Embryo 25DAF; Seed development; Rep 1 GSE9365 Expression data from barley maturing and germinating grains
6.2 98.0 GSM238429 Embryo 16DAF; Seed development; Rep 2 GSE9365 Expression data from barley maturing and germinating grains
5.8 97.8 GSM238434 Embryo 24 h; Seed germination; Rep 1 GSE9365 Expression data from barley maturing and germinating grains
5.5 97.6 GSM238432 Embryo 0 h; Seed germination; Rep 1 GSE9365 Expression data from barley maturing and germinating grains
4.7 96.9 GSM238431 Embryo 25DAF; Seed development; Rep 2 GSE9365 Expression data from barley maturing and germinating grains
4.5 96.7 GSM213443 Barley seeds with P. aeruginosa PA5021 mutant for 12hr GSE8618 P. aeruginosa virulent factor to barley
4.3 96.4 GSM238433 Embryo 0 h; Seed germination; Rep 2 GSE9365 Expression data from barley maturing and germinating grains
4.1 96.2 GSM213441 Barley seeds control in Hoagland solution for 12hr GSE8618 P. aeruginosa virulent factor to barley
3.9 95.8 GSM238435 Embryo 24 h; Seed germination; Rep 2 GSE9365 Expression data from barley maturing and germinating grains

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
8.5	98.8	GSM238428	Embryo 16DAF; Seed development; Rep 1	GSE9365	Expression data from barley maturing and germinating grains
8.4	98.8	GSM238430	Embryo 25DAF; Seed development; Rep 1	GSE9365	Expression data from barley maturing and germinating grains
6.2	98.0	GSM238429	Embryo 16DAF; Seed development; Rep 2	GSE9365	Expression data from barley maturing and germinating grains
5.8	97.8	GSM238434	Embryo 24 h; Seed germination; Rep 1	GSE9365	Expression data from barley maturing and germinating grains
5.5	97.6	GSM238432	Embryo 0 h; Seed germination; Rep 1	GSE9365	Expression data from barley maturing and germinating grains
4.7	96.9	GSM238431	Embryo 25DAF; Seed development; Rep 2	GSE9365	Expression data from barley maturing and germinating grains
4.5	96.7	GSM213443	Barley seeds with P. aeruginosa PA5021 mutant for 12hr	GSE8618	P. aeruginosa virulent factor to barley
4.3	96.4	GSM238433	Embryo 0 h; Seed germination; Rep 2	GSE9365	Expression data from barley maturing and germinating grains
4.1	96.2	GSM213441	Barley seeds control in Hoagland solution for 12hr	GSE8618	P. aeruginosa virulent factor to barley
3.9	95.8	GSM238435	Embryo 24 h; Seed germination; Rep 2	GSE9365	Expression data from barley maturing and germinating grains

Inter-species module comparison

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

Back to the CoP portal site

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Gene ID	EBem08_SQ002_D16_s_at
Gene name
Homology with Arabidopsis	Similar to At5g60460: sec61beta family protein (HF=2e-4)
Module size	7 genes
NF	0.45
%ile	62.5

Co-expression analysis

Gene ID EBem08_SQ002_D16_s_at Gene name Homology with ArabidopsisSimilar to At5g60460: sec61beta family protein (HF=2e-4) Module size 7 genes NF 0.45 %ile 62.5

Co-expressed genes

Specific experiments for the module

Inter-species module comparison

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

Gene ID EBem08_SQ002_D16_s_at

Gene name
Homology with Arabidopsis Similar to At5g60460: sec61beta family protein (HF=2e-4)

Module size 7 genes

NF 0.45

%ile 62.5

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