CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Ptp.4500.1.S1_at

Gene name thioredoxin m
Homology with Arabidopsis Similar to At3g15360: TRX-M4 (ARABIDOPSIS THIOREDOXIN M-TYPE 4) (HF=1e-7)

Module size 6 genes

NF 0.41

%ile 69.0

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
0.44 71.9 0.93 Ptp.4500.1.S1_at CV226875 thioredoxin m - 1e-7 At3g15360 TRX-M4 (ARABIDOPSIS THIOREDOXIN M-TYPE 4) O.I. H.G. S.X.
0.55 82.2 0.95 PtpAffx.45383.2.A1_a_at CV255277 hypothetical protein - 1e-9 At4g22000 unknown protein O.I. H.G. S.X.
0.50 78.6 0.95 PtpAffx.32368.1.S1_a_at CV278073 hypothetical protein - 7e-40 At2g33430 DAL1 (DIFFERENTIATION AND GREENING-LIKE 1) O.I. H.G. S.X.
0.37 62.3 0.94 PtpAffx.11494.1.S1_at CV260585 hypothetical protein - 1e-3 At3g44380 - O.I. H.G. S.X.
0.33 57.5 0.94 PtpAffx.32368.2.A1_at CV238018 hypothetical protein - 3e-49 At2g33430 DAL1 (DIFFERENTIATION AND GREENING-LIKE 1) O.I. H.G. S.X.
0.22 38.3 0.95 Ptp.6151.1.A1_at DN487970 hypothetical protein - 2e-6 At5g23040 CDF1 (CELL GROWTH DEFECT FACTOR 1) 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.
0.44	71.9	0.93	Ptp.4500.1.S1_at	CV226875	thioredoxin m	-	1e-7	At3g15360	TRX-M4 (ARABIDOPSIS THIOREDOXIN M-TYPE 4)	O.I.	H.G.	S.X.
0.55	82.2	0.95	PtpAffx.45383.2.A1_a_at	CV255277	hypothetical protein	-	1e-9	At4g22000	unknown protein	O.I.	H.G.	S.X.
0.50	78.6	0.95	PtpAffx.32368.1.S1_a_at	CV278073	hypothetical protein	-	7e-40	At2g33430	DAL1 (DIFFERENTIATION AND GREENING-LIKE 1)	O.I.	H.G.	S.X.
0.37	62.3	0.94	PtpAffx.11494.1.S1_at	CV260585	hypothetical protein	-	1e-3	At3g44380	-	O.I.	H.G.	S.X.
0.33	57.5	0.94	PtpAffx.32368.2.A1_at	CV238018	hypothetical protein	-	3e-49	At2g33430	DAL1 (DIFFERENTIATION AND GREENING-LIKE 1)	O.I.	H.G.	S.X.
0.22	38.3	0.95	Ptp.6151.1.A1_at	DN487970	hypothetical protein	-	2e-6	At5g23040	CDF1 (CELL GROWTH DEFECT FACTOR 1)	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.
0.67	91.1	0.93	Ptp.6828.1.A1_at	CV255971	hypothetical protein	-	2e+0	At4g18975	pentatricopeptide (PPR) repeat-containing protein	O.I.	H.G.	S.X.
0.57	84.2	0.93	PtpAffx.4964.1.S1_s_at	CV267529	hypothetical protein	-	2e+0	At2g20390	unknown protein	O.I.	H.G.	S.X.
0.46	73.7	0.93	PtpAffx.11859.1.A1_x_at	CV252937	hypothetical protein	-	1e-4	At4g29480	mitochondrial ATP synthase g subunit family protein	O.I.	H.G.	S.X.
0.46	73.7	0.93	Ptp.7737.1.S1_s_at	DN499091	hypothetical protein	-	8e-1	At5g10350	polyadenylate-binding protein family protein / PABP family protein	O.I.	H.G.	S.X.
0.40	67.0	0.91	PtpAffx.201470.1.S1_at	pmrna2888	hypothetical protein	-	3e-136	At5g63890	ATHDH (HISTIDINOL DEHYDROGENASE)	O.I.	H.G.	S.X.
0.40	67.0	0.94	PtpAffx.25022.2.S1_a_at	CV248623	hypothetical protein	-	2e-31	At3g53630	unknown protein	O.I.	H.G.	S.X.
0.38	63.7	0.94	PtpAffx.68666.1.S1_a_at	CV242588	hypothetical protein	-	4e-8	At3g03490	PEX19-1 (peroxin 19-1)	O.I.	H.G.	S.X.
0.37	62.3	0.93	PtpAffx.24915.1.A1_a_at	CV242437	hypothetical protein	-	4e-17	At5g15750	RNA-binding S4 domain-containing protein	O.I.	H.G.	S.X.
0.36	61.6	0.92	PtpAffx.203425.1.S1_at	pmrna6826	hypothetical protein	-	6e-12	At1g27385	unknown protein	O.I.	H.G.	S.X.
0.36	61.6	0.95	PtpAffx.3808.2.A1_at	BP936602	hypothetical protein	-	5e+0	At4g22440	unknown protein	O.I.	H.G.	S.X.
0.36	61.6	0.96	PtpAffx.1997.1.A1_x_at	CV236998	hypothetical protein	-	4e-34	At5g48870	SAD1 (SUPERSENSITIVE TO ABA AND DROUGHT 1)	O.I.	H.G.	S.X.
0.33	57.5	0.93	PtpAffx.206595.1.S1_at	pmrna13086	hypothetical protein	-	7e-1	At2g27390	proline-rich family protein	O.I.	H.G.	S.X.
0.33	57.5	0.94	PtpAffx.85599.1.S1_at	CV260946	hypothetical protein	-	1e-4	At1g20816	unknown protein	O.I.	H.G.	S.X.
0.33	57.5	0.96	PtpAffx.32368.1.S1_at	CV278073	hypothetical protein	-	7e-40	At2g33430	DAL1 (DIFFERENTIATION AND GREENING-LIKE 1)	O.I.	H.G.	S.X.
0.30	52.0	0.90	PtpAffx.86800.1.A1_at	DN490102	hypothetical protein	-	9e-2	At1g17745	PGDH (3-PHOSPHOGLYCERATE DEHYDROGENASE)	O.I.	H.G.	S.X.
0.29	50.5	0.92	PtpAffx.202396.1.S1_at	pmrna4810	hypothetical protein	-	2e-2	At4g27500	PPI1 (PROTON PUMP INTERACTOR 1)	O.I.	H.G.	S.X.
0.29	50.5	0.93	PtpAffx.28421.1.S1_at	CV264518	hypothetical protein	-	2e-103	At1g71230	CSN5B (COP9-SIGNALOSOME 5B)	O.I.	H.G.	S.X.
0.29	50.5	0.96	PtpAffx.4646.1.S1_a_at	CV283009	hypothetical protein	-	5e-25	At1g33810	unknown protein	O.I.	H.G.	S.X.
0.27	47.1	0.91	Ptp.5153.1.S1_at	CV244685	hypothetical protein	-	6e-22	At3g32930	unknown protein	O.I.	H.G.	S.X.
0.27	47.1	0.94	PtpAffx.54627.1.S1_at	CV271675	hypothetical protein	-	5e-1	At5g61660	glycine-rich protein	O.I.	H.G.	S.X.
0.27	47.1	0.94	PtpAffx.88369.1.A1_at	CV269685	hypothetical protein	-	2e-1	At3g09860	unknown protein	O.I.	H.G.	S.X.
0.25	43.6	0.87	PtpAffx.109125.1.A1_at	CV261593	hypothetical protein	-	3e+0	At4g20760	short-chain dehydrogenase/reductase (SDR) family protein	O.I.	H.G.	S.X.
0.25	43.6	0.92	Ptp.6680.1.S1_at	CK094754	hypothetical protein	-	2e-21	At3g51660	macrophage migration inhibitory factor family protein / MIF family protein	O.I.	H.G.	S.X.
0.25	43.6	0.94	PtpAffx.24003.1.A1_at	CV245118	hypothetical protein	-	8e-10	At4g38160	pde191 (pigment defective 191)	O.I.	H.G.	S.X.
0.25	43.6	0.94	PtpAffx.7355.1.S1_at	CV254967	hypothetical protein	-	3e-9	At4g12060	Clp amino terminal domain-containing 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
4.3 95.8 GSM327660 Populus balsamifera_Male_Catkin_midday_2 GSE13990 Populus balsamifera developmental tissue series
3.2 93.5 GSM327408 Populus balsamifera_1006_root_midday_2 GSE13990 Populus balsamifera developmental tissue series
3.0 92.9 GSM136936 Poplar in 1 x hrp + 0.25 % sucrose no bacteria GSE5887 Pseudomonas aeruginosa PAO1 virulent genes in the poplar rhizosphere
2.7 91.8 GSM327402 Populus balsamifera_20071015_Etiolated_seedling_6d_2 GSE13990 Populus balsamifera developmental tissue series
2.6 91.3 GSM327358 Populus balsamifera_20071015_Seedling_continuous_light_6d_2 GSE13990 Populus balsamifera developmental tissue series
2.6 91.3 GSM327400 Populus balsamifera_20071015_Etiolated_seedling_6d_1 GSE13990 Populus balsamifera developmental tissue series
2.6 91.3 GSM136938 Poplar contacted with P. aeruginosa PAO1 in 1 x hrp + 0.25 % sucrose GSE5887 Pseudomonas aeruginosa PAO1 virulent genes in the poplar rhizosphere
2.5 90.9 GSM328105 Populus x canescens leaf hypoxia_rep_01 GSE13109 Effect of hypoxia on gene expression in Grey poplar
2.5 90.9 GSM327661 Populus balsamifera_Male_Catkin_midday_3 GSE13990 Populus balsamifera developmental tissue series
2.2 89.3 GSM327405 Populus balsamifera_1006_young_leaf_midday_2 GSE13990 Populus balsamifera developmental tissue series

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
4.3	95.8	GSM327660	Populus balsamifera_Male_Catkin_midday_2	GSE13990	Populus balsamifera developmental tissue series
3.2	93.5	GSM327408	Populus balsamifera_1006_root_midday_2	GSE13990	Populus balsamifera developmental tissue series
3.0	92.9	GSM136936	Poplar in 1 x hrp + 0.25 % sucrose no bacteria	GSE5887	Pseudomonas aeruginosa PAO1 virulent genes in the poplar rhizosphere
2.7	91.8	GSM327402	Populus balsamifera_20071015_Etiolated_seedling_6d_2	GSE13990	Populus balsamifera developmental tissue series
2.6	91.3	GSM327358	Populus balsamifera_20071015_Seedling_continuous_light_6d_2	GSE13990	Populus balsamifera developmental tissue series
2.6	91.3	GSM327400	Populus balsamifera_20071015_Etiolated_seedling_6d_1	GSE13990	Populus balsamifera developmental tissue series
2.6	91.3	GSM136938	Poplar contacted with P. aeruginosa PAO1 in 1 x hrp + 0.25 % sucrose	GSE5887	Pseudomonas aeruginosa PAO1 virulent genes in the poplar rhizosphere
2.5	90.9	GSM328105	Populus x canescens leaf hypoxia_rep_01	GSE13109	Effect of hypoxia on gene expression in Grey poplar
2.5	90.9	GSM327661	Populus balsamifera_Male_Catkin_midday_3	GSE13990	Populus balsamifera developmental tissue series
2.2	89.3	GSM327405	Populus balsamifera_1006_young_leaf_midday_2	GSE13990	Populus balsamifera developmental tissue series

Inter-species module comparison

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

Back to the CoP portal site

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Gene ID	Ptp.4500.1.S1_at
Gene name	thioredoxin m
Homology with Arabidopsis	Similar to At3g15360: TRX-M4 (ARABIDOPSIS THIOREDOXIN M-TYPE 4) (HF=1e-7)
Module size	6 genes
NF	0.41
%ile	69.0

Co-expression analysis

Gene ID Ptp.4500.1.S1_at Gene name thioredoxin m Homology with ArabidopsisSimilar to At3g15360: TRX-M4 (ARABIDOPSIS THIOREDOXIN M-TYPE 4) (HF=1e-7) Module size 6 genes NF 0.41 %ile 69.0

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_sativaTriticum_aestivumVitis_viniferaZea_mays

Gene ID Ptp.4500.1.S1_at

Gene name thioredoxin m
Homology with Arabidopsis Similar to At3g15360: TRX-M4 (ARABIDOPSIS THIOREDOXIN M-TYPE 4) (HF=1e-7)

Module size 6 genes

NF 0.41

%ile 69.0

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