CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID PtpAffx.79594.1.S1_s_at

Gene name hypothetical protein
Homology with Arabidopsis Similar to At5g51970: sorbitol dehydrogenase, putative / L-iditol 2-dehydrogenase, putative (HF=2e-20)

Module size 6 genes

NF 0.45

%ile 74.6

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
0.63 88.1 0.93 PtpAffx.79594.1.S1_s_at CK098523 hypothetical protein - 2e-20 At5g51970 sorbitol dehydrogenase, putative / L-iditol 2-dehydrogenase, putative O.I. H.G. S.X.
0.50 78.6 0.93 Ptp.907.1.A1_at CV277484 hypothetical protein - 4e-32 At4g19160 unknown protein O.I. H.G. S.X.
0.50 78.6 0.94 PtpAffx.213643.1.S1_at pmrna26649 hypothetical protein - 1e-8 At5g61520 hexose transporter, putative O.I. H.G. S.X.
0.36 61.6 0.93 PtpAffx.16691.2.S1_a_at CV272539 hypothetical protein - 2e-8 At5g51970 sorbitol dehydrogenase, putative / L-iditol 2-dehydrogenase, putative O.I. H.G. S.X.
0.36 61.6 0.93 PtpAffx.211669.1.S1_x_at pmrna22876 hypothetical protein - 9e-6 At2g46940 unknown protein O.I. H.G. S.X.
0.21 36.5 0.94 PtpAffx.249.113.S1_at CV280925 hypothetical protein - 6e+0 At5g23140 NCLPP7 (NUCLEAR-ENCODED CLP PROTEASE P7) 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	88.1	0.93	PtpAffx.79594.1.S1_s_at	CK098523	hypothetical protein	-	2e-20	At5g51970	sorbitol dehydrogenase, putative / L-iditol 2-dehydrogenase, putative	O.I.	H.G.	S.X.
0.50	78.6	0.93	Ptp.907.1.A1_at	CV277484	hypothetical protein	-	4e-32	At4g19160	unknown protein	O.I.	H.G.	S.X.
0.50	78.6	0.94	PtpAffx.213643.1.S1_at	pmrna26649	hypothetical protein	-	1e-8	At5g61520	hexose transporter, putative	O.I.	H.G.	S.X.
0.36	61.6	0.93	PtpAffx.16691.2.S1_a_at	CV272539	hypothetical protein	-	2e-8	At5g51970	sorbitol dehydrogenase, putative / L-iditol 2-dehydrogenase, putative	O.I.	H.G.	S.X.
0.36	61.6	0.93	PtpAffx.211669.1.S1_x_at	pmrna22876	hypothetical protein	-	9e-6	At2g46940	unknown protein	O.I.	H.G.	S.X.
0.21	36.5	0.94	PtpAffx.249.113.S1_at	CV280925	hypothetical protein	-	6e+0	At5g23140	NCLPP7 (NUCLEAR-ENCODED CLP PROTEASE P7)	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
11.5 99.2 GSM136938 Poplar contacted with P. aeruginosa PAO1 in 1 x hrp + 0.25 % sucrose GSE5887 Pseudomonas aeruginosa PAO1 virulent genes in the poplar rhizosphere
4.8 96.4 GSM327409 Populus balsamifera_1006_root_midday_3 GSE13990 Populus balsamifera developmental tissue series
4.6 96.2 GSM327408 Populus balsamifera_1006_root_midday_2 GSE13990 Populus balsamifera developmental tissue series
4.0 95.3 GSM327407 Populus balsamifera_1006_root_midday_1 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
2.9 92.5 GSM334224 Populus balsamifera_1006_mature_leaf_midday_1 GSE13990 Populus balsamifera developmental tissue series
2.7 91.8 GSM327398 Populus balsamifera_20071015_Etiolated_seedling_6d_transfered_to_light_3h_3 GSE13990 Populus balsamifera developmental tissue series
2.6 91.3 GSM327397 Populus balsamifera_20071015_Etiolated_seedling_6d_transfered_to_light_3h_2 GSE13990 Populus balsamifera developmental tissue series
2.3 89.8 GSM327657 Populus balsamifera_Female_Catkin_midday_2 GSE13990 Populus balsamifera developmental tissue series
2.2 89.3 GSM334226 Populus balsamifera_1006_mature_leaf_midday_3 GSE13990 Populus balsamifera developmental tissue series

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
11.5	99.2	GSM136938	Poplar contacted with P. aeruginosa PAO1 in 1 x hrp + 0.25 % sucrose	GSE5887	Pseudomonas aeruginosa PAO1 virulent genes in the poplar rhizosphere
4.8	96.4	GSM327409	Populus balsamifera_1006_root_midday_3	GSE13990	Populus balsamifera developmental tissue series
4.6	96.2	GSM327408	Populus balsamifera_1006_root_midday_2	GSE13990	Populus balsamifera developmental tissue series
4.0	95.3	GSM327407	Populus balsamifera_1006_root_midday_1	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
2.9	92.5	GSM334224	Populus balsamifera_1006_mature_leaf_midday_1	GSE13990	Populus balsamifera developmental tissue series
2.7	91.8	GSM327398	Populus balsamifera_20071015_Etiolated_seedling_6d_transfered_to_light_3h_3	GSE13990	Populus balsamifera developmental tissue series
2.6	91.3	GSM327397	Populus balsamifera_20071015_Etiolated_seedling_6d_transfered_to_light_3h_2	GSE13990	Populus balsamifera developmental tissue series
2.3	89.8	GSM327657	Populus balsamifera_Female_Catkin_midday_2	GSE13990	Populus balsamifera developmental tissue series
2.2	89.3	GSM334226	Populus balsamifera_1006_mature_leaf_midday_3	GSE13990	Populus balsamifera developmental tissue series

Inter-species module comparison

A co-expression module including the Arabidopsis gene, At5g51970, orthologous to the query gene, PtpAffx.79594.1.S1_s_at

VF %ile Gene ID Repr. ID Gene Name Func. O.I. H.G. S.X. Other DB
0.79 89.1 At5g51970 835272 sorbitol dehydrogenase, putative / L-iditol 2-dehydrogenase, putative Encodes a putative sorbitol dehydrogenase that can be thiolated in vitro. O.I. H.G. S.X.
0.50 65.3 At1g63800 842683 UBC5 (ubiquitin-conjugating enzyme 5) F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:cellular_component unknown;MFOPV O.I. H.G. S.X.
0.45 58.3 At3g51840 824347 ACX4 (ACYL-COA OXIDASE 4) Encodes a short-chain acyl-CoA oxidase, which catalyzes the first step of peroxisomal fatty acid beta-oxidation during early, post-germinative growth in oilseed species. Null mutants virtually lack short-chain acyl-CoA and are resistant to 2,4-dichlorophenoxybutyric acid, which is converted to the herbicide and auxin analogue 2,4-dichlorophenoxyacetic acid by beta-oxidation. Despite the almost complete loss of short-chain activity, lipid catabolism and seedling growth and establishment was unaltered in the acx4 mutant. However, double mutants in acx3acx4 (acx3 encodes medium chain acyl CoA oxidase) were not viable and arrested during embryogenesis. O.I. H.G. S.X.
0.39 48.4 At5g59960 836118 unknown protein F:molecular_function unknown;P:biological_process unknown;C:nucleus;PO O.I. H.G. S.X.
0.38 46.7 At3g51730 824336 saposin B domain-containing protein F:molecular_function unknown;P:lipid metabolic process;C:vacuole;MOP O.I. H.G. S.X.
0.34 39.8 At3g06380 819812 ATTLP9 (TUBBY-LIKE PROTEIN 9) Member of TLP family O.I. H.G. S.X.
0.34 39.8 At5g47390 834786 myb family transcription factor F:transcription factor activity, DNA binding;P:in 8 processes;C:unknown;POFM O.I. H.G. S.X.
0.32 35.7 At5g58800 835997 quinone reductase family protein F:oxidoreductase activity, FMN binding;P:negative regulation of transcription;C:plasma membrane;BOFPAMV O.I. H.G. S.X.
0.30 32.1 At5g10450 830909 GRF6 (G-box regulating factor 6) Encodes a member of the 14-3-3 gene family that is a lambda isoform (14-3-3λ). Interacts with APX3 (ascorbate peroxidase) and AKR2 , suggesting a role in mediating oxidative metabolism in stress response. This protein was shown to colocalize and interact with SERK1 by which it is phosphorylated. This protein is also reported to interact with the phosphorylated form of the BZR1 transcription factor involved in brassinosteroid signaling and may affect the nucleocytoplasmic shuttling of BZR1. O.I. H.G. S.X.
0.28 30.3 At5g19860 832107 unknown protein F:unknown;P:biological_process unknown;C:vacuole;PO O.I. H.G. S.X.
0.25 22.6 At2g21950 816731 SKIP6 (SKP1 interacting partner 6) Encodes an SKP1 interacting partner (SKIP6). O.I. H.G. S.X.
0.23 19.3 At2g26670 817208 TED4 (REVERSAL OF THE DET PHENOTYPE 4) Encodes a plastid heme oxygenase necessary for phytochrome chromophore biosynthesis and for coupling the expression of some nuclear genes to the functional state of the chloroplast. O.I. H.G. S.X.
0.20 14.4 At5g39590 833955 - F:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;MOPF O.I. H.G. S.X.
0.20 14.4 At2g45980 819206 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.18 11.4 At4g02440 828008 EID1 (EMPFINDLICHER IM DUNKELROTEN LICHT 1) EID1 is an F-box protein that functions as a negative regulator in phytochrome A (phyA)-specific light signalling. Expressed at all stages of plant development independently of light conditions, localizes to the nucleus, and forms nuclear speckles under continuous far-red light. Forms stable dimeric and trimeric complexes with several ASK proteins and Cullin1 in yeast and in planta. O.I. H.G. S.X.
0.18 11.4 At4g18710 827605 BIN2 (BRASSINOSTEROID-INSENSITIVE 2) ATSK (shaggy-like kinase) family member that encodes an AtSK protein involved in the cross-talk between auxin and brassinosteroid signaling pathways. BR-INSENSITIVE 2 mutant indicated that the BR-insensitive dwarf phenotype was due to a semidominant mutation in the BIN2. BIN2 is not allelic to BRI1. BIN2-mediated phosphorylation appears to promote BZR1 export from the nucleus. O.I. H.G. S.X.
0.18 11.4 At5g10860 830953 CBS domain-containing protein F:unknown;P:response to salt stress;C:mitochondrion;BOAPFM O.I. H.G. S.X.
0.17 10.2 At1g04400 839529 CRY2 (CRYPTOCHROME 2) Blue light receptor mediating blue-light regulated cotyledon expansion and flowering time. Positive regulator of the flowering-time gene CONSTANS. This gene possesses a light-induced CNT2 N-terminal homodimerisation domain.Involved in blue-light induced stomatal opening. Involved in triggering chromatin decondensation. An 80-residue motif (NC80) is sufficient to confer CRY2's physiological function. It is proposed that the PHR domain and the C-terminal tail of the unphosphorylated CRY2 form a "closed" conformation to suppress the NC80 motif in the absence of light. In response to blue light, the C-terminal tail of CRY2 is phosphorylated and electrostatically repelled from the surface of the PHR domain to form an "open" conformation, resulting in derepression of the NC80 motif and signal transduction to trigger photomorphogenic responses. Cry2 phosphorylation and degradation both occur in the nucleus. O.I. H.G. S.X.
0.17 10.2 At1g19000 838481 myb family transcription factor F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:unknown;PO O.I. H.G. S.X.
0.17 10.2 At5g05930 830478 guanylyl cyclase-related (GC1) F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOA O.I. H.G. S.X.
0.17 10.2 At5g65430 836668 GRF8 (GENERAL REGULATORY FACTOR 8) member of 14-3-3 proteins. This protein is reported to interact with the BZR1 transcription factor involved in brassinosteroid signaling and may affect the nucleocytoplasmic shuttling of BZR1 O.I. H.G. S.X.
0.16 8.8 At2g25070 817045 protein phosphatase 2C, putative / PP2C, putative F:protein serine/threonine phosphatase activity, catalytic activity;P:protein amino acid dephosphorylation, N-terminal protein myristoylation;C:plasma membrane;MPOFBVA O.I. H.G. S.X.
0.15 7.8 At3g26030 822200 ATB' DELTA protein phosphatase 2A regulatory subunit isoform B' delta O.I. H.G. S.X.
0.15 7.8 At4g39100 830065 SHL1 (short life) Putative transcription factor containing a PHD finger and BAH motif, required for normal development O.I. H.G. S.X.
0.13 5.8 At1g56200 842073 emb1303 (embryo defective 1303) F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:chloroplast;PMBO O.I. H.G. S.X.

VF	%ile	Gene ID	Repr. ID	Gene Name	Func.	O.I.	H.G.	S.X.
0.79	89.1	At5g51970	835272	sorbitol dehydrogenase, putative / L-iditol 2-dehydrogenase, putative	Encodes a putative sorbitol dehydrogenase that can be thiolated in vitro.	O.I.	H.G.	S.X.
0.50	65.3	At1g63800	842683	UBC5 (ubiquitin-conjugating enzyme 5)	F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:cellular_component unknown;MFOPV	O.I.	H.G.	S.X.
0.45	58.3	At3g51840	824347	ACX4 (ACYL-COA OXIDASE 4)	Encodes a short-chain acyl-CoA oxidase, which catalyzes the first step of peroxisomal fatty acid beta-oxidation during early, post-germinative growth in oilseed species. Null mutants virtually lack short-chain acyl-CoA and are resistant to 2,4-dichlorophenoxybutyric acid, which is converted to the herbicide and auxin analogue 2,4-dichlorophenoxyacetic acid by beta-oxidation. Despite the almost complete loss of short-chain activity, lipid catabolism and seedling growth and establishment was unaltered in the acx4 mutant. However, double mutants in acx3acx4 (acx3 encodes medium chain acyl CoA oxidase) were not viable and arrested during embryogenesis.	O.I.	H.G.	S.X.
0.39	48.4	At5g59960	836118	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:nucleus;PO	O.I.	H.G.	S.X.
0.38	46.7	At3g51730	824336	saposin B domain-containing protein	F:molecular_function unknown;P:lipid metabolic process;C:vacuole;MOP	O.I.	H.G.	S.X.
0.34	39.8	At3g06380	819812	ATTLP9 (TUBBY-LIKE PROTEIN 9)	Member of TLP family	O.I.	H.G.	S.X.
0.34	39.8	At5g47390	834786	myb family transcription factor	F:transcription factor activity, DNA binding;P:in 8 processes;C:unknown;POFM	O.I.	H.G.	S.X.
0.32	35.7	At5g58800	835997	quinone reductase family protein	F:oxidoreductase activity, FMN binding;P:negative regulation of transcription;C:plasma membrane;BOFPAMV	O.I.	H.G.	S.X.
0.30	32.1	At5g10450	830909	GRF6 (G-box regulating factor 6)	Encodes a member of the 14-3-3 gene family that is a lambda isoform (14-3-3λ). Interacts with APX3 (ascorbate peroxidase) and AKR2 , suggesting a role in mediating oxidative metabolism in stress response. This protein was shown to colocalize and interact with SERK1 by which it is phosphorylated. This protein is also reported to interact with the phosphorylated form of the BZR1 transcription factor involved in brassinosteroid signaling and may affect the nucleocytoplasmic shuttling of BZR1.	O.I.	H.G.	S.X.
0.28	30.3	At5g19860	832107	unknown protein	F:unknown;P:biological_process unknown;C:vacuole;PO	O.I.	H.G.	S.X.
0.25	22.6	At2g21950	816731	SKIP6 (SKP1 interacting partner 6)	Encodes an SKP1 interacting partner (SKIP6).	O.I.	H.G.	S.X.
0.23	19.3	At2g26670	817208	TED4 (REVERSAL OF THE DET PHENOTYPE 4)	Encodes a plastid heme oxygenase necessary for phytochrome chromophore biosynthesis and for coupling the expression of some nuclear genes to the functional state of the chloroplast.	O.I.	H.G.	S.X.
0.20	14.4	At5g39590	833955	-	F:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;MOPF	O.I.	H.G.	S.X.
0.20	14.4	At2g45980	819206	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.18	11.4	At4g02440	828008	EID1 (EMPFINDLICHER IM DUNKELROTEN LICHT 1)	EID1 is an F-box protein that functions as a negative regulator in phytochrome A (phyA)-specific light signalling. Expressed at all stages of plant development independently of light conditions, localizes to the nucleus, and forms nuclear speckles under continuous far-red light. Forms stable dimeric and trimeric complexes with several ASK proteins and Cullin1 in yeast and in planta.	O.I.	H.G.	S.X.
0.18	11.4	At4g18710	827605	BIN2 (BRASSINOSTEROID-INSENSITIVE 2)	ATSK (shaggy-like kinase) family member that encodes an AtSK protein involved in the cross-talk between auxin and brassinosteroid signaling pathways. BR-INSENSITIVE 2 mutant indicated that the BR-insensitive dwarf phenotype was due to a semidominant mutation in the BIN2. BIN2 is not allelic to BRI1. BIN2-mediated phosphorylation appears to promote BZR1 export from the nucleus.	O.I.	H.G.	S.X.
0.18	11.4	At5g10860	830953	CBS domain-containing protein	F:unknown;P:response to salt stress;C:mitochondrion;BOAPFM	O.I.	H.G.	S.X.
0.17	10.2	At1g04400	839529	CRY2 (CRYPTOCHROME 2)	Blue light receptor mediating blue-light regulated cotyledon expansion and flowering time. Positive regulator of the flowering-time gene CONSTANS. This gene possesses a light-induced CNT2 N-terminal homodimerisation domain.Involved in blue-light induced stomatal opening. Involved in triggering chromatin decondensation. An 80-residue motif (NC80) is sufficient to confer CRY2's physiological function. It is proposed that the PHR domain and the C-terminal tail of the unphosphorylated CRY2 form a "closed" conformation to suppress the NC80 motif in the absence of light. In response to blue light, the C-terminal tail of CRY2 is phosphorylated and electrostatically repelled from the surface of the PHR domain to form an "open" conformation, resulting in derepression of the NC80 motif and signal transduction to trigger photomorphogenic responses. Cry2 phosphorylation and degradation both occur in the nucleus.	O.I.	H.G.	S.X.
0.17	10.2	At1g19000	838481	myb family transcription factor	F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:unknown;PO	O.I.	H.G.	S.X.
0.17	10.2	At5g05930	830478	guanylyl cyclase-related (GC1)	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOA	O.I.	H.G.	S.X.
0.17	10.2	At5g65430	836668	GRF8 (GENERAL REGULATORY FACTOR 8)	member of 14-3-3 proteins. This protein is reported to interact with the BZR1 transcription factor involved in brassinosteroid signaling and may affect the nucleocytoplasmic shuttling of BZR1	O.I.	H.G.	S.X.
0.16	8.8	At2g25070	817045	protein phosphatase 2C, putative / PP2C, putative	F:protein serine/threonine phosphatase activity, catalytic activity;P:protein amino acid dephosphorylation, N-terminal protein myristoylation;C:plasma membrane;MPOFBVA	O.I.	H.G.	S.X.
0.15	7.8	At3g26030	822200	ATB' DELTA	protein phosphatase 2A regulatory subunit isoform B' delta	O.I.	H.G.	S.X.
0.15	7.8	At4g39100	830065	SHL1 (short life)	Putative transcription factor containing a PHD finger and BAH motif, required for normal development	O.I.	H.G.	S.X.
0.13	5.8	At1g56200	842073	emb1303 (embryo defective 1303)	F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:chloroplast;PMBO	O.I.	H.G.	S.X.

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

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Gene ID	PtpAffx.79594.1.S1_s_at
Gene name	hypothetical protein
Homology with Arabidopsis	Similar to At5g51970: sorbitol dehydrogenase, putative / L-iditol 2-dehydrogenase, putative (HF=2e-20)
Module size	6 genes
NF	0.45
%ile	74.6

Co-expression analysis

Gene ID PtpAffx.79594.1.S1_s_at Gene name hypothetical protein Homology with ArabidopsisSimilar to At5g51970: sorbitol dehydrogenase, putative / L-iditol 2-dehydrogenase, putative (HF=2e-20) Module size 6 genes NF 0.45 %ile 74.6

Co-expressed genes

Click More genes

Specific experiments for the module

Inter-species module comparison

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

Gene ID PtpAffx.79594.1.S1_s_at

Gene name hypothetical protein
Homology with Arabidopsis Similar to At5g51970: sorbitol dehydrogenase, putative / L-iditol 2-dehydrogenase, putative (HF=2e-20)

Module size 6 genes

NF 0.45

%ile 74.6

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