CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID PtpAffx.135882.1.A1_at

Gene name hypothetical protein
Homology with Arabidopsis Similar to At1g78420: protein binding / zinc ion binding (HF=1e-7)

Module size 6 genes

NF 0.49

%ile 80.0

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
0.73 93.6 0.96 PtpAffx.135882.1.A1_at CV281275 hypothetical protein - 1e-7 At1g78420 protein binding / zinc ion binding O.I. H.G. S.X.
0.80 96.0 0.96 Ptp.7787.1.S1_s_at DN499212 - - 4e+0 At2g05642 - O.I. H.G. S.X.
0.46 73.7 0.96 Ptp.2558.1.S1_at CK096344 hypothetical protein - 0 At1g78900 VHA-A (VACUOLAR ATP SYNTHASE SUBUNIT A) O.I. H.G. S.X.
0.35 59.7 0.96 Ptp.5593.1.S1_at DN495608 hypothetical protein - 7e-15 At4g26240 unknown protein O.I. H.G. S.X.
0.33 57.5 0.96 PtpAffx.12253.1.A1_at CV225881 hypothetical protein - 3e+0 At4g32960 unknown protein O.I. H.G. S.X.
0.29 50.5 0.96 PtpAffx.121458.1.A1_s_at CV239175 hypothetical protein - 3e-14 At3g20650 mRNA capping enzyme family protein 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.
0.73	93.6	0.96	PtpAffx.135882.1.A1_at	CV281275	hypothetical protein	-	1e-7	At1g78420	protein binding / zinc ion binding	O.I.	H.G.	S.X.
0.80	96.0	0.96	Ptp.7787.1.S1_s_at	DN499212	-	-	4e+0	At2g05642	-	O.I.	H.G.	S.X.
0.46	73.7	0.96	Ptp.2558.1.S1_at	CK096344	hypothetical protein	-	0	At1g78900	VHA-A (VACUOLAR ATP SYNTHASE SUBUNIT A)	O.I.	H.G.	S.X.
0.35	59.7	0.96	Ptp.5593.1.S1_at	DN495608	hypothetical protein	-	7e-15	At4g26240	unknown protein	O.I.	H.G.	S.X.
0.33	57.5	0.96	PtpAffx.12253.1.A1_at	CV225881	hypothetical protein	-	3e+0	At4g32960	unknown protein	O.I.	H.G.	S.X.
0.29	50.5	0.96	PtpAffx.121458.1.A1_s_at	CV239175	hypothetical protein	-	3e-14	At3g20650	mRNA capping enzyme family protein	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
5.0 96.6 GSM328564 Populus x canescens root hypoxia_rep_06 GSE13109 Effect of hypoxia on gene expression in Grey poplar
3.9 95.1 GSM328567 Populus x canescens root hypoxia_rep_09 GSE13109 Effect of hypoxia on gene expression in Grey poplar
3.7 94.7 GSM328565 Populus x canescens root hypoxia_rep_07 GSE13109 Effect of hypoxia on gene expression in Grey poplar
2.3 89.8 GSM362888 Clone1979_LPI5_N+_4w_rep2 GSE14515 Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 1979
1.8 86.4 GSM328066 Populus x canescens leaf control_rep_04 GSE13109 Effect of hypoxia on gene expression in Grey poplar
1.8 86.4 GSM244438 Mmd infected tissue, biological rep3 GSE9673 Comparative transcriptomic reveals signatures specific to various interactions with Melampsora rust fungi
1.7 85.5 GSM328063 Populus x canescens leaf control_rep_03 GSE13109 Effect of hypoxia on gene expression in Grey poplar
1.7 85.5 GSM328275 Populus x canescens leaf hypoxia_rep_03 GSE13109 Effect of hypoxia on gene expression in Grey poplar
1.7 85.5 GSM244431 non infected tissue, biological rep2 GSE9673 Comparative transcriptomic reveals signatures specific to various interactions with Melampsora rust fungi
1.6 84.5 GSM328070 Populus x canescens leaf control_rep_05 GSE13109 Effect of hypoxia on gene expression in Grey poplar

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
5.0	96.6	GSM328564	Populus x canescens root hypoxia_rep_06	GSE13109	Effect of hypoxia on gene expression in Grey poplar
3.9	95.1	GSM328567	Populus x canescens root hypoxia_rep_09	GSE13109	Effect of hypoxia on gene expression in Grey poplar
3.7	94.7	GSM328565	Populus x canescens root hypoxia_rep_07	GSE13109	Effect of hypoxia on gene expression in Grey poplar
2.3	89.8	GSM362888	Clone1979_LPI5_N+_4w_rep2	GSE14515	Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 1979
1.8	86.4	GSM328066	Populus x canescens leaf control_rep_04	GSE13109	Effect of hypoxia on gene expression in Grey poplar
1.8	86.4	GSM244438	Mmd infected tissue, biological rep3	GSE9673	Comparative transcriptomic reveals signatures specific to various interactions with Melampsora rust fungi
1.7	85.5	GSM328063	Populus x canescens leaf control_rep_03	GSE13109	Effect of hypoxia on gene expression in Grey poplar
1.7	85.5	GSM328275	Populus x canescens leaf hypoxia_rep_03	GSE13109	Effect of hypoxia on gene expression in Grey poplar
1.7	85.5	GSM244431	non infected tissue, biological rep2	GSE9673	Comparative transcriptomic reveals signatures specific to various interactions with Melampsora rust fungi
1.6	84.5	GSM328070	Populus x canescens leaf control_rep_05	GSE13109	Effect of hypoxia on gene expression in Grey poplar

Inter-species module comparison

A co-expression module including the Arabidopsis gene, At1g78420, orthologous to the query gene, PtpAffx.135882.1.A1_at

VF %ile Gene ID Repr. ID Gene Name Func. O.I. H.G. S.X. Other DB
1.00 100.0 At1g78420 844178 protein binding / zinc ion binding F:protein binding, zinc ion binding;P:N-terminal protein myristoylation;C:unknown;FPMO O.I. H.G. S.X.
0.28 30.3 At4g11860 826793 - F:molecular_function unknown;P:biological_process unknown;C:cytosol, nucleus, plasma membrane;MFOPB O.I. H.G. S.X.
0.24 20.7 At5g52530 835329 dentin sialophosphoprotein-related F:molecular_function unknown;P:biological_process unknown;C:unknown;MOFBPVA O.I. H.G. S.X.
0.22 17.5 At5g42560 834262 abscisic acid-responsive HVA22 family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOBV O.I. H.G. S.X.
0.22 17.5 At5g02310 830916 PRT6 (PROTEOLYSIS 6) Encodes PROTEOLYSIS6 (PRT6), a component of the N-end rule pathway that targets protein degradation through the identity of the amino-terminal residue of specific protein substrates. Another component of the N-end rule pathway is arginyl-tRNA:protein arginyltransferase (ATE). Arabidopsis contains two ATE genes: At5g05700/ATE1, At3g11240/ATE2. PRT6 and ATE were shown to regulate seed after-ripening, seedling sugar sensitivity, seedling lipid breakdown, and abscisic acid (ABA) sensitivity of germination. O.I. H.G. S.X.
0.21 15.8 At5g63640 836484 VHS domain-containing protein / GAT domain-containing protein F:protein transporter activity;P:intracellular protein transport, intra-Golgi vesicle-mediated transport;C:Golgi stack, plasma membrane;MFPOB O.I. H.G. S.X.
0.20 14.4 At5g04410 830320 NAC2 NAC family member, hypothetical transcriptional regulator O.I. H.G. S.X.
0.19 12.7 At2g36960 818270 TKI1 (TSL-kinase interacting protein 1) Arabidopsis thaliana myb/SANT domain protein O.I. H.G. S.X.
0.18 11.4 At1g11020 837644 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:unknown;MOPFV O.I. H.G. S.X.
0.18 11.4 At5g66730 836806 zinc finger (C2H2 type) family protein F:transcription factor activity, zinc ion binding, nucleic acid binding;P:regulation of transcription;C:intracellular;MOPFB O.I. H.G. S.X.
0.17 10.2 At3g61710 825344 autophagy protein Apg6 family F:molecular_function unknown;P:autophagy;C:unknown;MOFBPVA O.I. H.G. S.X.
0.17 10.2 At5g37370 833711 ATSRL1 encodes a putative splicing factor. Over-expression in yeast and Arabidopsis result in increased tolerance to high salt. O.I. H.G. S.X.
0.15 7.8 At1g26830 839226 ATCUL3 (ARABIDOPSIS THALIANA CULLIN 3) Cullin, putative, similar to Cullin homolog 3 (CUL-3) SP:Q13618, GI:3639052 from (Homo sapiens); contains Pfam profile PF00888: Cullin family. Interacts with other components of E3 ligase complex suggesting it functions in RUB-modification. Forms complexes with BTB domain proteins forming a novel class of E3-based ubiquitin protein-ligase complexes. Mutant is early flowering and has a reduced sensitivity to far-red light. cul3a/cul3b homozygous/heterozygous plants are embryo lethal. O.I. H.G. S.X.
0.15 7.8 At2g27490 817294 ATCOAE AT2G27490 encodes dephospho-CoA kinase. The molecular function was shown to phosphorylate the ribosyl moiety forming CoA. O.I. H.G. S.X.
0.15 7.8 At3g05210 819685 ERCC1 encodes a homolog of human ERCC1 protein (yeast RAD10), which is a DNA repair endonuclease. Mutants are sensitive to UV-B and gamma radiation (G2 cell cycle phase arrest) and are defective in dark-repair of pyrimidine pyrimidone dimers. This protein incises the 5' end of damaged DNA, similar to ERCC1/RAD10. O.I. H.G. S.X.
0.13 5.8 At5g10270 830891 CDKC Encodes CDKC;1, part of a CDKC kinase complex that is targeted by Cauliflower mosaic virus (CaMV) for transcriptional activation of viral genes. Also regulates plant growth and development. O.I. H.G. S.X.
0.12 4.9 At4g15475 827219 F-box family protein (FBL4) F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:unknown;MPOFBV O.I. H.G. S.X.
0.10 3.4 At1g66340 842951 ETR1 (ETHYLENE RESPONSE 1) Similar to prokaryote sensory transduction proteins. Contains a histidine kinase and a response regulator domain. Homodimer. Membrane component. Binds ethylene. Mutations affect ethylene binding and metabolism of other plant hormones such as auxin, cytokinins, ABA and gibberellic acid. Ethylene receptor. Has histidine kinase activity. Is regulated by RTE1. O.I. H.G. S.X.
0.10 3.4 At5g49930 835056 emb1441 (embryo defective 1441) F:zinc ion binding, nucleic acid binding;P:embryonic development ending in seed dormancy;C:cellular_component unknown;OMBFAPV O.I. H.G. S.X.
0.09 2.8 At5g61500 836271 ATG3 F:molecular_function unknown;P:autophagy;C:cellular_component unknown;MFOP O.I. H.G. S.X.
0.09 2.8 At5g63200 836441 tetratricopeptide repeat (TPR)-containing protein F:binding;P:biological_process unknown;C:cellular_component unknown;OBMAFP O.I. H.G. S.X.
0.08 2.3 At3g15351 820769 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM O.I. H.G. S.X.

VF	%ile	Gene ID	Repr. ID	Gene Name	Func.	O.I.	H.G.	S.X.
1.00	100.0	At1g78420	844178	protein binding / zinc ion binding	F:protein binding, zinc ion binding;P:N-terminal protein myristoylation;C:unknown;FPMO	O.I.	H.G.	S.X.
0.28	30.3	At4g11860	826793	-	F:molecular_function unknown;P:biological_process unknown;C:cytosol, nucleus, plasma membrane;MFOPB	O.I.	H.G.	S.X.
0.24	20.7	At5g52530	835329	dentin sialophosphoprotein-related	F:molecular_function unknown;P:biological_process unknown;C:unknown;MOFBPVA	O.I.	H.G.	S.X.
0.22	17.5	At5g42560	834262	abscisic acid-responsive HVA22 family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOBV	O.I.	H.G.	S.X.
0.22	17.5	At5g02310	830916	PRT6 (PROTEOLYSIS 6)	Encodes PROTEOLYSIS6 (PRT6), a component of the N-end rule pathway that targets protein degradation through the identity of the amino-terminal residue of specific protein substrates. Another component of the N-end rule pathway is arginyl-tRNA:protein arginyltransferase (ATE). Arabidopsis contains two ATE genes: At5g05700/ATE1, At3g11240/ATE2. PRT6 and ATE were shown to regulate seed after-ripening, seedling sugar sensitivity, seedling lipid breakdown, and abscisic acid (ABA) sensitivity of germination.	O.I.	H.G.	S.X.
0.21	15.8	At5g63640	836484	VHS domain-containing protein / GAT domain-containing protein	F:protein transporter activity;P:intracellular protein transport, intra-Golgi vesicle-mediated transport;C:Golgi stack, plasma membrane;MFPOB	O.I.	H.G.	S.X.
0.20	14.4	At5g04410	830320	NAC2	NAC family member, hypothetical transcriptional regulator	O.I.	H.G.	S.X.
0.19	12.7	At2g36960	818270	TKI1 (TSL-kinase interacting protein 1)	Arabidopsis thaliana myb/SANT domain protein	O.I.	H.G.	S.X.
0.18	11.4	At1g11020	837644	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:unknown;MOPFV	O.I.	H.G.	S.X.
0.18	11.4	At5g66730	836806	zinc finger (C2H2 type) family protein	F:transcription factor activity, zinc ion binding, nucleic acid binding;P:regulation of transcription;C:intracellular;MOPFB	O.I.	H.G.	S.X.
0.17	10.2	At3g61710	825344	autophagy protein Apg6 family	F:molecular_function unknown;P:autophagy;C:unknown;MOFBPVA	O.I.	H.G.	S.X.
0.17	10.2	At5g37370	833711	ATSRL1	encodes a putative splicing factor. Over-expression in yeast and Arabidopsis result in increased tolerance to high salt.	O.I.	H.G.	S.X.
0.15	7.8	At1g26830	839226	ATCUL3 (ARABIDOPSIS THALIANA CULLIN 3)	Cullin, putative, similar to Cullin homolog 3 (CUL-3) SP:Q13618, GI:3639052 from (Homo sapiens); contains Pfam profile PF00888: Cullin family. Interacts with other components of E3 ligase complex suggesting it functions in RUB-modification. Forms complexes with BTB domain proteins forming a novel class of E3-based ubiquitin protein-ligase complexes. Mutant is early flowering and has a reduced sensitivity to far-red light. cul3a/cul3b homozygous/heterozygous plants are embryo lethal.	O.I.	H.G.	S.X.
0.15	7.8	At2g27490	817294	ATCOAE	AT2G27490 encodes dephospho-CoA kinase. The molecular function was shown to phosphorylate the ribosyl moiety forming CoA.	O.I.	H.G.	S.X.
0.15	7.8	At3g05210	819685	ERCC1	encodes a homolog of human ERCC1 protein (yeast RAD10), which is a DNA repair endonuclease. Mutants are sensitive to UV-B and gamma radiation (G2 cell cycle phase arrest) and are defective in dark-repair of pyrimidine pyrimidone dimers. This protein incises the 5' end of damaged DNA, similar to ERCC1/RAD10.	O.I.	H.G.	S.X.
0.13	5.8	At5g10270	830891	CDKC	Encodes CDKC;1, part of a CDKC kinase complex that is targeted by Cauliflower mosaic virus (CaMV) for transcriptional activation of viral genes. Also regulates plant growth and development.	O.I.	H.G.	S.X.
0.12	4.9	At4g15475	827219	F-box family protein (FBL4)	F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:unknown;MPOFBV	O.I.	H.G.	S.X.
0.10	3.4	At1g66340	842951	ETR1 (ETHYLENE RESPONSE 1)	Similar to prokaryote sensory transduction proteins. Contains a histidine kinase and a response regulator domain. Homodimer. Membrane component. Binds ethylene. Mutations affect ethylene binding and metabolism of other plant hormones such as auxin, cytokinins, ABA and gibberellic acid. Ethylene receptor. Has histidine kinase activity. Is regulated by RTE1.	O.I.	H.G.	S.X.
0.10	3.4	At5g49930	835056	emb1441 (embryo defective 1441)	F:zinc ion binding, nucleic acid binding;P:embryonic development ending in seed dormancy;C:cellular_component unknown;OMBFAPV	O.I.	H.G.	S.X.
0.09	2.8	At5g61500	836271	ATG3	F:molecular_function unknown;P:autophagy;C:cellular_component unknown;MFOP	O.I.	H.G.	S.X.
0.09	2.8	At5g63200	836441	tetratricopeptide repeat (TPR)-containing protein	F:binding;P:biological_process unknown;C:cellular_component unknown;OBMAFP	O.I.	H.G.	S.X.
0.08	2.3	At3g15351	820769	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM	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.135882.1.A1_at
Gene name	hypothetical protein
Homology with Arabidopsis	Similar to At1g78420: protein binding / zinc ion binding (HF=1e-7)
Module size	6 genes
NF	0.49
%ile	80.0

Co-expression analysis

Gene ID PtpAffx.135882.1.A1_at Gene name hypothetical protein Homology with ArabidopsisSimilar to At1g78420: protein binding / zinc ion binding (HF=1e-7) Module size 6 genes NF 0.49 %ile 80.0

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.135882.1.A1_at

Gene name hypothetical protein
Homology with Arabidopsis Similar to At1g78420: protein binding / zinc ion binding (HF=1e-7)

Module size 6 genes

NF 0.49

%ile 80.0

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