CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID 1620542_at

Gene name hypothetical protein LOC100255788
Homology with Arabidopsis Similar to At2g16800: high-affinity nickel-transport family protein (HF=9e-31)

Module size 6 genes

NF 0.46

%ile 69.2

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
0.53 75.2 0.95 1620542_at CB344230 hypothetical protein LOC100255788 - 9e-31 At2g16800 high-affinity nickel-transport family protein O.I. H.G. S.X.
0.67 87.9 0.95 1607286_at CF207311 hypothetical protein LOC100267511 - 3e-69 At3g12150 unknown protein O.I. H.G. S.X.
0.47 67.7 0.95 1616579_at CF514965 hypothetical protein LOC100260111 - 6e-2 At3g12360 ITN1 (INCREASED TOLERANCE TO NACL) O.I. H.G. S.X.
0.46 66.5 0.95 1619252_at CF206010.1 hypothetical protein LOC100242409 - 1e-28 At3g01850 ribulose-phosphate 3-epimerase, cytosolic, putative / pentose-5-phosphate 3-epimerase, putative O.I. H.G. S.X.
0.29 37.7 0.95 1610068_at CD711769 hypothetical protein LOC100252154 - 2e-19 At2g36670 aspartyl protease family protein O.I. H.G. S.X.
0.27 34.0 0.95 1615832_at BQ792735 hypothetical protein LOC100242360 - 1e-10 At2g24860 chaperone protein dnaJ-related 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.
0.53	75.2	0.95	1620542_at	CB344230	hypothetical protein LOC100255788	-	9e-31	At2g16800	high-affinity nickel-transport family protein	O.I.	H.G.	S.X.
0.67	87.9	0.95	1607286_at	CF207311	hypothetical protein LOC100267511	-	3e-69	At3g12150	unknown protein	O.I.	H.G.	S.X.
0.47	67.7	0.95	1616579_at	CF514965	hypothetical protein LOC100260111	-	6e-2	At3g12360	ITN1 (INCREASED TOLERANCE TO NACL)	O.I.	H.G.	S.X.
0.46	66.5	0.95	1619252_at	CF206010.1	hypothetical protein LOC100242409	-	1e-28	At3g01850	ribulose-phosphate 3-epimerase, cytosolic, putative / pentose-5-phosphate 3-epimerase, putative	O.I.	H.G.	S.X.
0.29	37.7	0.95	1610068_at	CD711769	hypothetical protein LOC100252154	-	2e-19	At2g36670	aspartyl protease family protein	O.I.	H.G.	S.X.
0.27	34.0	0.95	1615832_at	BQ792735	hypothetical protein LOC100242360	-	1e-10	At2g24860	chaperone protein dnaJ-related	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
5.7 98.5 GSM287877 Green hard berry B12 from plant 2 cluster distal position, biological rep 1 GSE11406 Expression data in individual grape berries during ripening initation
4.5 97.5 GSM287890 Pink soft berry C25 from plant 2 cluster proximal position, biological rep 1 GSE11406 Expression data in individual grape berries during ripening initation
3.7 96.2 GSM287875 Green hard berry C17 from plant 2 cluster proximal position, biological rep 2 GSE11406 Expression data in individual grape berries during ripening initation
3.5 95.7 GSM287886 Green soft berry C22 from plant 2 cluster proximal position, biological rep 2 GSE11406 Expression data in individual grape berries during ripening initation
3.4 95.5 GSM287873 Green hard berry B9 from plant 2 cluster proximal position, biological rep 1 GSE11406 Expression data in individual grape berries during ripening initation
3.2 94.9 GSM287888 Green soft berry C24 from plant 2 cluster distal position, biological rep 2 GSE11406 Expression data in individual grape berries during ripening initation
3.0 94.2 GSM287879 Green hard berry C19 from plant 2 cluster distal position, biological rep 2 GSE11406 Expression data in individual grape berries during ripening initation
3.0 94.2 GSM287885 Green soft berry A22 from plant 2 cluster proximal position, biological rep 1 GSE11406 Expression data in individual grape berries during ripening initation
2.7 93.0 GSM322368 genotype: Incrocio Manzoni - disease type: Bois Noir infected - rep2 GSE12842 Gene expression in grapevine in response to Bois noir infection
2.7 93.0 GSM147729 Vitis aestivalis 'Norton ' mock inoculated at 12 h post inoculation 58

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
5.7	98.5	GSM287877	Green hard berry B12 from plant 2 cluster distal position, biological rep 1	GSE11406	Expression data in individual grape berries during ripening initation
4.5	97.5	GSM287890	Pink soft berry C25 from plant 2 cluster proximal position, biological rep 1	GSE11406	Expression data in individual grape berries during ripening initation
3.7	96.2	GSM287875	Green hard berry C17 from plant 2 cluster proximal position, biological rep 2	GSE11406	Expression data in individual grape berries during ripening initation
3.5	95.7	GSM287886	Green soft berry C22 from plant 2 cluster proximal position, biological rep 2	GSE11406	Expression data in individual grape berries during ripening initation
3.4	95.5	GSM287873	Green hard berry B9 from plant 2 cluster proximal position, biological rep 1	GSE11406	Expression data in individual grape berries during ripening initation
3.2	94.9	GSM287888	Green soft berry C24 from plant 2 cluster distal position, biological rep 2	GSE11406	Expression data in individual grape berries during ripening initation
3.0	94.2	GSM287879	Green hard berry C19 from plant 2 cluster distal position, biological rep 2	GSE11406	Expression data in individual grape berries during ripening initation
3.0	94.2	GSM287885	Green soft berry A22 from plant 2 cluster proximal position, biological rep 1	GSE11406	Expression data in individual grape berries during ripening initation
2.7	93.0	GSM322368	genotype: Incrocio Manzoni - disease type: Bois Noir infected - rep2	GSE12842	Gene expression in grapevine in response to Bois noir infection
2.7	93.0	GSM147729	Vitis aestivalis 'Norton ' mock inoculated at 12 h post inoculation	58

Inter-species module comparison

A co-expression module including the Arabidopsis gene, At2g16800, orthologous to the query gene, 1620542_at

VF %ile Gene ID Repr. ID Gene Name Func. O.I. H.G. S.X. Other DB
1.00 100.0 At2g16800 816181 high-affinity nickel-transport family protein F:nickel ion transmembrane transporter activity, metal ion binding;P:nickel ion transport, metal ion transport;C:integral to membrane, chloroplast;OBPA O.I. H.G. S.X.
0.50 65.3 At4g19210 827661 ATRLI2 member of RLI subfamily O.I. H.G. S.X.
0.47 61.2 At2g43770 818980 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MFOBPAV O.I. H.G. S.X.
0.43 55.3 At4g26300 828736 emb1027 (embryo defective 1027) F:nucleotide binding, aminoacyl-tRNA ligase activity, arginine-tRNA ligase activity, ATP binding;P:embryonic development ending in seed dormancy, arginyl-tRNA aminoacylation;C:mitochondrion, chloroplast;OBMAFPV O.I. H.G. S.X.
0.39 48.4 At3g57610 824930 ADSS (ADENYLOSUCCINATE SYNTHASE) encoding adenylosuccinate synthetase (AdSS), the enzyme involved in the first step of the formation of the purine nucleotide AMP (conversion of IMP to adenylo-succinate) O.I. H.G. S.X.
0.35 41.6 At3g14390 820660 diaminopimelate decarboxylase, putative / DAP carboxylase, putative F:diaminopimelate decarboxylase activity;P:lysine biosynthetic process via diaminopimelate;C:chloroplast;BOMPFAV O.I. H.G. S.X.
0.33 38.1 At4g14000 827036 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;MFOPB O.I. H.G. S.X.
0.33 38.1 At3g07300 819918 eukaryotic translation initiation factor 2B family protein / eIF-2B family protein F:GTP binding, translation initiation factor activity;P:translational initiation, cellular metabolic process;C:eukaryotic translation initiation factor 2B complex;OBMFAP O.I. H.G. S.X.
0.32 35.7 At4g39280 830084 phenylalanyl-tRNA synthetase, putative / phenylalanine--tRNA ligase, putative F:phenylalanine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:phenylalanyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:cytoplasm;BOMAFP O.I. H.G. S.X.
0.32 35.7 At5g27470 832806 seryl-tRNA synthetase / serine--tRNA ligase F:serine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:response to cadmium ion, seryl-tRNA aminoacylation;C:cytosol;OBMFAP O.I. H.G. S.X.
0.31 33.8 At1g43190 840918 polypyrimidine tract-binding protein, putative / heterogeneous nuclear ribonucleoprotein, putative F:RNA binding, nucleotide binding, nucleic acid binding;P:mRNA processing;C:nucleus;MPOF O.I. H.G. S.X.
0.31 33.8 At1g04170 839238 EIF2 GAMMA protein synthesis initiation factor eIF2 gamma O.I. H.G. S.X.
0.31 33.8 At4g25550 828660 protein binding F:protein binding;P:biological_process unknown;C:cellular_component unknown;MOFP O.I. H.G. S.X.
0.29 30.3 At3g57290 824896 EIF3E (EUKARYOTIC TRANSLATION INITIATION FACTOR 3E) Encodes a protein that is found in not only the eif3 complex but also in association with subunits of the COP9 signalosome. eIF3e appears to be subjected to proteasome-dependent degradation that requires the PCI domain of eIF3e. The level of eIF3e present in cells appears to affect the rate of translation. O.I. H.G. S.X.
0.28 30.3 At2g39990 818587 EIF2 translation initiation factor eIF2 p47 subunit homolog O.I. H.G. S.X.
0.28 30.3 At2g39290 818514 PGP1 (PHOSPHATIDYLGLYCEROLPHOSPHATE SYNTHASE 1) Encodes a phosphatidylglycerolphosphate synthase 2C which is dual-targeted into chloroplasts and mitochondria. Mutant plants have mutant chloroplasts but normal mitochondria. O.I. H.G. S.X.
0.26 24.4 At3g58610 825030 ketol-acid reductoisomerase F:coenzyme binding, oxidoreductase activity, binding, ketol-acid reductoisomerase activity, catalytic activity;P:response to cadmium ion, branched chain family amino acid biosynthetic process;C:in 6 components;BOFAP O.I. H.G. S.X.
0.25 22.6 At4g33250 829461 EIF3K (EUKARYOTIC TRANSLATION INITIATION FACTOR 3K) Encodes initiation factor 3k (EIF3k). O.I. H.G. S.X.
0.25 22.6 At1g09620 837489 ATP binding / aminoacyl-tRNA ligase/ leucine-tRNA ligase/ nucleotide binding F:nucleotide binding, aminoacyl-tRNA ligase activity, leucine-tRNA ligase activity, ATP binding;P:leucyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:chloroplast;BOMAFP O.I. H.G. S.X.
0.23 19.3 At3g09630 820120 60S ribosomal protein L4/L1 (RPL4A) F:structural constituent of ribosome;P:translation;C:in 9 components;MOAFPB O.I. H.G. S.X.
0.21 15.8 At1g09640 837491 elongation factor 1B-gamma, putative / eEF-1B gamma, putative F:translation elongation factor activity;P:translational elongation;C:plasma membrane;BMOPFA O.I. H.G. S.X.
0.20 14.4 At3g59990 825169 MAP2B (METHIONINE AMINOPEPTIDASE 2B) Encodes a MAP2 like methionine aminopeptidase O.I. H.G. S.X.
0.20 14.4 At5g02870 831756 60S ribosomal protein L4/L1 (RPL4D) F:structural constituent of ribosome;P:translation;C:in 8 components;MOAFPB O.I. H.G. S.X.
0.18 11.4 At1g13320 837892 PP2AA3 (PROTEIN PHOSPHATASE 2A SUBUNIT A3) one of three genes encoding the 65 kDa regulatory subunit of protein phosphatase 2A (PP2A) 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	At2g16800	816181	high-affinity nickel-transport family protein	F:nickel ion transmembrane transporter activity, metal ion binding;P:nickel ion transport, metal ion transport;C:integral to membrane, chloroplast;OBPA	O.I.	H.G.	S.X.
0.50	65.3	At4g19210	827661	ATRLI2	member of RLI subfamily	O.I.	H.G.	S.X.
0.47	61.2	At2g43770	818980	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MFOBPAV	O.I.	H.G.	S.X.
0.43	55.3	At4g26300	828736	emb1027 (embryo defective 1027)	F:nucleotide binding, aminoacyl-tRNA ligase activity, arginine-tRNA ligase activity, ATP binding;P:embryonic development ending in seed dormancy, arginyl-tRNA aminoacylation;C:mitochondrion, chloroplast;OBMAFPV	O.I.	H.G.	S.X.
0.39	48.4	At3g57610	824930	ADSS (ADENYLOSUCCINATE SYNTHASE)	encoding adenylosuccinate synthetase (AdSS), the enzyme involved in the first step of the formation of the purine nucleotide AMP (conversion of IMP to adenylo-succinate)	O.I.	H.G.	S.X.
0.35	41.6	At3g14390	820660	diaminopimelate decarboxylase, putative / DAP carboxylase, putative	F:diaminopimelate decarboxylase activity;P:lysine biosynthetic process via diaminopimelate;C:chloroplast;BOMPFAV	O.I.	H.G.	S.X.
0.33	38.1	At4g14000	827036	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;MFOPB	O.I.	H.G.	S.X.
0.33	38.1	At3g07300	819918	eukaryotic translation initiation factor 2B family protein / eIF-2B family protein	F:GTP binding, translation initiation factor activity;P:translational initiation, cellular metabolic process;C:eukaryotic translation initiation factor 2B complex;OBMFAP	O.I.	H.G.	S.X.
0.32	35.7	At4g39280	830084	phenylalanyl-tRNA synthetase, putative / phenylalanine--tRNA ligase, putative	F:phenylalanine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:phenylalanyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:cytoplasm;BOMAFP	O.I.	H.G.	S.X.
0.32	35.7	At5g27470	832806	seryl-tRNA synthetase / serine--tRNA ligase	F:serine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:response to cadmium ion, seryl-tRNA aminoacylation;C:cytosol;OBMFAP	O.I.	H.G.	S.X.
0.31	33.8	At1g43190	840918	polypyrimidine tract-binding protein, putative / heterogeneous nuclear ribonucleoprotein, putative	F:RNA binding, nucleotide binding, nucleic acid binding;P:mRNA processing;C:nucleus;MPOF	O.I.	H.G.	S.X.
0.31	33.8	At1g04170	839238	EIF2 GAMMA	protein synthesis initiation factor eIF2 gamma	O.I.	H.G.	S.X.
0.31	33.8	At4g25550	828660	protein binding	F:protein binding;P:biological_process unknown;C:cellular_component unknown;MOFP	O.I.	H.G.	S.X.
0.29	30.3	At3g57290	824896	EIF3E (EUKARYOTIC TRANSLATION INITIATION FACTOR 3E)	Encodes a protein that is found in not only the eif3 complex but also in association with subunits of the COP9 signalosome. eIF3e appears to be subjected to proteasome-dependent degradation that requires the PCI domain of eIF3e. The level of eIF3e present in cells appears to affect the rate of translation.	O.I.	H.G.	S.X.
0.28	30.3	At2g39990	818587	EIF2	translation initiation factor eIF2 p47 subunit homolog	O.I.	H.G.	S.X.
0.28	30.3	At2g39290	818514	PGP1 (PHOSPHATIDYLGLYCEROLPHOSPHATE SYNTHASE 1)	Encodes a phosphatidylglycerolphosphate synthase 2C which is dual-targeted into chloroplasts and mitochondria. Mutant plants have mutant chloroplasts but normal mitochondria.	O.I.	H.G.	S.X.
0.26	24.4	At3g58610	825030	ketol-acid reductoisomerase	F:coenzyme binding, oxidoreductase activity, binding, ketol-acid reductoisomerase activity, catalytic activity;P:response to cadmium ion, branched chain family amino acid biosynthetic process;C:in 6 components;BOFAP	O.I.	H.G.	S.X.
0.25	22.6	At4g33250	829461	EIF3K (EUKARYOTIC TRANSLATION INITIATION FACTOR 3K)	Encodes initiation factor 3k (EIF3k).	O.I.	H.G.	S.X.
0.25	22.6	At1g09620	837489	ATP binding / aminoacyl-tRNA ligase/ leucine-tRNA ligase/ nucleotide binding	F:nucleotide binding, aminoacyl-tRNA ligase activity, leucine-tRNA ligase activity, ATP binding;P:leucyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:chloroplast;BOMAFP	O.I.	H.G.	S.X.
0.23	19.3	At3g09630	820120	60S ribosomal protein L4/L1 (RPL4A)	F:structural constituent of ribosome;P:translation;C:in 9 components;MOAFPB	O.I.	H.G.	S.X.
0.21	15.8	At1g09640	837491	elongation factor 1B-gamma, putative / eEF-1B gamma, putative	F:translation elongation factor activity;P:translational elongation;C:plasma membrane;BMOPFA	O.I.	H.G.	S.X.
0.20	14.4	At3g59990	825169	MAP2B (METHIONINE AMINOPEPTIDASE 2B)	Encodes a MAP2 like methionine aminopeptidase	O.I.	H.G.	S.X.
0.20	14.4	At5g02870	831756	60S ribosomal protein L4/L1 (RPL4D)	F:structural constituent of ribosome;P:translation;C:in 8 components;MOAFPB	O.I.	H.G.	S.X.
0.18	11.4	At1g13320	837892	PP2AA3 (PROTEIN PHOSPHATASE 2A SUBUNIT A3)	one of three genes encoding the 65 kDa regulatory subunit of protein phosphatase 2A (PP2A)	O.I.	H.G.	S.X.

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

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Gene ID	1620542_at
Gene name	hypothetical protein LOC100255788
Homology with Arabidopsis	Similar to At2g16800: high-affinity nickel-transport family protein (HF=9e-31)
Module size	6 genes
NF	0.46
%ile	69.2

Co-expression analysis

Gene ID 1620542_at Gene name hypothetical protein LOC100255788 Homology with ArabidopsisSimilar to At2g16800: high-affinity nickel-transport family protein (HF=9e-31) Module size 6 genes NF 0.46 %ile 69.2

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_sativaPopulus_trichocarpaTriticum_aestivumZea_mays

Gene ID 1620542_at

Gene name hypothetical protein LOC100255788
Homology with Arabidopsis Similar to At2g16800: high-affinity nickel-transport family protein (HF=9e-31)

Module size 6 genes

NF 0.46

%ile 69.2

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