CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID 1607287_a_at

Gene name hypothetical protein LOC100248273
Homology with Arabidopsis Similar to At3g56910: PSRP5 (PLASTID-SPECIFIC 50S RIBOSOMAL PROTEIN 5) (HF=3e-16)

Module size 6 genes

NF 0.65

%ile 91.0

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
0.91 98.8 0.98 1607287_a_at CA817984 hypothetical protein LOC100248273 - 3e-16 At3g56910 PSRP5 (PLASTID-SPECIFIC 50S RIBOSOMAL PROTEIN 5) O.I. H.G. S.X.
0.73 90.8 0.99 1607466_at CF413978 similar to EMB2394 (EMBRYO DEFECTIVE 2394); structural constituent of ribosome - 2e-17 At1g05190 emb2394 (embryo defective 2394) O.I. H.G. S.X.
0.67 87.9 0.98 1620684_at CA811105 hypothetical protein LOC100244408 - 5e-10 At1g64510 ribosomal protein S6 family protein O.I. H.G. S.X.
0.53 75.2 0.98 1608691_at CB345817 hypothetical protein LOC100248623 - 6e-27 At1g78630 emb1473 (embryo defective 1473) O.I. H.G. S.X.
0.46 66.5 0.99 1606458_at BQ792397 hypothetical protein LOC100251697 - 4e-11 At3g44890 RPL9 (RIBOSOMAL PROTEIN L9) O.I. H.G. S.X.
0.33 45.7 0.98 1606797_at CD714405 similar to 50S ribosomal protein L17, chloroplastic - 3e-8 At3g54210 ribosomal protein L17 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.
0.91	98.8	0.98	1607287_a_at	CA817984	hypothetical protein LOC100248273	-	3e-16	At3g56910	PSRP5 (PLASTID-SPECIFIC 50S RIBOSOMAL PROTEIN 5)	O.I.	H.G.	S.X.
0.73	90.8	0.99	1607466_at	CF413978	similar to EMB2394 (EMBRYO DEFECTIVE 2394); structural constituent of ribosome	-	2e-17	At1g05190	emb2394 (embryo defective 2394)	O.I.	H.G.	S.X.
0.67	87.9	0.98	1620684_at	CA811105	hypothetical protein LOC100244408	-	5e-10	At1g64510	ribosomal protein S6 family protein	O.I.	H.G.	S.X.
0.53	75.2	0.98	1608691_at	CB345817	hypothetical protein LOC100248623	-	6e-27	At1g78630	emb1473 (embryo defective 1473)	O.I.	H.G.	S.X.
0.46	66.5	0.99	1606458_at	BQ792397	hypothetical protein LOC100251697	-	4e-11	At3g44890	RPL9 (RIBOSOMAL PROTEIN L9)	O.I.	H.G.	S.X.
0.33	45.7	0.98	1606797_at	CD714405	similar to 50S ribosomal protein L17, chloroplastic	-	3e-8	At3g54210	ribosomal protein L17 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
8.8 99.5 GSM299457 C_i_rep2 GSE11857 Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
6.8 99.0 GSM147717 Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 12 h post inoculation 46
5.8 98.6 GSM299461 C_ni_rep1 GSE11857 Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
5.5 98.4 GSM299453 B_i_rep1 GSE11857 Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
3.2 94.9 GSM299459 D_i_rep1 GSE11857 Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
3.0 94.2 GSM299455 C_ni_rep2 GSE11857 Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
2.9 93.8 GSM299451 B_ni_rep1 GSE11857 Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
2.9 93.8 GSM299456 C_i_rep1 GSE11857 Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
2.8 93.4 GSM299454 B_i_rep2 GSE11857 Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
2.5 91.9 GSM147735 Vitis aestivalis 'Norton ' mock inoculated at 12 h post inoculation 64

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
8.8	99.5	GSM299457	C_i_rep2	GSE11857	Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
6.8	99.0	GSM147717	Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 12 h post inoculation	46
5.8	98.6	GSM299461	C_ni_rep1	GSE11857	Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
5.5	98.4	GSM299453	B_i_rep1	GSE11857	Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
3.2	94.9	GSM299459	D_i_rep1	GSE11857	Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
3.0	94.2	GSM299455	C_ni_rep2	GSE11857	Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
2.9	93.8	GSM299451	B_ni_rep1	GSE11857	Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
2.9	93.8	GSM299456	C_i_rep1	GSE11857	Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
2.8	93.4	GSM299454	B_i_rep2	GSE11857	Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes
2.5	91.9	GSM147735	Vitis aestivalis 'Norton ' mock inoculated at 12 h post inoculation	64

Inter-species module comparison

A co-expression module including the Arabidopsis gene, At3g56910, orthologous to the query gene, 1607287_a_at

VF %ile Gene ID Repr. ID Gene Name Func. O.I. H.G. S.X. Other DB
0.79 89.1 At3g56910 824858 PSRP5 (PLASTID-SPECIFIC 50S RIBOSOMAL PROTEIN 5) F:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast, chloroplast envelope;PM O.I. H.G. S.X.
0.93 96.4 At1g79850 844324 RPS17 (RIBOSOMAL PROTEIN S17) nuclear-encoded 30S chloroplast ribosomal protein S17 O.I. H.G. S.X.
0.91 95.6 At2g33450 817910 50S ribosomal protein L28, chloroplast (CL28) F:structural constituent of ribosome;P:translation;C:ribosome, chloroplast, membrane;BOPF O.I. H.G. S.X.
0.90 95.1 At5g47190 834765 ribosomal protein L19 family protein F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, chloroplast stroma, chloroplast, membrane, chloroplast envelope;BOPMF O.I. H.G. S.X.
0.89 94.6 At1g48350 841255 ribosomal protein L18 family protein F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, chloroplast, chloroplast envelope;BOPM O.I. H.G. S.X.
0.89 94.6 At1g64510 842759 ribosomal protein S6 family protein F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:thylakoid, chloroplast thylakoid membrane, ribosome, chloroplast;BOP O.I. H.G. S.X.
0.89 94.6 At1g78630 844199 emb1473 (embryo defective 1473) F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation;C:thylakoid, ribosome, chloroplast, chloroplast stroma;BOMFAP O.I. H.G. S.X.
0.89 94.6 At2g33800 817947 ribosomal protein S5 family protein F:structural constituent of ribosome, RNA binding;P:response to cadmium ion, response to cold, translation;C:in 8 components;BOMAFP O.I. H.G. S.X.
0.87 93.5 At3g52150 824379 RNA recognition motif (RRM)-containing protein F:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast stroma, chloroplast, chloroplast envelope;MPOFBA O.I. H.G. S.X.
0.85 92.4 At2g24090 816943 ribosomal protein L35 family protein F:structural constituent of ribosome;P:translation;C:ribosome, chloroplast;BOPMF O.I. H.G. S.X.
0.85 92.4 At4g01310 827947 ribosomal protein L5 family protein F:structural constituent of ribosome;P:translation;C:in 6 components;BOPAFM O.I. H.G. S.X.
0.85 92.4 At3g54210 824588 ribosomal protein L17 family protein F:structural constituent of ribosome;P:translation;C:ribosome, chloroplast;BOMFP O.I. H.G. S.X.
0.83 91.4 At3g13120 820500 30S ribosomal protein S10, chloroplast, putative F:structural constituent of ribosome, RNA binding;P:translation;C:small ribosomal subunit, chloroplast;BOMAPF O.I. H.G. S.X.
0.82 90.9 At1g07320 837243 RPL4 encodes a plastid ribosomal protein L4 O.I. H.G. S.X.
0.82 90.9 At2g43030 818905 ribosomal protein L3 family protein F:structural constituent of ribosome;P:translation;C:ribosome, chloroplast stroma, chloroplast, membrane;BOAMFP O.I. H.G. S.X.
0.82 90.9 At4g24770 828579 RBP31 (31-KDA RNA BINDING PROTEIN) Encodes a chloroplast RNA-binding protein. A substrate of the type III effector HopU1 (mono-ADP-ribosyltransferase). O.I. H.G. S.X.
0.81 90.4 At5g14910 831343 heavy-metal-associated domain-containing protein F:metal ion binding;P:metal ion transport;C:thylakoid, chloroplast thylakoid membrane, chloroplast stroma, chloroplast;P O.I. H.G. S.X.
0.81 90.4 At3g15190 820750 chloroplast 30S ribosomal protein S20, putative F:structural constituent of ribosome, RNA binding;P:translation, ribosome biogenesis;C:ribosome, chloroplast stroma, chloroplast, membrane;BOPM O.I. H.G. S.X.
0.81 90.4 At1g29070 839781 ribosomal protein L34 family protein F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, intracellular, chloroplast;BPOF O.I. H.G. S.X.
0.80 89.8 At1g05190 839273 emb2394 (embryo defective 2394) F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation;C:chloroplast stroma, chloroplast, large ribosomal subunit, membrane, chloroplast envelope;BOAFPM O.I. H.G. S.X.
0.78 88.6 At1g74970 843836 RPS9 (RIBOSOMAL PROTEIN S9) ribosomal protein S9, nuclear encoded component of the chloroplast ribosome O.I. H.G. S.X.
0.75 86.9 At5g08280 830724 HEMC (HYDROXYMETHYLBILANE SYNTHASE) Encodes a protein with porphobilinogen deaminase activity. This protein is targeted to the chloroplast. O.I. H.G. S.X.
0.71 84.2 At1g68590 843189 plastid-specific 30S ribosomal protein 3, putative / PSRP-3, putative F:structural constituent of ribosome;P:translation;C:thylakoid, chloroplast thylakoid membrane, chloroplast;OBP O.I. H.G. S.X.
0.71 84.2 At3g08740 820021 elongation factor P (EF-P) family protein F:translation elongation factor activity;P:translational elongation;C:chloroplast, chloroplast stroma;BOPA O.I. H.G. S.X.
0.71 84.2 At5g13510 831195 ribosomal protein L10 family protein F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic ribosome, ribosome, chloroplast, chloroplast stroma;BOAPMF O.I. H.G. S.X.
0.70 83.5 At1g75350 843871 emb2184 (embryo defective 2184) F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation, ribosome biogenesis;C:ribosome, chloroplast, chloroplast stroma, chloroplast envelope;BOP O.I. H.G. S.X.
0.70 83.5 At4g18480 827580 CHLI1 Encodes the CHLI subunit of magnesium chelatase which is required for chlorophyll biosynthesis. All four cysteine residues of the protein form two disulfide bonds (Cys102-Cys193 and Cys354-Cys396) under oxidized conditions but are fully reduced by reduction. It was suggested that the redox state of CHLI is regulated in vivo by the change of the redox environment in the chloroplasts probably via the Trx system. O.I. H.G. S.X.
0.68 82.2 At1g32990 840194 PRPL11 (PLASTID RIBOSOMAL PROTEIN L11) mutant has Decreased effective quantum yield of photosystem II; Pale green plants; Reduced growth rate; Plastid Ribosomal Protein L11 O.I. H.G. S.X.
0.63 78.1 At3g11630 820335 2-cys peroxiredoxin, chloroplast (BAS1) Encodes a 2-Cys peroxiredoxin (2-Cys PrxA) that contains two catalytic Cys residues. 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	At3g56910	824858	PSRP5 (PLASTID-SPECIFIC 50S RIBOSOMAL PROTEIN 5)	F:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast, chloroplast envelope;PM	O.I.	H.G.	S.X.
0.93	96.4	At1g79850	844324	RPS17 (RIBOSOMAL PROTEIN S17)	nuclear-encoded 30S chloroplast ribosomal protein S17	O.I.	H.G.	S.X.
0.91	95.6	At2g33450	817910	50S ribosomal protein L28, chloroplast (CL28)	F:structural constituent of ribosome;P:translation;C:ribosome, chloroplast, membrane;BOPF	O.I.	H.G.	S.X.
0.90	95.1	At5g47190	834765	ribosomal protein L19 family protein	F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, chloroplast stroma, chloroplast, membrane, chloroplast envelope;BOPMF	O.I.	H.G.	S.X.
0.89	94.6	At1g48350	841255	ribosomal protein L18 family protein	F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, chloroplast, chloroplast envelope;BOPM	O.I.	H.G.	S.X.
0.89	94.6	At1g64510	842759	ribosomal protein S6 family protein	F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:thylakoid, chloroplast thylakoid membrane, ribosome, chloroplast;BOP	O.I.	H.G.	S.X.
0.89	94.6	At1g78630	844199	emb1473 (embryo defective 1473)	F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation;C:thylakoid, ribosome, chloroplast, chloroplast stroma;BOMFAP	O.I.	H.G.	S.X.
0.89	94.6	At2g33800	817947	ribosomal protein S5 family protein	F:structural constituent of ribosome, RNA binding;P:response to cadmium ion, response to cold, translation;C:in 8 components;BOMAFP	O.I.	H.G.	S.X.
0.87	93.5	At3g52150	824379	RNA recognition motif (RRM)-containing protein	F:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast stroma, chloroplast, chloroplast envelope;MPOFBA	O.I.	H.G.	S.X.
0.85	92.4	At2g24090	816943	ribosomal protein L35 family protein	F:structural constituent of ribosome;P:translation;C:ribosome, chloroplast;BOPMF	O.I.	H.G.	S.X.
0.85	92.4	At4g01310	827947	ribosomal protein L5 family protein	F:structural constituent of ribosome;P:translation;C:in 6 components;BOPAFM	O.I.	H.G.	S.X.
0.85	92.4	At3g54210	824588	ribosomal protein L17 family protein	F:structural constituent of ribosome;P:translation;C:ribosome, chloroplast;BOMFP	O.I.	H.G.	S.X.
0.83	91.4	At3g13120	820500	30S ribosomal protein S10, chloroplast, putative	F:structural constituent of ribosome, RNA binding;P:translation;C:small ribosomal subunit, chloroplast;BOMAPF	O.I.	H.G.	S.X.
0.82	90.9	At1g07320	837243	RPL4	encodes a plastid ribosomal protein L4	O.I.	H.G.	S.X.
0.82	90.9	At2g43030	818905	ribosomal protein L3 family protein	F:structural constituent of ribosome;P:translation;C:ribosome, chloroplast stroma, chloroplast, membrane;BOAMFP	O.I.	H.G.	S.X.
0.82	90.9	At4g24770	828579	RBP31 (31-KDA RNA BINDING PROTEIN)	Encodes a chloroplast RNA-binding protein. A substrate of the type III effector HopU1 (mono-ADP-ribosyltransferase).	O.I.	H.G.	S.X.
0.81	90.4	At5g14910	831343	heavy-metal-associated domain-containing protein	F:metal ion binding;P:metal ion transport;C:thylakoid, chloroplast thylakoid membrane, chloroplast stroma, chloroplast;P	O.I.	H.G.	S.X.
0.81	90.4	At3g15190	820750	chloroplast 30S ribosomal protein S20, putative	F:structural constituent of ribosome, RNA binding;P:translation, ribosome biogenesis;C:ribosome, chloroplast stroma, chloroplast, membrane;BOPM	O.I.	H.G.	S.X.
0.81	90.4	At1g29070	839781	ribosomal protein L34 family protein	F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, intracellular, chloroplast;BPOF	O.I.	H.G.	S.X.
0.80	89.8	At1g05190	839273	emb2394 (embryo defective 2394)	F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation;C:chloroplast stroma, chloroplast, large ribosomal subunit, membrane, chloroplast envelope;BOAFPM	O.I.	H.G.	S.X.
0.78	88.6	At1g74970	843836	RPS9 (RIBOSOMAL PROTEIN S9)	ribosomal protein S9, nuclear encoded component of the chloroplast ribosome	O.I.	H.G.	S.X.
0.75	86.9	At5g08280	830724	HEMC (HYDROXYMETHYLBILANE SYNTHASE)	Encodes a protein with porphobilinogen deaminase activity. This protein is targeted to the chloroplast.	O.I.	H.G.	S.X.
0.71	84.2	At1g68590	843189	plastid-specific 30S ribosomal protein 3, putative / PSRP-3, putative	F:structural constituent of ribosome;P:translation;C:thylakoid, chloroplast thylakoid membrane, chloroplast;OBP	O.I.	H.G.	S.X.
0.71	84.2	At3g08740	820021	elongation factor P (EF-P) family protein	F:translation elongation factor activity;P:translational elongation;C:chloroplast, chloroplast stroma;BOPA	O.I.	H.G.	S.X.
0.71	84.2	At5g13510	831195	ribosomal protein L10 family protein	F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic ribosome, ribosome, chloroplast, chloroplast stroma;BOAPMF	O.I.	H.G.	S.X.
0.70	83.5	At1g75350	843871	emb2184 (embryo defective 2184)	F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation, ribosome biogenesis;C:ribosome, chloroplast, chloroplast stroma, chloroplast envelope;BOP	O.I.	H.G.	S.X.
0.70	83.5	At4g18480	827580	CHLI1	Encodes the CHLI subunit of magnesium chelatase which is required for chlorophyll biosynthesis. All four cysteine residues of the protein form two disulfide bonds (Cys102-Cys193 and Cys354-Cys396) under oxidized conditions but are fully reduced by reduction. It was suggested that the redox state of CHLI is regulated in vivo by the change of the redox environment in the chloroplasts probably via the Trx system.	O.I.	H.G.	S.X.
0.68	82.2	At1g32990	840194	PRPL11 (PLASTID RIBOSOMAL PROTEIN L11)	mutant has Decreased effective quantum yield of photosystem II; Pale green plants; Reduced growth rate; Plastid Ribosomal Protein L11	O.I.	H.G.	S.X.
0.63	78.1	At3g11630	820335	2-cys peroxiredoxin, chloroplast (BAS1)	Encodes a 2-Cys peroxiredoxin (2-Cys PrxA) that contains two catalytic Cys residues.	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	1607287_a_at
Gene name	hypothetical protein LOC100248273
Homology with Arabidopsis	Similar to At3g56910: PSRP5 (PLASTID-SPECIFIC 50S RIBOSOMAL PROTEIN 5) (HF=3e-16)
Module size	6 genes
NF	0.65
%ile	91.0

Co-expression analysis

Gene ID 1607287_a_at Gene name hypothetical protein LOC100248273 Homology with ArabidopsisSimilar to At3g56910: PSRP5 (PLASTID-SPECIFIC 50S RIBOSOMAL PROTEIN 5) (HF=3e-16) Module size 6 genes NF 0.65 %ile 91.0

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_sativaPopulus_trichocarpaTriticum_aestivumZea_mays

Gene ID 1607287_a_at

Gene name hypothetical protein LOC100248273
Homology with Arabidopsis Similar to At3g56910: PSRP5 (PLASTID-SPECIFIC 50S RIBOSOMAL PROTEIN 5) (HF=3e-16)

Module size 6 genes

NF 0.65

%ile 91.0

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