CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Os06g0608600

Gene name
Homology with Arabidopsis Similar to At5g56020: - (HF=9e-3)

Module size 6 genes

NF 0.33

%ile 36.7

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
0.67 87.2 0.95 Os06g0608600 AK061418.1 - Conserved hypothetical protein 9e-3 At5g56020 - O.I. H.G. S.X.
0.61 81.2 0.94 Os04g0600400 AK072894.1 - Conserved hypothetical protein 6e-1 At2g35470 unknown protein O.I. H.G. S.X.
0.60 79.7 0.94 Os06g0300300 AK068813.1 - Conserved hypothetical protein 2e-3 At4g26550 - O.I. H.G. S.X.
0.30 32.7 0.94 Os05g0279600 AK070566.1 - Conserved hypothetical protein 3e-9 At4g30900 - O.I. H.G. S.X.
0.22 19.4 0.94 Os04g0687300 AK060617.1 - Heat shock protein DnaJ, N-terminal domaincontaining protein 7e-1 At3g08000 RNA-binding protein, putative O.I. H.G. S.X.
0.11 6.5 0.94 Os03g0729900 BE040070 - BSD protein (Fragment) 2e+0 At5g27930 protein phosphatase 2C, putative / PP2C, putative 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	87.2	0.95	Os06g0608600	AK061418.1	-	Conserved hypothetical protein	9e-3	At5g56020	-	O.I.	H.G.	S.X.
0.61	81.2	0.94	Os04g0600400	AK072894.1	-	Conserved hypothetical protein	6e-1	At2g35470	unknown protein	O.I.	H.G.	S.X.
0.60	79.7	0.94	Os06g0300300	AK068813.1	-	Conserved hypothetical protein	2e-3	At4g26550	-	O.I.	H.G.	S.X.
0.30	32.7	0.94	Os05g0279600	AK070566.1	-	Conserved hypothetical protein	3e-9	At4g30900	-	O.I.	H.G.	S.X.
0.22	19.4	0.94	Os04g0687300	AK060617.1	-	Heat shock protein DnaJ, N-terminal domaincontaining protein	7e-1	At3g08000	RNA-binding protein, putative	O.I.	H.G.	S.X.
0.11	6.5	0.94	Os03g0729900	BE040070	-	BSD protein (Fragment)	2e+0	At5g27930	protein phosphatase 2C, putative / PP2C, putative	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
31.3 99.7 GSM422672 Drought GSE16865 Heterologous microarrays for the study of drought stress in Musa
25.3 99.5 GSM422674 Musa_DNA_RICE GSE16865 Heterologous microarrays for the study of drought stress in Musa
13.8 98.5 GSM100446 Rice Bala 1ppm Arsenate Rep2 GSE4471 Expression data from rice varieties Azucena and Bala grown in 0 and 1ppm arsenate
9.9 98.0 GSM422676 Control GSE16865 Heterologous microarrays for the study of drought stress in Musa
9.0 97.8 GSM174886 F FR13 4 dpi rep 1 with array type rice from Affymetrix GSE7256 Identification of rice genes differentially expressed upon virulent infection by Magnaporthe grisea
8.4 97.7 GSM377074 Genomic DNA - 45 day old leaf sample - mutant g282 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.0 97.6 GSM377078 Genomic DNA - 45 day old leaf sample - mutant g6603 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.4 97.5 GSM377081 Genomic DNA - 45 day old leaf sample - mutant g7534 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.2 97.4 GSM174889 H FR13 4 dpi rep 2 with array type rice from Affymetrix GSE7256 Identification of rice genes differentially expressed upon virulent infection by Magnaporthe grisea
7.0 97.4 GSM377082 Genomic DNA - 45 day old leaf sample - mutant g9799 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
31.3	99.7	GSM422672	Drought	GSE16865	Heterologous microarrays for the study of drought stress in Musa
25.3	99.5	GSM422674	Musa_DNA_RICE	GSE16865	Heterologous microarrays for the study of drought stress in Musa
13.8	98.5	GSM100446	Rice Bala 1ppm Arsenate Rep2	GSE4471	Expression data from rice varieties Azucena and Bala grown in 0 and 1ppm arsenate
9.9	98.0	GSM422676	Control	GSE16865	Heterologous microarrays for the study of drought stress in Musa
9.0	97.8	GSM174886	F FR13 4 dpi rep 1 with array type rice from Affymetrix	GSE7256	Identification of rice genes differentially expressed upon virulent infection by Magnaporthe grisea
8.4	97.7	GSM377074	Genomic DNA - 45 day old leaf sample - mutant g282	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.0	97.6	GSM377078	Genomic DNA - 45 day old leaf sample - mutant g6603	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.4	97.5	GSM377081	Genomic DNA - 45 day old leaf sample - mutant g7534	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.2	97.4	GSM174889	H FR13 4 dpi rep 2 with array type rice from Affymetrix	GSE7256	Identification of rice genes differentially expressed upon virulent infection by Magnaporthe grisea
7.0	97.4	GSM377082	Genomic DNA - 45 day old leaf sample - mutant g9799	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO

Inter-species module comparison

A co-expression module including the Arabidopsis gene, At5g56020, orthologous to the query gene, Os06g0608600

VF %ile Gene ID Repr. ID Gene Name Func. O.I. H.G. S.X. Other DB
0.63 78.1 At5g56020 835700 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFP O.I. H.G. S.X.
0.63 78.1 At3g21610 821715 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BOP O.I. H.G. S.X.
0.53 68.6 At5g64500 836571 membrane protein-related F:molecular_function unknown;P:biological_process unknown;C:membrane;BOFMAP O.I. H.G. S.X.
0.51 66.3 At1g71190 843459 SAG18 (SENESCENCE ASSOCIATED GENE 18) Senescence associated gene (SAG). Expression induced by ozone. Encodes a plant-specific protein of unknown function. Based on a personal communication from David Meinke (08/21/2007), this gene is not allelic to TTN4, even though this has been stated previously in a publication. O.I. H.G. S.X.
0.46 59.8 At3g05010 819662 transmembrane protein, putative F:molecular_function unknown;P:biological_process unknown;C:membrane;MPBO O.I. H.G. S.X.
0.44 57.2 At3g51040 824268 RTH (RTE1-HOMOLOG) Encodes a protein of 231 amino acids with 51% identity to RTE1 over 209 amino acids. O.I. H.G. S.X.
0.44 57.2 At4g07390 826170 PQ-loop repeat family protein / transmembrane family protein F:unknown;P:unknown;C:membrane;MPFO O.I. H.G. S.X.
0.42 53.9 At5g09310 830790 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO O.I. H.G. S.X.
0.36 43.6 At5g60620 836183 phospholipid/glycerol acyltransferase family protein F:acyltransferase activity;P:triglyceride biosynthetic process, diacylglycerol biosynthetic process, metabolic process;C:plasma membrane, membrane;MOBPF O.I. H.G. S.X.
0.35 41.6 At1g68070 843135 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:plasma membrane;PMOFVB O.I. H.G. S.X.
0.33 38.1 At1g80950 844435 phospholipid/glycerol acyltransferase family protein F:acyltransferase activity;P:metabolic process;C:endoplasmic reticulum, nucleus;BOMPF O.I. H.G. S.X.
0.33 38.1 At2g04900 815037 unknown protein F:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;BOMPF O.I. H.G. S.X.
0.33 38.1 At3g58460 825015 ATRBL15 (ARABIDOPSIS RHOMBOID-LIKE PROTEIN 15) F:molecular_function unknown;P:biological_process unknown;C:integral to membrane;BOPMFAV O.I. H.G. S.X.
0.32 35.7 At5g48810 834939 CB5-D (CYTOCHROME B5 ISOFORM D) Encodes a cytochrome b5 isoform that localizes to the ER. The C-terminal portion of the protein appears to be capable of inserting into a plant microsomal membrane in vitro and the protein appears to be subject to glycosylation. O.I. H.G. S.X.
0.31 33.8 At1g16890 838260 ubiquitin-conjugating enzyme, putative UBC36/UBC13B encodes a protein that may play a role in DNA damage responses and error-free post-replicative DNA repair. It can bind to the MMZ/UEV1 proteins in vitro. O.I. H.G. S.X.
0.30 32.1 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.
0.30 32.1 At1g68100 843138 IAR1 (IAA-ALANINE RESISTANT 1) member of IAA-alanine resistance protein 1 O.I. H.G. S.X.
0.30 32.1 At3g18430 821372 calcium-binding EF hand family protein F:calcium ion binding;P:N-terminal protein myristoylation;C:vacuole;MPOFB O.I. H.G. S.X.
0.29 30.3 At5g02040 831904 PRA1.A1 (PRENYLATED RAB ACCEPTOR 1.A1) F:molecular_function unknown;P:vesicle-mediated transport;C:endoplasmic reticulum;MPF O.I. H.G. S.X.
0.29 30.3 At5g51400 835214 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMF O.I. H.G. S.X.
0.29 30.3 At4g05000 825842 VPS28-2 F:transporter activity;P:transport;C:ESCRT I complex;MFPO O.I. H.G. S.X.
0.29 30.3 At1g04260 839565 MPI7 (CAMV MOVEMENT PROTEIN INTERACTING PROTEIN 7) Encodes protein that interacts with CaMV movement protein. Colocalizes in the cytoplasm with the movement protein. Has similarity to mammalian proteins (such as the rat PRA1) which have been described as rab acceptors. O.I. H.G. S.X.
0.28 30.3 At3g59950 825165 autophagy 4b (APG4b) F:peptidase activity;P:autophagy;C:chloroplast;MOFP O.I. H.G. S.X.
0.27 26.2 At2g47760 819388 ALG3 F:alpha-1,3-mannosyltransferase activity, catalytic activity;P:protein amino acid glycosylation;C:endoplasmic reticulum;MFOPAB O.I. H.G. S.X.
0.24 20.7 At4g04860 825823 DER2.2 (DERLIN-2.2) F:unknown;P:proteolysis;C:cellular_component unknown;MOFP O.I. H.G. S.X.
0.24 20.7 At5g08290 830725 YLS8 Encodes Dim1 homolog. O.I. H.G. S.X.
0.23 19.3 At5g52240 835300 MSBP1 (membrane steroid binding protein 1) Encodes a protein with similarity to progesterone-binding proteins in animals. Has been shown to bind steroids in vitro. Expressed in aerial portions of the plant excluding mature flowers and siliques. Antisense experiments suggest a role in inhibition of hypocotyl cell elongation. Expression is suppressed light grown seedlings transferred to the dark. O.I. H.G. S.X.
0.23 19.3 At1g79975 - - - O.I. H.G. S.X.
0.23 19.3 At5g11810 831054 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO O.I. H.G. S.X.
0.22 17.5 At2g25280 817066 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BAMOFP O.I. H.G. S.X.
0.21 15.8 At5g51510 835225 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO O.I. H.G. S.X.
0.21 15.8 At2g30710 817622 RabGAP/TBC domain-containing protein F:RAB GTPase activator activity;P:regulation of Rab GTPase activity;C:intracellular;MOFP O.I. H.G. S.X.

VF	%ile	Gene ID	Repr. ID	Gene Name	Func.	O.I.	H.G.	S.X.
0.63	78.1	At5g56020	835700	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFP	O.I.	H.G.	S.X.
0.63	78.1	At3g21610	821715	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BOP	O.I.	H.G.	S.X.
0.53	68.6	At5g64500	836571	membrane protein-related	F:molecular_function unknown;P:biological_process unknown;C:membrane;BOFMAP	O.I.	H.G.	S.X.
0.51	66.3	At1g71190	843459	SAG18 (SENESCENCE ASSOCIATED GENE 18)	Senescence associated gene (SAG). Expression induced by ozone. Encodes a plant-specific protein of unknown function. Based on a personal communication from David Meinke (08/21/2007), this gene is not allelic to TTN4, even though this has been stated previously in a publication.	O.I.	H.G.	S.X.
0.46	59.8	At3g05010	819662	transmembrane protein, putative	F:molecular_function unknown;P:biological_process unknown;C:membrane;MPBO	O.I.	H.G.	S.X.
0.44	57.2	At3g51040	824268	RTH (RTE1-HOMOLOG)	Encodes a protein of 231 amino acids with 51% identity to RTE1 over 209 amino acids.	O.I.	H.G.	S.X.
0.44	57.2	At4g07390	826170	PQ-loop repeat family protein / transmembrane family protein	F:unknown;P:unknown;C:membrane;MPFO	O.I.	H.G.	S.X.
0.42	53.9	At5g09310	830790	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO	O.I.	H.G.	S.X.
0.36	43.6	At5g60620	836183	phospholipid/glycerol acyltransferase family protein	F:acyltransferase activity;P:triglyceride biosynthetic process, diacylglycerol biosynthetic process, metabolic process;C:plasma membrane, membrane;MOBPF	O.I.	H.G.	S.X.
0.35	41.6	At1g68070	843135	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:plasma membrane;PMOFVB	O.I.	H.G.	S.X.
0.33	38.1	At1g80950	844435	phospholipid/glycerol acyltransferase family protein	F:acyltransferase activity;P:metabolic process;C:endoplasmic reticulum, nucleus;BOMPF	O.I.	H.G.	S.X.
0.33	38.1	At2g04900	815037	unknown protein	F:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;BOMPF	O.I.	H.G.	S.X.
0.33	38.1	At3g58460	825015	ATRBL15 (ARABIDOPSIS RHOMBOID-LIKE PROTEIN 15)	F:molecular_function unknown;P:biological_process unknown;C:integral to membrane;BOPMFAV	O.I.	H.G.	S.X.
0.32	35.7	At5g48810	834939	CB5-D (CYTOCHROME B5 ISOFORM D)	Encodes a cytochrome b5 isoform that localizes to the ER. The C-terminal portion of the protein appears to be capable of inserting into a plant microsomal membrane in vitro and the protein appears to be subject to glycosylation.	O.I.	H.G.	S.X.
0.31	33.8	At1g16890	838260	ubiquitin-conjugating enzyme, putative	UBC36/UBC13B encodes a protein that may play a role in DNA damage responses and error-free post-replicative DNA repair. It can bind to the MMZ/UEV1 proteins in vitro.	O.I.	H.G.	S.X.
0.30	32.1	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.
0.30	32.1	At1g68100	843138	IAR1 (IAA-ALANINE RESISTANT 1)	member of IAA-alanine resistance protein 1	O.I.	H.G.	S.X.
0.30	32.1	At3g18430	821372	calcium-binding EF hand family protein	F:calcium ion binding;P:N-terminal protein myristoylation;C:vacuole;MPOFB	O.I.	H.G.	S.X.
0.29	30.3	At5g02040	831904	PRA1.A1 (PRENYLATED RAB ACCEPTOR 1.A1)	F:molecular_function unknown;P:vesicle-mediated transport;C:endoplasmic reticulum;MPF	O.I.	H.G.	S.X.
0.29	30.3	At5g51400	835214	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMF	O.I.	H.G.	S.X.
0.29	30.3	At4g05000	825842	VPS28-2	F:transporter activity;P:transport;C:ESCRT I complex;MFPO	O.I.	H.G.	S.X.
0.29	30.3	At1g04260	839565	MPI7 (CAMV MOVEMENT PROTEIN INTERACTING PROTEIN 7)	Encodes protein that interacts with CaMV movement protein. Colocalizes in the cytoplasm with the movement protein. Has similarity to mammalian proteins (such as the rat PRA1) which have been described as rab acceptors.	O.I.	H.G.	S.X.
0.28	30.3	At3g59950	825165	autophagy 4b (APG4b)	F:peptidase activity;P:autophagy;C:chloroplast;MOFP	O.I.	H.G.	S.X.
0.27	26.2	At2g47760	819388	ALG3	F:alpha-1,3-mannosyltransferase activity, catalytic activity;P:protein amino acid glycosylation;C:endoplasmic reticulum;MFOPAB	O.I.	H.G.	S.X.
0.24	20.7	At4g04860	825823	DER2.2 (DERLIN-2.2)	F:unknown;P:proteolysis;C:cellular_component unknown;MOFP	O.I.	H.G.	S.X.
0.24	20.7	At5g08290	830725	YLS8	Encodes Dim1 homolog.	O.I.	H.G.	S.X.
0.23	19.3	At5g52240	835300	MSBP1 (membrane steroid binding protein 1)	Encodes a protein with similarity to progesterone-binding proteins in animals. Has been shown to bind steroids in vitro. Expressed in aerial portions of the plant excluding mature flowers and siliques. Antisense experiments suggest a role in inhibition of hypocotyl cell elongation. Expression is suppressed light grown seedlings transferred to the dark.	O.I.	H.G.	S.X.
0.23	19.3	At1g79975	-	-	-	O.I.	H.G.	S.X.
0.23	19.3	At5g11810	831054	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO	O.I.	H.G.	S.X.
0.22	17.5	At2g25280	817066	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BAMOFP	O.I.	H.G.	S.X.
0.21	15.8	At5g51510	835225	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO	O.I.	H.G.	S.X.
0.21	15.8	At2g30710	817622	RabGAP/TBC domain-containing protein	F:RAB GTPase activator activity;P:regulation of Rab GTPase activity;C:intracellular;MOFP	O.I.	H.G.	S.X.

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

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Gene ID	Os06g0608600
Gene name
Homology with Arabidopsis	Similar to At5g56020: - (HF=9e-3)
Module size	6 genes
NF	0.33
%ile	36.7

Co-expression analysis

Gene ID Os06g0608600 Gene name Homology with ArabidopsisSimilar to At5g56020: - (HF=9e-3) Module size 6 genes NF 0.33 %ile 36.7

Co-expressed genes

Click More genes

Specific experiments for the module

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO

Inter-species module comparison

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

Gene ID Os06g0608600

Gene name
Homology with Arabidopsis Similar to At5g56020: - (HF=9e-3)

Module size 6 genes

NF 0.33

%ile 36.7

SF Genes GO ID Process Name Link to AmiGO

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