CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Os04g0555500

Gene name
Homology with Arabidopsis Similar to At2g45540: WD-40 repeat family protein / beige-related (HF=4e-3)

Module size 20 genes

NF 0.55

%ile 73.8

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
0.72 89.8 0.96 Os04g0555500 AK108782.1 - The start codon is not identified. 4e-3 At2g45540 WD-40 repeat family protein / beige-related O.I. H.G. S.X.
0.79 93.6 0.97 Os03g0227000 AK068454.1 - Coatomer gamma subunit (Gamma-coat protein)(Gamma-COP) 1e-25 At4g34450 coatomer gamma-2 subunit, putative / gamma-2 coat protein, putative / gamma-2 COP, putative O.I. H.G. S.X.
0.68 87.5 0.97 Os03g0265700 AK068453.1 - SH3 domain containing protein 6e-50 At2g07360 SH3 domain-containing protein O.I. H.G. S.X.
0.62 81.5 0.97 Os05g0230600 AK070398.1 - WD40-like domain containing protein 1e-7 At5g11560 catalytic O.I. H.G. S.X.
0.60 79.7 0.96 Os07g0564700 AK059018.1 - Hypothetical protein 5e-18 At3g43300 ATMIN7 (ARABIDOPSIS THALIANA HOPM INTERACTOR 7) O.I. H.G. S.X.
0.60 79.7 0.97 Os03g0355600 AK068938.1 - Adapter-related protein complex 1 beta 1 subunit(Beta-adaptin 1) (Adaptor protein complex AP-1 beta-1subunit) (Golgi adaptor HA1/AP1 adaptin beta subunit)(Clathrin assembly protein complex 1 beta large chain).Splice isoform B 0 At4g23460 beta-adaptin, putative O.I. H.G. S.X.
0.60 79.7 0.98 Os02g0537900 AK070310.1 - Vacuolar-type H+-translocating inorganicpyrophosphatase (EC 3.6.1.1) 5e-87 At1g16780 vacuolar-type H+-translocating inorganic pyrophosphatase, putative O.I. H.G. S.X.
0.59 78.0 0.97 Os06g0143900 AK111584.1 - Coatomer protein complex, beta prime 6e-99 At1g52360 coatomer protein complex, subunit beta 2 (beta prime), putative O.I. H.G. S.X.
0.56 76.3 0.98 Os07g0657200 AK072927.1 - WD40-like domain containing protein 3e-8 At3g63460 WD-40 repeat family protein O.I. H.G. S.X.
0.56 76.3 0.98 Os05g0556100 AK065908.1 - SDL5A 1e-43 At3g61760 ADL1B (ARABIDOPSIS DYNAMIN-LIKE 1B) O.I. H.G. S.X.
0.51 68.7 0.96 Os05g0154700 AK064328.1 - Kinesin heavy chain (Fragment) 5e-18 At3g16630 KINESIN-13A O.I. H.G. S.X.
0.51 68.7 0.97 Os02g0832800 AK101526.1 - Alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase (EC 2.4.1.101) 5e-15 At4g38240 CGL1 (COMPLEX GLYCAN LESS 1) O.I. H.G. S.X.
0.50 68.0 0.97 Os02g0722300 AK064958.1 - Nonaspanin (TM9SF) family protein 6e-21 At4g12650 - O.I. H.G. S.X.
0.49 64.4 0.97 Os06g0568000 AK071892.1 - Nonaspanin (TM9SF) family protein 4e-107 At3g13772 endomembrane protein 70, putative O.I. H.G. S.X.
0.47 62.3 0.97 Os06g0618600 AK060212.1 - Conserved hypothetical protein 8e-8 At1g50120 - O.I. H.G. S.X.
0.47 62.3 0.98 Os03g0112400 AK063082.1 - AP2 adaptor, appendage domain containing protein 5e-2 At5g22770 alpha-ADR (alpha-adaptin) O.I. H.G. S.X.
0.45 58.8 0.97 Os01g0911200 AK101333.1 - Ribophorin II family protein 1e-6 At4g21150 HAP6 (HAPLESS 6) O.I. H.G. S.X.
0.40 51.1 0.97 Os12g0104800 AK058259.1 - - 2e-138 At3g08530 clathrin heavy chain, putative O.I. H.G. S.X.
0.33 38.8 0.97 Os03g0694900 AK121157.1 - Valyl-tRNA synthetase (EC 6.1.1.9) (Valine--tRNAligase) (ValRS) 2e-28 At1g14610 TWN2 (TWIN 2) O.I. H.G. S.X.
0.30 32.7 0.97 Os04g0129500 AK071986.1 - Sec23/Sec24 zinc finger domain containing protein 7e-31 At3g07100 protein transport protein Sec24, 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.
0.72	89.8	0.96	Os04g0555500	AK108782.1	-	The start codon is not identified.	4e-3	At2g45540	WD-40 repeat family protein / beige-related	O.I.	H.G.	S.X.
0.79	93.6	0.97	Os03g0227000	AK068454.1	-	Coatomer gamma subunit (Gamma-coat protein)(Gamma-COP)	1e-25	At4g34450	coatomer gamma-2 subunit, putative / gamma-2 coat protein, putative / gamma-2 COP, putative	O.I.	H.G.	S.X.
0.68	87.5	0.97	Os03g0265700	AK068453.1	-	SH3 domain containing protein	6e-50	At2g07360	SH3 domain-containing protein	O.I.	H.G.	S.X.
0.62	81.5	0.97	Os05g0230600	AK070398.1	-	WD40-like domain containing protein	1e-7	At5g11560	catalytic	O.I.	H.G.	S.X.
0.60	79.7	0.96	Os07g0564700	AK059018.1	-	Hypothetical protein	5e-18	At3g43300	ATMIN7 (ARABIDOPSIS THALIANA HOPM INTERACTOR 7)	O.I.	H.G.	S.X.
0.60	79.7	0.97	Os03g0355600	AK068938.1	-	Adapter-related protein complex 1 beta 1 subunit(Beta-adaptin 1) (Adaptor protein complex AP-1 beta-1subunit) (Golgi adaptor HA1/AP1 adaptin beta subunit)(Clathrin assembly protein complex 1 beta large chain).Splice isoform B	0	At4g23460	beta-adaptin, putative	O.I.	H.G.	S.X.
0.60	79.7	0.98	Os02g0537900	AK070310.1	-	Vacuolar-type H+-translocating inorganicpyrophosphatase (EC 3.6.1.1)	5e-87	At1g16780	vacuolar-type H+-translocating inorganic pyrophosphatase, putative	O.I.	H.G.	S.X.
0.59	78.0	0.97	Os06g0143900	AK111584.1	-	Coatomer protein complex, beta prime	6e-99	At1g52360	coatomer protein complex, subunit beta 2 (beta prime), putative	O.I.	H.G.	S.X.
0.56	76.3	0.98	Os07g0657200	AK072927.1	-	WD40-like domain containing protein	3e-8	At3g63460	WD-40 repeat family protein	O.I.	H.G.	S.X.
0.56	76.3	0.98	Os05g0556100	AK065908.1	-	SDL5A	1e-43	At3g61760	ADL1B (ARABIDOPSIS DYNAMIN-LIKE 1B)	O.I.	H.G.	S.X.
0.51	68.7	0.96	Os05g0154700	AK064328.1	-	Kinesin heavy chain (Fragment)	5e-18	At3g16630	KINESIN-13A	O.I.	H.G.	S.X.
0.51	68.7	0.97	Os02g0832800	AK101526.1	-	Alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase (EC 2.4.1.101)	5e-15	At4g38240	CGL1 (COMPLEX GLYCAN LESS 1)	O.I.	H.G.	S.X.
0.50	68.0	0.97	Os02g0722300	AK064958.1	-	Nonaspanin (TM9SF) family protein	6e-21	At4g12650	-	O.I.	H.G.	S.X.
0.49	64.4	0.97	Os06g0568000	AK071892.1	-	Nonaspanin (TM9SF) family protein	4e-107	At3g13772	endomembrane protein 70, putative	O.I.	H.G.	S.X.
0.47	62.3	0.97	Os06g0618600	AK060212.1	-	Conserved hypothetical protein	8e-8	At1g50120	-	O.I.	H.G.	S.X.
0.47	62.3	0.98	Os03g0112400	AK063082.1	-	AP2 adaptor, appendage domain containing protein	5e-2	At5g22770	alpha-ADR (alpha-adaptin)	O.I.	H.G.	S.X.
0.45	58.8	0.97	Os01g0911200	AK101333.1	-	Ribophorin II family protein	1e-6	At4g21150	HAP6 (HAPLESS 6)	O.I.	H.G.	S.X.
0.40	51.1	0.97	Os12g0104800	AK058259.1	-	-	2e-138	At3g08530	clathrin heavy chain, putative	O.I.	H.G.	S.X.
0.33	38.8	0.97	Os03g0694900	AK121157.1	-	Valyl-tRNA synthetase (EC 6.1.1.9) (Valine--tRNAligase) (ValRS)	2e-28	At1g14610	TWN2 (TWIN 2)	O.I.	H.G.	S.X.
0.30	32.7	0.97	Os04g0129500	AK071986.1	-	Sec23/Sec24 zinc finger domain containing protein	7e-31	At3g07100	protein transport protein Sec24, 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
14.9 98.6 GSM195228 Embryo GSE7951 Genome-wide gene expression profiling of rice stigma
13.8 98.5 GSM422676 Control GSE16865 Heterologous microarrays for the study of drought stress in Musa
6.4 97.2 GSM422672 Drought GSE16865 Heterologous microarrays for the study of drought stress in Musa
5.1 96.6 GSM377085 Genomic DNA - 45 day old leaf sample - mutant f2045 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
4.6 96.3 GSM377086 Genomic DNA - 45 day old leaf sample - IR64 wtcheck GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
4.5 96.3 GSM377078 Genomic DNA - 45 day old leaf sample - mutant g6603 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
4.2 96.0 GSM377081 Genomic DNA - 45 day old leaf sample - mutant g7534 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
4.0 95.9 GSM377077 Genomic DNA - 45 day old leaf sample - mutant g6489 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
4.0 95.9 GSM377080 Genomic DNA - 45 day old leaf sample - mutant g6728 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
3.9 95.8 GSM377076 Genomic DNA - 45 day old leaf sample - mutant g6485 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
14.9	98.6	GSM195228	Embryo	GSE7951	Genome-wide gene expression profiling of rice stigma
13.8	98.5	GSM422676	Control	GSE16865	Heterologous microarrays for the study of drought stress in Musa
6.4	97.2	GSM422672	Drought	GSE16865	Heterologous microarrays for the study of drought stress in Musa
5.1	96.6	GSM377085	Genomic DNA - 45 day old leaf sample - mutant f2045	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
4.6	96.3	GSM377086	Genomic DNA - 45 day old leaf sample - IR64 wtcheck	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
4.5	96.3	GSM377078	Genomic DNA - 45 day old leaf sample - mutant g6603	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
4.2	96.0	GSM377081	Genomic DNA - 45 day old leaf sample - mutant g7534	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
4.0	95.9	GSM377077	Genomic DNA - 45 day old leaf sample - mutant g6489	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
4.0	95.9	GSM377080	Genomic DNA - 45 day old leaf sample - mutant g6728	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
3.9	95.8	GSM377076	Genomic DNA - 45 day old leaf sample - mutant g6485	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
0.091 1 GO:0006438 The process of coupling valine to valyl-tRNA, catalyzed by valyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
0.074 1 GO:0006487 The posttranslational glycosylation of protein via the N4 atom of peptidyl-asparagine or the N1' atom peptidyl-tryptophan.
0.043 1 GO:0015992 The directed movement of protons (hydrogen ions) into, out of, within or between cells.

SF	Genes	GO ID	Process Name
0.091	1	GO:0006438	The process of coupling valine to valyl-tRNA, catalyzed by valyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
0.074	1	GO:0006487	The posttranslational glycosylation of protein via the N4 atom of peptidyl-asparagine or the N1' atom peptidyl-tryptophan.
0.043	1	GO:0015992	The directed movement of protons (hydrogen ions) into, out of, within or between cells.

Inter-species module comparison

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

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Gene ID	Os04g0555500
Gene name
Homology with Arabidopsis	Similar to At2g45540: WD-40 repeat family protein / beige-related (HF=4e-3)
Module size	20 genes
NF	0.55
%ile	73.8

Co-expression analysis

Gene ID Os04g0555500 Gene name Homology with ArabidopsisSimilar to At2g45540: WD-40 repeat family protein / beige-related (HF=4e-3) Module size 20 genes NF 0.55 %ile 73.8

Co-expressed genes

Click More genes

Specific experiments for the module

Biological processes inferred to relate to the module

Inter-species module comparison

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

Gene ID Os04g0555500

Gene name
Homology with Arabidopsis Similar to At2g45540: WD-40 repeat family protein / beige-related (HF=4e-3)

Module size 20 genes

NF 0.55

%ile 73.8

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