CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Os09g0541900

Gene name
Homology with Arabidopsis Similar to At1g20200: EMB2719 (EMBRYO DEFECTIVE 2719) (HF=1e-24)

Module size 6 genes

NF 0.59

%ile 80.3

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
0.71 89.6 0.97 Os09g0541900 AB031299.1 - Proteasome component region PCI domain containingprotein 1e-24 At1g20200 EMB2719 (EMBRYO DEFECTIVE 2719) O.I. H.G. S.X.
0.73 91.1 0.98 Os05g0301500 AK067027.1 - Ribophorin I (Fragment) 7e-5 At1g76400 ribophorin I family protein O.I. H.G. S.X.
0.67 87.2 0.98 Os07g0209000 AK058399.1 - Dolichyl-di-phosphooligosaccharide-proteinglycotransferase (Oligosaccharyltransferase)-like 1e-24 At5g66680 DGL1 O.I. H.G. S.X.
0.67 87.2 0.98 Os05g0147400 AK062146.1 - T-complex protein 1, zeta subunit (TCP-1-zeta)(CCT-zeta) (CCT-zeta- 1) 6e-67 At5g16070 chaperonin, putative O.I. H.G. S.X.
0.44 58.1 0.98 Os06g0538000 AK069949.1 - Chaperonin Cpn60/TCP-1 family protein 5e-83 At5g26360 chaperonin, putative O.I. H.G. S.X.
0.32 36.3 0.97 Os01g0911200 AK101333.1 - Ribophorin II family protein 1e-6 At4g21150 HAP6 (HAPLESS 6) 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.
0.71	89.6	0.97	Os09g0541900	AB031299.1	-	Proteasome component region PCI domain containingprotein	1e-24	At1g20200	EMB2719 (EMBRYO DEFECTIVE 2719)	O.I.	H.G.	S.X.
0.73	91.1	0.98	Os05g0301500	AK067027.1	-	Ribophorin I (Fragment)	7e-5	At1g76400	ribophorin I family protein	O.I.	H.G.	S.X.
0.67	87.2	0.98	Os07g0209000	AK058399.1	-	Dolichyl-di-phosphooligosaccharide-proteinglycotransferase (Oligosaccharyltransferase)-like	1e-24	At5g66680	DGL1	O.I.	H.G.	S.X.
0.67	87.2	0.98	Os05g0147400	AK062146.1	-	T-complex protein 1, zeta subunit (TCP-1-zeta)(CCT-zeta) (CCT-zeta- 1)	6e-67	At5g16070	chaperonin, putative	O.I.	H.G.	S.X.
0.44	58.1	0.98	Os06g0538000	AK069949.1	-	Chaperonin Cpn60/TCP-1 family protein	5e-83	At5g26360	chaperonin, putative	O.I.	H.G.	S.X.
0.32	36.3	0.97	Os01g0911200	AK101333.1	-	Ribophorin II family protein	1e-6	At4g21150	HAP6 (HAPLESS 6)	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.
0.57	77.0	0.97	Os06g0687700	AK109357.2	-	T-complex protein 1, eta subunit (TCP-1-eta)(CCT-eta) (HIV-1 Nef interacting protein)	2e-44	At3g11830	chaperonin, putative	O.I.	H.G.	S.X.
0.55	73.7	0.96	Os10g0377400	AK111872.1	-	Ras-related protein Rab11D	7e-10	At4g39990	RABA4B (RAB GTPASE HOMOLOG A4B)	O.I.	H.G.	S.X.
0.55	73.7	0.97	Os12g0611700	AK062659.1	-	Conserved hypothetical protein	1e+0	At2g04220	unknown protein	O.I.	H.G.	S.X.
0.55	73.7	0.98	Os02g0332200	AK067672.1	-	T-complex protein 1 delta subunit	2e-29	At3g18190	chaperonin, putative	O.I.	H.G.	S.X.
0.50	68.0	0.96	Os02g0465400	AK100199.1	-	7-dehydrocholesterol reductase (EC 1.3.1.21)(7-DHC reductase) (Sterol delta-7-reductase) (Dwarf5protein)	9e-32	At1g50430	DWF5 (DWARF 5)	O.I.	H.G.	S.X.
0.50	68.0	0.97	Os01g0300600	AK058273.1	-	Intradiol ring-cleavage dioxygenase domaincontaining protein	4e-11	At3g62360	carbohydrate binding	O.I.	H.G.	S.X.
0.48	63.7	0.97	Os03g0113800	AK065925.1	-	ARM repeat fold domain containing protein	6e-11	At5g41950	binding	O.I.	H.G.	S.X.
0.46	60.9	0.94	Os03g0136200	AF042333.1	-	-	2e-11	At1g20330	SMT2 (STEROL METHYLTRANSFERASE 2)	O.I.	H.G.	S.X.
0.46	60.9	0.97	Os04g0372800	AK101615.1	-	Nuclear transport factor 2 domain containingprotein	2e-1	At3g61260	DNA-binding family protein / remorin family protein	O.I.	H.G.	S.X.
0.46	60.9	0.97	Os03g0619400	CB653322	-	Chaperonin Cpn60 family protein	1e-57	At5g20890	chaperonin, putative	O.I.	H.G.	S.X.
0.44	58.1	0.98	Os04g0551800	AK121568.1	-	T-complex protein 1, alpha subunit (TCP-1-alpha)(CCT-alpha)	4e-40	At3g20050	ATTCP-1	O.I.	H.G.	S.X.
0.43	55.4	0.96	Os03g0713100	BE040116	-	Dynamin family protein	2e-6	At1g14830	ADL1C (ARABIDOPSIS DYNAMIN-LIKE PROTEIN 1C)	O.I.	H.G.	S.X.
0.43	55.4	0.97	Os03g0336300	AK068503.1	-	Peptidase M16, C-terminal domain containingprotein	1e-13	At1g06900	catalytic/ metal ion binding / metalloendopeptidase/ zinc ion binding	O.I.	H.G.	S.X.
0.43	55.4	0.98	Os06g0562600	AK067114.1	-	T-complex protein 1, epsilon subunit(TCP-1-epsilon) (CCT-epsilon) (TCP-K36)	2e-88	At1g24510	T-complex protein 1 epsilon subunit, putative / TCP-1-epsilon, putative / chaperonin, putative	O.I.	H.G.	S.X.
0.39	48.3	0.96	Os03g0804800	AK100651.1	-	-	2e-39	At3g03960	chaperonin, putative	O.I.	H.G.	S.X.
0.35	41.7	0.97	Os12g0178100	AK061107.1	-	Thylakoid-bound ascorbate peroxidase (EC1.11.1.11) (Fragment)	4e-27	At4g08390	SAPX (STROMAL ASCORBATE PEROXIDASE)	O.I.	H.G.	S.X.
0.33	38.8	0.96	Os02g0497700	AK066155.1	-	Ras-GTPase-activating protein SH3-domain bindingprotein-like	7e-2	At5g60980	nuclear transport factor 2 (NTF2) family protein / RNA recognition motif (RRM)-containing protein	O.I.	H.G.	S.X.
0.33	38.8	0.96	Os08g0386300	AK070379.1	-	Cytochrome b5 domain containing protein	2e+0	At2g40500	protein kinase family protein	O.I.	H.G.	S.X.
0.33	38.8	0.97	Os07g0201100	AK100095.1	-	Coatomer gamma subunit (Gamma-coat protein)(Gamma-COP)	2e-37	At4g34450	coatomer gamma-2 subunit, putative / gamma-2 coat protein, putative / gamma-2 COP, putative	O.I.	H.G.	S.X.
0.33	38.8	0.97	Os05g0104800	AK070215.1	-	Eukaryotic translation initiation factor 3 subunit5 (eIF-3 epsilon) (eIF3 p32 subunit) (eIF3f)	6e-4	At2g39990	EIF2	O.I.	H.G.	S.X.
0.33	38.8	0.97	Os08g0295300	AK070378.1	-	Threonyl-tRNA synthetase, mitochondrial precursor(EC 6.1.1.3) (Threonine--tRNA ligase) (ThrRS)	6e-12	At5g26830	threonyl-tRNA synthetase / threonine--tRNA ligase (THRRS)	O.I.	H.G.	S.X.
0.32	36.3	0.96	Os10g0483000	AK121674.1	-	Transcription factor homolog BTF3-like protein	6e-31	At1g73230	nascent polypeptide-associated complex (NAC) domain-containing protein	O.I.	H.G.	S.X.
0.32	36.3	0.98	Os08g0207000	AK058705.1	-	40S ribosomal protein S11 (S18) (YS12) (RP41)	4e-60	At3g48930	EMB1080 (embryo defective 1080)	O.I.	H.G.	S.X.
0.29	31.1	0.96	Os11g0568500	AK059656.1	-	Prefoldin beta-like family protein	7e-3	At3g22480	prefoldin-related KE2 family protein	O.I.	H.G.	S.X.
0.29	31.1	0.96	Os05g0295300	AK059261.1	-	Acetyl-coenzyme A carboxylase (EC 6.4.1.2)	2e+0	At3g24280	SMAP2 (small acidic protein 2)	O.I.	H.G.	S.X.
0.27	27.5	0.94	Os01g0883900	AK119636.1	-	Putative methyltransferase DUF248 family protein	2e-12	At5g64030	dehydration-responsive protein-related	O.I.	H.G.	S.X.
0.27	27.5	0.96	Os06g0156900	AK110688.1	-	Glycosyl transferase, family 31 protein	1e-18	At1g53290	galactosyltransferase family protein	O.I.	H.G.	S.X.
0.27	27.5	0.96	Os05g0482700	AK065541.1	-	2,3-bisphosphoglycerate-independentphosphoglycerate mutase (EC 5.4.2.1)(Phosphoglyceromutase) (BPG-independent PGAM) (PGAM-I)	3e-38	At1g09780	2,3-biphosphoglycerate-independent phosphoglycerate mutase, putative / phosphoglyceromutase, putative	O.I.	H.G.	S.X.
0.27	27.5	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.
0.27	27.5	0.97	Os03g0282900	AK102161.1	-	Conserved hypothetical protein	9e-3	At5g03380	heavy-metal-associated domain-containing protein	O.I.	H.G.	S.X.
0.26	25.6	0.95	Os02g0738900	AK099699.1	-	Dynamin-like protein 6	4e-26	At1g59610	ADL3 (ARABIDOPSIS DYNAMIN-LIKE 3)	O.I.	H.G.	S.X.
0.25	24.1	0.94	Os01g0180800	AK059244.1	-	Heat shock protein Hsp70 family protein	1e-25	At1g79930	HSP91	O.I.	H.G.	S.X.
0.25	24.1	0.96	Os03g0350300	AK073164.1	-	SAR DNA-binding protein-like protein	3e-16	At3g05060	SAR DNA-binding protein, putative	O.I.	H.G.	S.X.
0.25	24.1	0.97	Os03g0853800	AK102872.1	-	Conserved hypothetical protein	2e+0	At3g15720	glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein	O.I.	H.G.	S.X.

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
15.9 98.7 GSM422676 Control GSE16865 Heterologous microarrays for the study of drought stress in Musa
8.2 97.7 GSM377073 Genomic DNA - 45 day old leaf sample - mutant d2943 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.7 97.6 GSM377085 Genomic DNA - 45 day old leaf sample - mutant f2045 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.5 97.5 GSM377075 Genomic DNA - 45 day old leaf sample - mutant g650 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.4 97.5 GSM377070 Genomic DNA - 45 day old leaf sample - mutant d1 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
6.5 97.2 GSM377084 Genomic DNA - 45 day old leaf sample - mutant f1856 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
6.3 97.2 GSM377074 Genomic DNA - 45 day old leaf sample - mutant g282 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
6.3 97.2 GSM377081 Genomic DNA - 45 day old leaf sample - mutant g7534 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
6.3 97.2 GSM377076 Genomic DNA - 45 day old leaf sample - mutant g6485 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
6.2 97.1 GSM377080 Genomic DNA - 45 day old leaf sample - mutant g6728 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
15.9	98.7	GSM422676	Control	GSE16865	Heterologous microarrays for the study of drought stress in Musa
8.2	97.7	GSM377073	Genomic DNA - 45 day old leaf sample - mutant d2943	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.7	97.6	GSM377085	Genomic DNA - 45 day old leaf sample - mutant f2045	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.5	97.5	GSM377075	Genomic DNA - 45 day old leaf sample - mutant g650	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.4	97.5	GSM377070	Genomic DNA - 45 day old leaf sample - mutant d1	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
6.5	97.2	GSM377084	Genomic DNA - 45 day old leaf sample - mutant f1856	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
6.3	97.2	GSM377074	Genomic DNA - 45 day old leaf sample - mutant g282	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
6.3	97.2	GSM377081	Genomic DNA - 45 day old leaf sample - mutant g7534	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
6.3	97.2	GSM377076	Genomic DNA - 45 day old leaf sample - mutant g6485	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
6.2	97.1	GSM377080	Genomic DNA - 45 day old leaf sample - mutant g6728	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
0.286 1 GO:0018279 The posttranslational glycosylation of protein via the N4 atom of peptidyl-asparagine forming N4-glycosyl-L-asparagine; the most common form is N-acetylglucosaminyl asparagine; N-acetylgalactosaminyl asparagine also occurs; this modification typically occurs in extracellular peptides with an N-X-(ST) motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position; secondary structure features are important, and proline in the second or fourth positions inhibits modification.
0.024 1 GO:0006457 The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.286	1	GO:0018279	The posttranslational glycosylation of protein via the N4 atom of peptidyl-asparagine forming N4-glycosyl-L-asparagine; the most common form is N-acetylglucosaminyl asparagine; N-acetylgalactosaminyl asparagine also occurs; this modification typically occurs in extracellular peptides with an N-X-(ST) motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position; secondary structure features are important, and proline in the second or fourth positions inhibits modification.
0.024	1	GO:0006457	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.

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	Os09g0541900
Gene name
Homology with Arabidopsis	Similar to At1g20200: EMB2719 (EMBRYO DEFECTIVE 2719) (HF=1e-24)
Module size	6 genes
NF	0.59
%ile	80.3

Co-expression analysis

Gene ID Os09g0541900 Gene name Homology with ArabidopsisSimilar to At1g20200: EMB2719 (EMBRYO DEFECTIVE 2719) (HF=1e-24) Module size 6 genes NF 0.59 %ile 80.3

Co-expressed 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 Os09g0541900

Gene name
Homology with Arabidopsis Similar to At1g20200: EMB2719 (EMBRYO DEFECTIVE 2719) (HF=1e-24)

Module size 6 genes

NF 0.59

%ile 80.3

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