CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Os01g0138900

Gene name
Homology with Arabidopsis Similar to At1g34370: STOP1 (sensitive to proton rhizotoxicity 1) (HF=5e-19)

Module size 31 genes

NF 0.37

%ile 42.6

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
0.95 99.6 0.91 Os01g0138900 AK072417.1 - Mandelate racemase/muconate lactonizing enzymefamily protein 5e-19 At1g34370 STOP1 (sensitive to proton rhizotoxicity 1) O.I. H.G. S.X.
0.56 76.3 0.93 Os10g0363600 AK111523.1 - Cyclin-like F-box domain containing protein 4e-3 At1g22040 kelch repeat-containing F-box family protein O.I. H.G. S.X.
0.50 68.0 0.93 Os02g0830100 AK065077.1 - Oligopeptidase A 7e-24 At5g65620 peptidase M3 family protein / thimet oligopeptidase family protein O.I. H.G. S.X.
0.47 62.3 0.92 Os10g0502500 AK061824.1 - Cytochrome b5 domain containing protein 4e-14 At3g48890 ATMP2 O.I. H.G. S.X.
0.45 58.8 0.94 Os03g0425200 AK101293.1 - Inosine/uridine-preferring nucleoside hydrolasedomain containing protein 5e-14 At2g36310 URH1 (URIDINE-RIBOHYDROLASE 1) O.I. H.G. S.X.
0.44 58.1 0.94 Os08g0562700 AK066773.1 - Aminopeptidase N 4e-44 At1g63770 peptidase M1 family protein O.I. H.G. S.X.
0.43 55.4 0.92 Os07g0142000 AK099414.1 - Reticulon family protein 3e-9 At3g10260 reticulon family protein O.I. H.G. S.X.
0.42 53.9 0.93 Os06g0646600 CB659494 - KNOX family class 2 homeodomain protein 3e-14 At4g32040 KNAT5 (KNOTTED1-LIKE HOMEOBOX GENE 5) O.I. H.G. S.X.
0.42 53.9 0.92 Os01g0871200 AK065024.1 - Zn-finger, C2H2 type domain containing protein 3e-19 At1g34370 STOP1 (sensitive to proton rhizotoxicity 1) O.I. H.G. S.X.
0.41 52.4 0.92 Os02g0745700 AK103058.1 - Sterol desaturase family protein 2e-25 At1g69640 SBH1 (SPHINGOID BASE HYDROXYLASE 1) O.I. H.G. S.X.
0.41 52.4 0.95 Os02g0634500 AK065162.1 - ATP-dependent Clp protease, proteolytic subunitClpP (EC 3.4.21.92) 2e-3 At5g23140 NCLPP7 (NUCLEAR-ENCODED CLP PROTEASE P7) O.I. H.G. S.X.
0.41 52.4 0.91 Os01g0255000 AK109484.1 - Soluble epoxide hydrolase 1e-11 At3g05600 epoxide hydrolase, putative O.I. H.G. S.X.
0.40 51.1 0.93 Os04g0437600 AK061622.1 - MAP protein kinase 1e-3 At1g53570 MAP3KA O.I. H.G. S.X.
0.39 48.3 0.92 Os03g0284100 AK099526.1 - Expressed protein (Pseudo-response regulator 9)(Timing of CAB expression 1-like protein) 4e-19 At5g02810 PRR7 (PSEUDO-RESPONSE REGULATOR 7) O.I. H.G. S.X.
0.38 46.9 0.94 Os02g0773300 AK071811.1 - Pyridoxal phosphate-dependent deaminase familyprotein 3e-12 At1g48420 D-CDES (D-CYSTEINE DESULFHYDRASE) O.I. H.G. S.X.
0.38 46.9 0.94 Os01g0662600 AK119723.1 - ISCU1 1e-4 At3g01020 ISU2 (ISCU-LIKE 2) O.I. H.G. S.X.
0.37 45.0 0.94 Os12g0620400 AK072503.1 - Methyl-CpG binding domain containing protein 8e-1 At5g43175 basic helix-loop-helix (bHLH) family protein O.I. H.G. S.X.
0.33 38.8 0.93 Os02g0125100 AK101889.1 - Cis-homoaconitase family protein 1e-24 At4g13430 IIL1 (ISOPROPYL MALATE ISOMERASE LARGE SUBUNIT 1) O.I. H.G. S.X.
0.33 38.8 0.93 Os06g0728500 AK099928.1 - Hypothetical protein 2e-2 At1g70190 ribosomal protein L12 family protein O.I. H.G. S.X.
0.32 36.3 0.93 Os07g0646300 AK066044.1 - Conserved hypothetical protein 9e-1 At3g11630 2-cys peroxiredoxin, chloroplast (BAS1) O.I. H.G. S.X.
0.32 36.3 0.93 Os07g0185300 AK071133.1 - Protein of unknown function YGGT family protein 5e-1 At1g64750 ATDSS1(I) (ARABIDOPSIS THALIANA DELETION OF SUV3 SUPRESSOR 1(I)) O.I. H.G. S.X.
0.31 34.5 0.92 Os04g0528100 AK065957.1 - Conserved hypothetical protein 2e+0 At2g10970 invertase/pectin methylesterase inhibitor family protein O.I. H.G. S.X.
0.31 34.5 0.90 Os09g0442300 CB666183 - Oryzain gamma chain precursor (EC 3.4.22.-) 4e-30 At5g60360 AALP (Arabidopsis aleurain-like protease) O.I. H.G. S.X.
0.29 31.1 0.95 Os12g0276100 AK062912.1 - Hypothetical protein 2e+0 At3g17830 DNAJ heat shock family protein O.I. H.G. S.X.
0.27 27.5 0.95 Os01g0963400 AK062343.1 - The start codon is not identified. 9e-11 At1g43560 Aty2 (Arabidopsis thioredoxin y2) O.I. H.G. S.X.
0.25 24.1 0.95 Os02g0768600 AK059725.1 - - 2e-68 At5g09650 AtPPa6 (Arabidopsis thaliana pyrophosphorylase 6) O.I. H.G. S.X.
0.24 22.4 0.96 Os01g0104100 AK072797.1 - The start codon is not identified. 1e-2 At3g54360 protein binding / zinc ion binding O.I. H.G. S.X.
0.23 21.2 0.95 Os05g0101200 AY262026.1 - Peroxisomal membrane anchor protein (Pex14p)domain containing protein 1e+0 At5g61660 glycine-rich protein O.I. H.G. S.X.
0.22 19.4 0.92 Os03g0307100 AK102205.1 - TolB, C-terminal domain containing protein 7e-37 At2g47390 serine-type endopeptidase/ serine-type peptidase O.I. H.G. S.X.
0.21 17.9 0.93 Os03g0428800 AK060233.1 - TPR-like domain containing protein 2e-4 At3g26580 - O.I. H.G. S.X.
0.17 12.6 0.93 Os07g0204900 AK065213.1 - Zeta-carotene desaturase (Fragment) 1e-19 At3g04870 ZDS (ZETA-CAROTENE DESATURASE) 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.
0.95	99.6	0.91	Os01g0138900	AK072417.1	-	Mandelate racemase/muconate lactonizing enzymefamily protein	5e-19	At1g34370	STOP1 (sensitive to proton rhizotoxicity 1)	O.I.	H.G.	S.X.
0.56	76.3	0.93	Os10g0363600	AK111523.1	-	Cyclin-like F-box domain containing protein	4e-3	At1g22040	kelch repeat-containing F-box family protein	O.I.	H.G.	S.X.
0.50	68.0	0.93	Os02g0830100	AK065077.1	-	Oligopeptidase A	7e-24	At5g65620	peptidase M3 family protein / thimet oligopeptidase family protein	O.I.	H.G.	S.X.
0.47	62.3	0.92	Os10g0502500	AK061824.1	-	Cytochrome b5 domain containing protein	4e-14	At3g48890	ATMP2	O.I.	H.G.	S.X.
0.45	58.8	0.94	Os03g0425200	AK101293.1	-	Inosine/uridine-preferring nucleoside hydrolasedomain containing protein	5e-14	At2g36310	URH1 (URIDINE-RIBOHYDROLASE 1)	O.I.	H.G.	S.X.
0.44	58.1	0.94	Os08g0562700	AK066773.1	-	Aminopeptidase N	4e-44	At1g63770	peptidase M1 family protein	O.I.	H.G.	S.X.
0.43	55.4	0.92	Os07g0142000	AK099414.1	-	Reticulon family protein	3e-9	At3g10260	reticulon family protein	O.I.	H.G.	S.X.
0.42	53.9	0.93	Os06g0646600	CB659494	-	KNOX family class 2 homeodomain protein	3e-14	At4g32040	KNAT5 (KNOTTED1-LIKE HOMEOBOX GENE 5)	O.I.	H.G.	S.X.
0.42	53.9	0.92	Os01g0871200	AK065024.1	-	Zn-finger, C2H2 type domain containing protein	3e-19	At1g34370	STOP1 (sensitive to proton rhizotoxicity 1)	O.I.	H.G.	S.X.
0.41	52.4	0.92	Os02g0745700	AK103058.1	-	Sterol desaturase family protein	2e-25	At1g69640	SBH1 (SPHINGOID BASE HYDROXYLASE 1)	O.I.	H.G.	S.X.
0.41	52.4	0.95	Os02g0634500	AK065162.1	-	ATP-dependent Clp protease, proteolytic subunitClpP (EC 3.4.21.92)	2e-3	At5g23140	NCLPP7 (NUCLEAR-ENCODED CLP PROTEASE P7)	O.I.	H.G.	S.X.
0.41	52.4	0.91	Os01g0255000	AK109484.1	-	Soluble epoxide hydrolase	1e-11	At3g05600	epoxide hydrolase, putative	O.I.	H.G.	S.X.
0.40	51.1	0.93	Os04g0437600	AK061622.1	-	MAP protein kinase	1e-3	At1g53570	MAP3KA	O.I.	H.G.	S.X.
0.39	48.3	0.92	Os03g0284100	AK099526.1	-	Expressed protein (Pseudo-response regulator 9)(Timing of CAB expression 1-like protein)	4e-19	At5g02810	PRR7 (PSEUDO-RESPONSE REGULATOR 7)	O.I.	H.G.	S.X.
0.38	46.9	0.94	Os02g0773300	AK071811.1	-	Pyridoxal phosphate-dependent deaminase familyprotein	3e-12	At1g48420	D-CDES (D-CYSTEINE DESULFHYDRASE)	O.I.	H.G.	S.X.
0.38	46.9	0.94	Os01g0662600	AK119723.1	-	ISCU1	1e-4	At3g01020	ISU2 (ISCU-LIKE 2)	O.I.	H.G.	S.X.
0.37	45.0	0.94	Os12g0620400	AK072503.1	-	Methyl-CpG binding domain containing protein	8e-1	At5g43175	basic helix-loop-helix (bHLH) family protein	O.I.	H.G.	S.X.
0.33	38.8	0.93	Os02g0125100	AK101889.1	-	Cis-homoaconitase family protein	1e-24	At4g13430	IIL1 (ISOPROPYL MALATE ISOMERASE LARGE SUBUNIT 1)	O.I.	H.G.	S.X.
0.33	38.8	0.93	Os06g0728500	AK099928.1	-	Hypothetical protein	2e-2	At1g70190	ribosomal protein L12 family protein	O.I.	H.G.	S.X.
0.32	36.3	0.93	Os07g0646300	AK066044.1	-	Conserved hypothetical protein	9e-1	At3g11630	2-cys peroxiredoxin, chloroplast (BAS1)	O.I.	H.G.	S.X.
0.32	36.3	0.93	Os07g0185300	AK071133.1	-	Protein of unknown function YGGT family protein	5e-1	At1g64750	ATDSS1(I) (ARABIDOPSIS THALIANA DELETION OF SUV3 SUPRESSOR 1(I))	O.I.	H.G.	S.X.
0.31	34.5	0.92	Os04g0528100	AK065957.1	-	Conserved hypothetical protein	2e+0	At2g10970	invertase/pectin methylesterase inhibitor family protein	O.I.	H.G.	S.X.
0.31	34.5	0.90	Os09g0442300	CB666183	-	Oryzain gamma chain precursor (EC 3.4.22.-)	4e-30	At5g60360	AALP (Arabidopsis aleurain-like protease)	O.I.	H.G.	S.X.
0.29	31.1	0.95	Os12g0276100	AK062912.1	-	Hypothetical protein	2e+0	At3g17830	DNAJ heat shock family protein	O.I.	H.G.	S.X.
0.27	27.5	0.95	Os01g0963400	AK062343.1	-	The start codon is not identified.	9e-11	At1g43560	Aty2 (Arabidopsis thioredoxin y2)	O.I.	H.G.	S.X.
0.25	24.1	0.95	Os02g0768600	AK059725.1	-	-	2e-68	At5g09650	AtPPa6 (Arabidopsis thaliana pyrophosphorylase 6)	O.I.	H.G.	S.X.
0.24	22.4	0.96	Os01g0104100	AK072797.1	-	The start codon is not identified.	1e-2	At3g54360	protein binding / zinc ion binding	O.I.	H.G.	S.X.
0.23	21.2	0.95	Os05g0101200	AY262026.1	-	Peroxisomal membrane anchor protein (Pex14p)domain containing protein	1e+0	At5g61660	glycine-rich protein	O.I.	H.G.	S.X.
0.22	19.4	0.92	Os03g0307100	AK102205.1	-	TolB, C-terminal domain containing protein	7e-37	At2g47390	serine-type endopeptidase/ serine-type peptidase	O.I.	H.G.	S.X.
0.21	17.9	0.93	Os03g0428800	AK060233.1	-	TPR-like domain containing protein	2e-4	At3g26580	-	O.I.	H.G.	S.X.
0.17	12.6	0.93	Os07g0204900	AK065213.1	-	Zeta-carotene desaturase (Fragment)	1e-19	At3g04870	ZDS (ZETA-CAROTENE DESATURASE)	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
12.6 98.4 GSM422672 Drought GSE16865 Heterologous microarrays for the study of drought stress in Musa
9.5 97.9 GSM377075 Genomic DNA - 45 day old leaf sample - mutant g650 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
9.0 97.8 GSM377071 Genomic DNA - 45 day old leaf sample - mutant d256 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.9 97.8 GSM377078 Genomic DNA - 45 day old leaf sample - mutant g6603 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.9 97.8 GSM377070 Genomic DNA - 45 day old leaf sample - mutant d1 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.7 97.8 GSM377076 Genomic DNA - 45 day old leaf sample - mutant g6485 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.7 97.8 GSM377073 Genomic DNA - 45 day old leaf sample - mutant d2943 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.3 97.7 GSM377084 Genomic DNA - 45 day old leaf sample - mutant f1856 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.9 97.6 GSM377077 Genomic DNA - 45 day old leaf sample - mutant g6489 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.9 97.6 GSM377081 Genomic DNA - 45 day old leaf sample - mutant g7534 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
12.6	98.4	GSM422672	Drought	GSE16865	Heterologous microarrays for the study of drought stress in Musa
9.5	97.9	GSM377075	Genomic DNA - 45 day old leaf sample - mutant g650	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
9.0	97.8	GSM377071	Genomic DNA - 45 day old leaf sample - mutant d256	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.9	97.8	GSM377078	Genomic DNA - 45 day old leaf sample - mutant g6603	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.9	97.8	GSM377070	Genomic DNA - 45 day old leaf sample - mutant d1	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.7	97.8	GSM377076	Genomic DNA - 45 day old leaf sample - mutant g6485	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.7	97.8	GSM377073	Genomic DNA - 45 day old leaf sample - mutant d2943	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.3	97.7	GSM377084	Genomic DNA - 45 day old leaf sample - mutant f1856	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.9	97.6	GSM377077	Genomic DNA - 45 day old leaf sample - mutant g6489	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.9	97.6	GSM377081	Genomic DNA - 45 day old leaf sample - mutant g7534	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
0.061 1 GO:0009409 A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
0.061 1 GO:0009414 A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a water deprivation stimulus, prolonged deprivation of water.
0.061 1 GO:0009651 A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.

SF	Genes	GO ID	Process Name
0.061	1	GO:0009409	A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
0.061	1	GO:0009414	A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a water deprivation stimulus, prolonged deprivation of water.
0.061	1	GO:0009651	A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.

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

Back to the CoP portal site

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Gene ID	Os01g0138900
Gene name
Homology with Arabidopsis	Similar to At1g34370: STOP1 (sensitive to proton rhizotoxicity 1) (HF=5e-19)
Module size	31 genes
NF	0.37
%ile	42.6

Co-expression analysis

Gene ID Os01g0138900 Gene name Homology with ArabidopsisSimilar to At1g34370: STOP1 (sensitive to proton rhizotoxicity 1) (HF=5e-19) Module size 31 genes NF 0.37 %ile 42.6

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 Os01g0138900

Gene name
Homology with Arabidopsis Similar to At1g34370: STOP1 (sensitive to proton rhizotoxicity 1) (HF=5e-19)

Module size 31 genes

NF 0.37

%ile 42.6

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