CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Os03g0189400

Gene name
Homology with Arabidopsis Similar to At5g42250: alcohol dehydrogenase, putative (HF=4e-2)

Module size 25 genes

NF 0.25

%ile 24.7

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
0.92 99.1 0.85 Os03g0189400 AK067720.1 - Alcohol dehydrogenase ADH 4e-2 At5g42250 alcohol dehydrogenase, putative O.I. H.G. S.X.
0.36 44.0 0.89 Os05g0163700 AK071561.1 - Acyl-CoA dehydrogenase, N-terminal domaincontaining protein 2e-13 At3g51840 ACX4 (ACYL-COA OXIDASE 4) O.I. H.G. S.X.
0.35 41.7 0.92 Os03g0843100 AK111499.1 - Ras-related protein Rab-11B 4e-11 At1g09630 ATRAB11C (ARABIDOPSIS RAB GTPASE 11C) O.I. H.G. S.X.
0.33 38.8 0.89 Os03g0582200 AK099288.1 - SCAMP family protein 1e-9 At2g20840 secretory carrier membrane protein (SCAMP) family protein O.I. H.G. S.X.
0.33 38.8 0.91 Os06g0354500 AK066934.1 - Acyl-CoA oxidase ACX3 2e-15 At1g06310 ACX6 (ACYL-COA OXIDASE 6) O.I. H.G. S.X.
0.32 36.3 0.92 Os12g0596800 AK065760.1 - Ubiquitin interacting motif domain containingprotein 1e-12 At4g36860 zinc ion binding O.I. H.G. S.X.
0.31 34.5 0.92 Os12g0623500 CB629004 - Cationic amino acid transporter-like protein 3e-17 At1g58030 CAT2 (CATIONIC AMINO ACID TRANSPORTER 2) O.I. H.G. S.X.
0.29 31.1 0.91 Os11g0186200 BI806335 - Aldehyde dehydrogenase (EC 1.2.1.3) 1e+0 At1g01520 myb family transcription factor O.I. H.G. S.X.
0.29 31.1 0.92 Os05g0475300 AK065069.1 - VHS domain containing protein 1e-6 At5g01760 VHS domain-containing protein / GAT domain-containing protein O.I. H.G. S.X.
0.28 31.1 0.91 Os01g0796400 AK060287.1 - - 2e-11 At3g15290 3-hydroxybutyryl-CoA dehydrogenase, putative O.I. H.G. S.X.
0.27 27.5 0.94 Os03g0318600 AB051294.1 - Transcription factor HBP-1b(c38) 4e-15 At5g06950 AHBP-1B O.I. H.G. S.X.
0.26 25.6 0.90 Os02g0690200 AK070868.1 - Conserved hypothetical protein 4e-1 At4g31150 endonuclease V family protein O.I. H.G. S.X.
0.23 21.2 0.93 Os07g0687700 AB051295.1 - - 8e-8 At5g06950 AHBP-1B O.I. H.G. S.X.
0.22 19.4 0.90 Os04g0390500 AK100148.1 - Iron-phytosiderophore transporter protein yellowstripe 1 1e-21 At3g27020 YSL6 (YELLOW STRIPE LIKE 6) O.I. H.G. S.X.
0.20 16.5 0.91 Os03g0788800 AK071670.1 - Zn-finger, RING domain containing protein 4e-15 At5g22000 RHF2A (RING-H2 GROUP F2A) O.I. H.G. S.X.
0.19 15.1 0.90 Os06g0716000 AK067426.1 - Protein of unknown function DUF668 family protein 4e-3 At1g34320 unknown protein O.I. H.G. S.X.
0.17 12.6 0.93 Os04g0550700 AK106156.1 - Conserved hypothetical protein 3e+0 At3g05560 60S ribosomal protein L22-2 (RPL22B) O.I. H.G. S.X.
0.16 11.3 0.92 Os04g0451900 9632.m03567 - Protein phosphatase 2C-like domain containingprotein 6e-11 At1g22280 protein phosphatase 2C, putative / PP2C, putative O.I. H.G. S.X.
0.16 11.3 0.91 Os03g0170400 AU057487 - Protein kinase APK1B (EC 2.7.1.-) 5e-9 At2g28930 APK1B O.I. H.G. S.X.
0.15 10.3 0.92 Os11g0588300 AF402793.1 - Glutathione transferase AtGST 10 (EC 2.5.1.18) 2e-3 At5g41210 ATGSTT1 (GLUTATHIONE S-TRANSFERASE THETA 1) O.I. H.G. S.X.
0.15 10.3 0.91 Os03g0335300 AK111847.1 - PV72 6e-18 At3g52850 VSR1 (VACUOLAR SORTING RECEPTOR HOMOLOG 1) O.I. H.G. S.X.
0.14 9.3 0.94 Os02g0750600 AK066145.1 - Ubiquitin domain containing protein 6e-7 At1g22050 MUB6 (MEMBRANE-ANCHORED UBIQUITIN-FOLD PROTEIN 6 PRECURSOR) O.I. H.G. S.X.
0.13 8.2 0.95 Os02g0601100 AK120475.1 - Nucleotide-binding protein 3e-46 At5g50960 NBP35 (NUCLEOTIDE BINDING PROTEIN 35) O.I. H.G. S.X.
0.13 8.2 0.93 Os08g0518100 AK066731.1 - RabGAP/TBC domain containing protein 2e-3 At2g19240 RabGAP/TBC domain-containing protein O.I. H.G. S.X.
0.12 7.2 0.93 Os02g0763200 AK072854.1 - - 3e-1 At5g14690 unknown 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.
0.92	99.1	0.85	Os03g0189400	AK067720.1	-	Alcohol dehydrogenase ADH	4e-2	At5g42250	alcohol dehydrogenase, putative	O.I.	H.G.	S.X.
0.36	44.0	0.89	Os05g0163700	AK071561.1	-	Acyl-CoA dehydrogenase, N-terminal domaincontaining protein	2e-13	At3g51840	ACX4 (ACYL-COA OXIDASE 4)	O.I.	H.G.	S.X.
0.35	41.7	0.92	Os03g0843100	AK111499.1	-	Ras-related protein Rab-11B	4e-11	At1g09630	ATRAB11C (ARABIDOPSIS RAB GTPASE 11C)	O.I.	H.G.	S.X.
0.33	38.8	0.89	Os03g0582200	AK099288.1	-	SCAMP family protein	1e-9	At2g20840	secretory carrier membrane protein (SCAMP) family protein	O.I.	H.G.	S.X.
0.33	38.8	0.91	Os06g0354500	AK066934.1	-	Acyl-CoA oxidase ACX3	2e-15	At1g06310	ACX6 (ACYL-COA OXIDASE 6)	O.I.	H.G.	S.X.
0.32	36.3	0.92	Os12g0596800	AK065760.1	-	Ubiquitin interacting motif domain containingprotein	1e-12	At4g36860	zinc ion binding	O.I.	H.G.	S.X.
0.31	34.5	0.92	Os12g0623500	CB629004	-	Cationic amino acid transporter-like protein	3e-17	At1g58030	CAT2 (CATIONIC AMINO ACID TRANSPORTER 2)	O.I.	H.G.	S.X.
0.29	31.1	0.91	Os11g0186200	BI806335	-	Aldehyde dehydrogenase (EC 1.2.1.3)	1e+0	At1g01520	myb family transcription factor	O.I.	H.G.	S.X.
0.29	31.1	0.92	Os05g0475300	AK065069.1	-	VHS domain containing protein	1e-6	At5g01760	VHS domain-containing protein / GAT domain-containing protein	O.I.	H.G.	S.X.
0.28	31.1	0.91	Os01g0796400	AK060287.1	-	-	2e-11	At3g15290	3-hydroxybutyryl-CoA dehydrogenase, putative	O.I.	H.G.	S.X.
0.27	27.5	0.94	Os03g0318600	AB051294.1	-	Transcription factor HBP-1b(c38)	4e-15	At5g06950	AHBP-1B	O.I.	H.G.	S.X.
0.26	25.6	0.90	Os02g0690200	AK070868.1	-	Conserved hypothetical protein	4e-1	At4g31150	endonuclease V family protein	O.I.	H.G.	S.X.
0.23	21.2	0.93	Os07g0687700	AB051295.1	-	-	8e-8	At5g06950	AHBP-1B	O.I.	H.G.	S.X.
0.22	19.4	0.90	Os04g0390500	AK100148.1	-	Iron-phytosiderophore transporter protein yellowstripe 1	1e-21	At3g27020	YSL6 (YELLOW STRIPE LIKE 6)	O.I.	H.G.	S.X.
0.20	16.5	0.91	Os03g0788800	AK071670.1	-	Zn-finger, RING domain containing protein	4e-15	At5g22000	RHF2A (RING-H2 GROUP F2A)	O.I.	H.G.	S.X.
0.19	15.1	0.90	Os06g0716000	AK067426.1	-	Protein of unknown function DUF668 family protein	4e-3	At1g34320	unknown protein	O.I.	H.G.	S.X.
0.17	12.6	0.93	Os04g0550700	AK106156.1	-	Conserved hypothetical protein	3e+0	At3g05560	60S ribosomal protein L22-2 (RPL22B)	O.I.	H.G.	S.X.
0.16	11.3	0.92	Os04g0451900	9632.m03567	-	Protein phosphatase 2C-like domain containingprotein	6e-11	At1g22280	protein phosphatase 2C, putative / PP2C, putative	O.I.	H.G.	S.X.
0.16	11.3	0.91	Os03g0170400	AU057487	-	Protein kinase APK1B (EC 2.7.1.-)	5e-9	At2g28930	APK1B	O.I.	H.G.	S.X.
0.15	10.3	0.92	Os11g0588300	AF402793.1	-	Glutathione transferase AtGST 10 (EC 2.5.1.18)	2e-3	At5g41210	ATGSTT1 (GLUTATHIONE S-TRANSFERASE THETA 1)	O.I.	H.G.	S.X.
0.15	10.3	0.91	Os03g0335300	AK111847.1	-	PV72	6e-18	At3g52850	VSR1 (VACUOLAR SORTING RECEPTOR HOMOLOG 1)	O.I.	H.G.	S.X.
0.14	9.3	0.94	Os02g0750600	AK066145.1	-	Ubiquitin domain containing protein	6e-7	At1g22050	MUB6 (MEMBRANE-ANCHORED UBIQUITIN-FOLD PROTEIN 6 PRECURSOR)	O.I.	H.G.	S.X.
0.13	8.2	0.95	Os02g0601100	AK120475.1	-	Nucleotide-binding protein	3e-46	At5g50960	NBP35 (NUCLEOTIDE BINDING PROTEIN 35)	O.I.	H.G.	S.X.
0.13	8.2	0.93	Os08g0518100	AK066731.1	-	RabGAP/TBC domain containing protein	2e-3	At2g19240	RabGAP/TBC domain-containing protein	O.I.	H.G.	S.X.
0.12	7.2	0.93	Os02g0763200	AK072854.1	-	-	3e-1	At5g14690	unknown 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
19.3 99.0 GSM422672 Drought GSE16865 Heterologous microarrays for the study of drought stress in Musa
15.2 98.7 GSM422674 Musa_DNA_RICE GSE16865 Heterologous microarrays for the study of drought stress in Musa
13.8 98.5 GSM377070 Genomic DNA - 45 day old leaf sample - mutant d1 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
12.9 98.4 GSM377078 Genomic DNA - 45 day old leaf sample - mutant g6603 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
12.9 98.4 GSM377076 Genomic DNA - 45 day old leaf sample - mutant g6485 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
12.8 98.4 GSM377080 Genomic DNA - 45 day old leaf sample - mutant g6728 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
12.5 98.3 GSM377073 Genomic DNA - 45 day old leaf sample - mutant d2943 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
12.0 98.3 GSM377074 Genomic DNA - 45 day old leaf sample - mutant g282 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
11.9 98.3 GSM377071 Genomic DNA - 45 day old leaf sample - mutant d256 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
11.8 98.3 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
19.3	99.0	GSM422672	Drought	GSE16865	Heterologous microarrays for the study of drought stress in Musa
15.2	98.7	GSM422674	Musa_DNA_RICE	GSE16865	Heterologous microarrays for the study of drought stress in Musa
13.8	98.5	GSM377070	Genomic DNA - 45 day old leaf sample - mutant d1	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
12.9	98.4	GSM377078	Genomic DNA - 45 day old leaf sample - mutant g6603	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
12.9	98.4	GSM377076	Genomic DNA - 45 day old leaf sample - mutant g6485	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
12.8	98.4	GSM377080	Genomic DNA - 45 day old leaf sample - mutant g6728	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
12.5	98.3	GSM377073	Genomic DNA - 45 day old leaf sample - mutant d2943	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
12.0	98.3	GSM377074	Genomic DNA - 45 day old leaf sample - mutant g282	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
11.9	98.3	GSM377071	Genomic DNA - 45 day old leaf sample - mutant d256	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
11.8	98.3	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
0.074 1 GO:0006635 A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
0.063 1 GO:0006891 The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).
0.049 1 GO:0042546 The process by which a cell wall is synthesized, aggregates, and bonds together. A cell wall is the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.

SF	Genes	GO ID	Process Name
0.074	1	GO:0006635	A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
0.063	1	GO:0006891	The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).
0.049	1	GO:0042546	The process by which a cell wall is synthesized, aggregates, and bonds together. A cell wall is the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.

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	Os03g0189400
Gene name
Homology with Arabidopsis	Similar to At5g42250: alcohol dehydrogenase, putative (HF=4e-2)
Module size	25 genes
NF	0.25
%ile	24.7

Co-expression analysis

Gene ID Os03g0189400 Gene name Homology with ArabidopsisSimilar to At5g42250: alcohol dehydrogenase, putative (HF=4e-2) Module size 25 genes NF 0.25 %ile 24.7

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 Os03g0189400

Gene name
Homology with Arabidopsis Similar to At5g42250: alcohol dehydrogenase, putative (HF=4e-2)

Module size 25 genes

NF 0.25

%ile 24.7

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