CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g17990

Gene name 12-oxophytodienoate reductase, putative

Module size 29 genes

NF 0.20

%ile 19.0

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

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. O.I. H.G. S.X. Other DB
1.00 100.0 1.00 At1g17990 838379 12-oxophytodienoate reductase, putative F:unknown;P:unknown;C:unknown;BOFPAM O.I. H.G. S.X.
0.48 62.5 0.77 At4g08920 826470 CRY1 (CRYPTOCHROME 1) Encodes CRY1, a flavin-type blue-light photoreceptor with ATP binding and autophosphorylation activity. The photoreceptor may be involved in electron transport. Mutant phenotype displays a blue light-dependent inhibition of hypocotyl elongation. Photoreceptor activity requires light-induced homodimerisation of the N-terminal CNT1 domains of CRY1. Involved in blue-light induced stomatal opening. The C-terminal domain of the protein undergoes a light dependent conformational change. Also involved in response to circadian rhythm. Mutants exhibit long hypocotyl under blue light and are out of phase in their response to circadian rhythm. CRY1 is present in the nucleus and cytoplasm. Different subcellular pools of CRY1 have different functions during photomorphogenesis of Arabidopsis seedlings. O.I. H.G. S.X.
0.30 32.1 0.75 At2g46220 819229 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;BPMO O.I. H.G. S.X.
0.29 30.3 0.75 At4g13830 827017 J20 (DNAJ-LIKE 20) DnaJ-like protein (J20); nuclear gene O.I. H.G. S.X.
0.29 30.3 0.75 At1g19660 838553 wound-responsive family protein F:unknown;P:response to wounding;C:unknown;BOPA O.I. H.G. S.X.
0.29 30.3 0.75 At2g30950 817646 VAR2 (VARIEGATED 2) Metalloprotease that functions in thylakoid membrane biogenesis. Involved in the repair of PSII following damaged incurred during photoinhibition. Forms a complex with VAR1. Mutants show a variegated phenotype, which decreases during development. Transcript and protein levels increase with light intensity. O.I. H.G. S.X.
0.27 26.2 0.75 At5g50920 835165 CLPC1 Encodes a protein that is similar to ATP-dependent Clp protease ATP-binding subunit / ClpC. Involved in protein import into the chloroplast. May provide ATP source that drives the TIC (Translocon at the Inner envelope membrane of Chloroplasts) translocation machinery. O.I. H.G. S.X.
0.25 22.6 0.75 At2g14910 815980 unknown protein F:unknown;P:unknown;C:chloroplast;BOPM O.I. H.G. S.X.
0.25 22.6 0.75 At5g44870 834517 disease resistance protein (TIR-NBS-LRR class), putative F:protein binding, transmembrane receptor activity, ATP binding;P:signal transduction, defense response, apoptosis, innate immune response;C:intrinsic to membrane;PMBOFA O.I. H.G. S.X.
0.25 22.6 0.75 At1g77930 844128 DNAJ heat shock N-terminal domain-containing protein F:heat shock protein binding;P:protein folding;C:chloroplast;BOMFPAV O.I. H.G. S.X.
0.23 19.3 0.77 At3g59060 825075 PIL6 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 6) Encodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family. Involved in shade avoidance. Functions as negative regulator of PhyB. Protein levels are modulated by phytochrome B. O.I. H.G. S.X.
0.22 17.5 0.76 At1g49970 841420 CLPR1 Encodes a ClpP-related sequence. Though similar to ClpP proteins, this does not contains the highly conserved catalytic triad of Ser-type proteases (Ser-His-Asp). The name reflects nomenclature described in Adam et. al (2001). O.I. H.G. S.X.
0.22 17.5 0.75 At1g54520 841894 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;BPOM O.I. H.G. S.X.
0.21 15.8 0.76 At1g06650 837175 2-oxoglutarate-dependent dioxygenase, putative encodes a protein whose sequence is similar to 2-oxoglutarate-dependent dioxygenase O.I. H.G. S.X.
0.20 14.4 0.75 At4g25650 828670 ACD1-LIKE (ACD1-LIKE) Similar to ACD1. Leaves of antisense ACD1-like plants turn yellow in darkness like wild-type whereas antisense ACD1 plants remain dark after five days of dark treatment. O.I. H.G. S.X.
0.17 10.2 0.76 At3g07310 819919 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;PBO O.I. H.G. S.X.
0.17 10.2 0.76 At4g34350 829585 HDR (4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE) Arabidopsis ISPH is involved in the plastid nonmevalonate pathway of isoprenoid biosynthesis. It was shown to complement the lethal phenotype of E. coli ispH mutant and is therefore most likely encodes a protein with 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity involved in the last step of mevalonate-independent isopentenyl biosynthesis. Mutant has Albino seedling. O.I. H.G. S.X.
0.17 10.2 0.77 At1g23310 838940 GGT1 (GLUTAMATE:GLYOXYLATE AMINOTRANSFERASE) Identified by cloning the gene that corresponded to a purified protein having glyoxylate aminotransferase activity. Localized to the peroxisome and thought to be involved in photorespiration/ metabolic salvage pathway. O.I. H.G. S.X.
0.17 10.2 0.75 At1g58200 842187 MSL3 (MscS-LIKE 3) A member of MscS-like gene family, structurally very similar to MSL2, comprising of an N-terminal chloroplast transit peptide, five trans-membrane helices and a C-terminal cytoplasmic domain. Mutant plants showed abnormalities in the size and shape of plastids. MSL3-GFP was localized to discrete foci on the plastid envelope and co-localize with the plastid division protein AtMinE. MSL3 was capable of increasing the osmotic-shock survival of a mutant bacterial strain lacking MS-ion-channel activity. O.I. H.G. S.X.
0.14 6.8 0.75 At1g65260 842833 PTAC4 (PLASTID TRANSCRIPTIONALLY ACTIVE4) F:unknown;P:biological_process unknown;C:in 8 components;BOMVFPA O.I. H.G. S.X.
0.14 6.8 0.76 At4g23180 828417 CRK10 (CYSTEINE-RICH RLK10) Encodes a receptor-like protein kinase. Naming convention from Chen et al 2003 (PMID 14756307) O.I. H.G. S.X.
0.12 4.9 0.76 At4g32060 829337 calcium-binding EF hand family protein F:calcium ion binding;P:unknown;C:unknown;MOFP O.I. H.G. S.X.
0.11 4.1 0.76 At2g28800 817429 ALB3 (ALBINO 3) member of Chloroplast membrane protein ALBINO3 family O.I. H.G. S.X.
0.08 2.3 0.78 At1g18000 838380 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;FMBPO O.I. H.G. S.X.
0.07 1.9 0.75 At5g01530 830325 chlorophyll A-B binding protein CP29 (LHCB4) F:chlorophyll binding;P:response to blue light, response to red light, response to far red light, photosynthesis;C:in 6 components;POM O.I. H.G. S.X.
0.06 1.4 0.75 At3g47560 823910 esterase/lipase/thioesterase family protein F:catalytic activity;P:unknown;C:unknown;OBPFAM O.I. H.G. S.X.
0.05 1.1 0.76 At2g41430 818741 ERD15 (EARLY RESPONSIVE TO DEHYDRATION 15) Encodes hydrophilic protein lacking Cys residues that is expressed in response to drought stress, light stress and treatment with plant-growth-promoting rhizobacteria (Paenibacillus polymyxa), possibly revealing a connection between responses to biotic and abiotic stress. Also identified as a CTC Interacting Domain (CID) protein in a yeast two hybrid screen using the PAB2 protein as bait. Contains PAM2 like domain which mediates interaction with PABC domain in PAB2. O.I. H.G. S.X.
0.05 1.1 0.75 At5g02290 831880 NAK Encodes a candidate protein kinase NAK that is similar to the oncogenes met and abl. O.I. H.G. S.X.
0.04 0.9 0.75 At5g24520 832523 TTG1 (TRANSPARENT TESTA GLABRA 1) Required for the accumulation of purple anthocyanins in leaves and stems. Involved in trichome and root hair development. Controls epidermal cell fate specification. Affects dihydroflavonol 4-reductase gene expression. It is thought that a ternary complex composed of TT2, TT8 and TTG1 is necessary for correct expression of BAN in seed endothelium. Based on clonal analysis and other methonds TTG1 has been shown to act non-cell autonomously and to move via plasmodesmata between cells.Localization and levels of TTG1 affect patterning of leaf trichomes. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
1.00	100.0	1.00	At1g17990	838379	12-oxophytodienoate reductase, putative	F:unknown;P:unknown;C:unknown;BOFPAM	O.I.	H.G.	S.X.
0.48	62.5	0.77	At4g08920	826470	CRY1 (CRYPTOCHROME 1)	Encodes CRY1, a flavin-type blue-light photoreceptor with ATP binding and autophosphorylation activity. The photoreceptor may be involved in electron transport. Mutant phenotype displays a blue light-dependent inhibition of hypocotyl elongation. Photoreceptor activity requires light-induced homodimerisation of the N-terminal CNT1 domains of CRY1. Involved in blue-light induced stomatal opening. The C-terminal domain of the protein undergoes a light dependent conformational change. Also involved in response to circadian rhythm. Mutants exhibit long hypocotyl under blue light and are out of phase in their response to circadian rhythm. CRY1 is present in the nucleus and cytoplasm. Different subcellular pools of CRY1 have different functions during photomorphogenesis of Arabidopsis seedlings.	O.I.	H.G.	S.X.
0.30	32.1	0.75	At2g46220	819229	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;BPMO	O.I.	H.G.	S.X.
0.29	30.3	0.75	At4g13830	827017	J20 (DNAJ-LIKE 20)	DnaJ-like protein (J20); nuclear gene	O.I.	H.G.	S.X.
0.29	30.3	0.75	At1g19660	838553	wound-responsive family protein	F:unknown;P:response to wounding;C:unknown;BOPA	O.I.	H.G.	S.X.
0.29	30.3	0.75	At2g30950	817646	VAR2 (VARIEGATED 2)	Metalloprotease that functions in thylakoid membrane biogenesis. Involved in the repair of PSII following damaged incurred during photoinhibition. Forms a complex with VAR1. Mutants show a variegated phenotype, which decreases during development. Transcript and protein levels increase with light intensity.	O.I.	H.G.	S.X.
0.27	26.2	0.75	At5g50920	835165	CLPC1	Encodes a protein that is similar to ATP-dependent Clp protease ATP-binding subunit / ClpC. Involved in protein import into the chloroplast. May provide ATP source that drives the TIC (Translocon at the Inner envelope membrane of Chloroplasts) translocation machinery.	O.I.	H.G.	S.X.
0.25	22.6	0.75	At2g14910	815980	unknown protein	F:unknown;P:unknown;C:chloroplast;BOPM	O.I.	H.G.	S.X.
0.25	22.6	0.75	At5g44870	834517	disease resistance protein (TIR-NBS-LRR class), putative	F:protein binding, transmembrane receptor activity, ATP binding;P:signal transduction, defense response, apoptosis, innate immune response;C:intrinsic to membrane;PMBOFA	O.I.	H.G.	S.X.
0.25	22.6	0.75	At1g77930	844128	DNAJ heat shock N-terminal domain-containing protein	F:heat shock protein binding;P:protein folding;C:chloroplast;BOMFPAV	O.I.	H.G.	S.X.
0.23	19.3	0.77	At3g59060	825075	PIL6 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 6)	Encodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family. Involved in shade avoidance. Functions as negative regulator of PhyB. Protein levels are modulated by phytochrome B.	O.I.	H.G.	S.X.
0.22	17.5	0.76	At1g49970	841420	CLPR1	Encodes a ClpP-related sequence. Though similar to ClpP proteins, this does not contains the highly conserved catalytic triad of Ser-type proteases (Ser-His-Asp). The name reflects nomenclature described in Adam et. al (2001).	O.I.	H.G.	S.X.
0.22	17.5	0.75	At1g54520	841894	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;BPOM	O.I.	H.G.	S.X.
0.21	15.8	0.76	At1g06650	837175	2-oxoglutarate-dependent dioxygenase, putative	encodes a protein whose sequence is similar to 2-oxoglutarate-dependent dioxygenase	O.I.	H.G.	S.X.
0.20	14.4	0.75	At4g25650	828670	ACD1-LIKE (ACD1-LIKE)	Similar to ACD1. Leaves of antisense ACD1-like plants turn yellow in darkness like wild-type whereas antisense ACD1 plants remain dark after five days of dark treatment.	O.I.	H.G.	S.X.
0.17	10.2	0.76	At3g07310	819919	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;PBO	O.I.	H.G.	S.X.
0.17	10.2	0.76	At4g34350	829585	HDR (4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE)	Arabidopsis ISPH is involved in the plastid nonmevalonate pathway of isoprenoid biosynthesis. It was shown to complement the lethal phenotype of E. coli ispH mutant and is therefore most likely encodes a protein with 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity involved in the last step of mevalonate-independent isopentenyl biosynthesis. Mutant has Albino seedling.	O.I.	H.G.	S.X.
0.17	10.2	0.77	At1g23310	838940	GGT1 (GLUTAMATE:GLYOXYLATE AMINOTRANSFERASE)	Identified by cloning the gene that corresponded to a purified protein having glyoxylate aminotransferase activity. Localized to the peroxisome and thought to be involved in photorespiration/ metabolic salvage pathway.	O.I.	H.G.	S.X.
0.17	10.2	0.75	At1g58200	842187	MSL3 (MscS-LIKE 3)	A member of MscS-like gene family, structurally very similar to MSL2, comprising of an N-terminal chloroplast transit peptide, five trans-membrane helices and a C-terminal cytoplasmic domain. Mutant plants showed abnormalities in the size and shape of plastids. MSL3-GFP was localized to discrete foci on the plastid envelope and co-localize with the plastid division protein AtMinE. MSL3 was capable of increasing the osmotic-shock survival of a mutant bacterial strain lacking MS-ion-channel activity.	O.I.	H.G.	S.X.
0.14	6.8	0.75	At1g65260	842833	PTAC4 (PLASTID TRANSCRIPTIONALLY ACTIVE4)	F:unknown;P:biological_process unknown;C:in 8 components;BOMVFPA	O.I.	H.G.	S.X.
0.14	6.8	0.76	At4g23180	828417	CRK10 (CYSTEINE-RICH RLK10)	Encodes a receptor-like protein kinase. Naming convention from Chen et al 2003 (PMID 14756307)	O.I.	H.G.	S.X.
0.12	4.9	0.76	At4g32060	829337	calcium-binding EF hand family protein	F:calcium ion binding;P:unknown;C:unknown;MOFP	O.I.	H.G.	S.X.
0.11	4.1	0.76	At2g28800	817429	ALB3 (ALBINO 3)	member of Chloroplast membrane protein ALBINO3 family	O.I.	H.G.	S.X.
0.08	2.3	0.78	At1g18000	838380	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;FMBPO	O.I.	H.G.	S.X.
0.07	1.9	0.75	At5g01530	830325	chlorophyll A-B binding protein CP29 (LHCB4)	F:chlorophyll binding;P:response to blue light, response to red light, response to far red light, photosynthesis;C:in 6 components;POM	O.I.	H.G.	S.X.
0.06	1.4	0.75	At3g47560	823910	esterase/lipase/thioesterase family protein	F:catalytic activity;P:unknown;C:unknown;OBPFAM	O.I.	H.G.	S.X.
0.05	1.1	0.76	At2g41430	818741	ERD15 (EARLY RESPONSIVE TO DEHYDRATION 15)	Encodes hydrophilic protein lacking Cys residues that is expressed in response to drought stress, light stress and treatment with plant-growth-promoting rhizobacteria (Paenibacillus polymyxa), possibly revealing a connection between responses to biotic and abiotic stress. Also identified as a CTC Interacting Domain (CID) protein in a yeast two hybrid screen using the PAB2 protein as bait. Contains PAM2 like domain which mediates interaction with PABC domain in PAB2.	O.I.	H.G.	S.X.
0.05	1.1	0.75	At5g02290	831880	NAK	Encodes a candidate protein kinase NAK that is similar to the oncogenes met and abl.	O.I.	H.G.	S.X.
0.04	0.9	0.75	At5g24520	832523	TTG1 (TRANSPARENT TESTA GLABRA 1)	Required for the accumulation of purple anthocyanins in leaves and stems. Involved in trichome and root hair development. Controls epidermal cell fate specification. Affects dihydroflavonol 4-reductase gene expression. It is thought that a ternary complex composed of TT2, TT8 and TTG1 is necessary for correct expression of BAN in seed endothelium. Based on clonal analysis and other methonds TTG1 has been shown to act non-cell autonomously and to move via plasmodesmata between cells.Localization and levels of TTG1 affect patterning of leaf trichomes.	O.I.	H.G.	S.X.

Click More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
71.6 99.9 GSM184556 Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
50.4 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
48.5 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
47.9 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
46.3 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.1 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
44.2 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
44.2 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.3 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
43.2 99.8 GSM184551 Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
43.0 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.9 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
42.8 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.3 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.3 99.8 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
40.1 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.0 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
39.1 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.8 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.7 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.8 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.6 99.7 GSM67087 Arabidopsis_Stigma03 GSE3056 Arabidopsis Pollination Study
34.4 99.7 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
33.2 99.7 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
31.4 99.7 GSM67086 Arabidopsis_Stigma02 GSE3056 Arabidopsis Pollination Study
27.2 99.7 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
19.4 99.6 GSM311291 Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
18.8 99.5 GSM311282 Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
17.2 99.5 GSM311292 Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
16.5 99.5 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
15.3 99.4 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.8 99.4 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.1 99.4 GSM311281 Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 1 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
12.8 99.3 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.0 99.2 GSM142750 MJ001_ATH1_A1-jones-WT1 GSE6165 The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
10.7 99.2 GSM133760 Lindsey_1-12_heart-stage-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.7 99.1 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
8.6 99.0 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
71.6	99.9	GSM184556	Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
50.4	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
48.5	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
47.9	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
46.3	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.1	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
44.2	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
44.2	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.3	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
43.2	99.8	GSM184551	Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
43.0	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.9	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
42.8	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.3	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.3	99.8	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
40.1	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.0	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
39.1	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.8	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.7	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.8	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.6	99.7	GSM67087	Arabidopsis_Stigma03	GSE3056	Arabidopsis Pollination Study
34.4	99.7	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
33.2	99.7	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
31.4	99.7	GSM67086	Arabidopsis_Stigma02	GSE3056	Arabidopsis Pollination Study
27.2	99.7	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
19.4	99.6	GSM311291	Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
18.8	99.5	GSM311282	Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
17.2	99.5	GSM311292	Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
16.5	99.5	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
15.3	99.4	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.8	99.4	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.1	99.4	GSM311281	Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
12.8	99.3	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.0	99.2	GSM142750	MJ001_ATH1_A1-jones-WT1	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
10.7	99.2	GSM133760	Lindsey_1-12_heart-stage-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.7	99.1	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
8.6	99.0	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.128 3 GO:0010027 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the thylakoid membrane.
0.067 1 GO:0010343 Programmed cell death induced by singlet oxygen. Programmed cell death is the cell death resulting from activation of endogenous cellular processes.
0.067 1 GO:0016050 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.

SF	Genes	GO ID	Process Name
0.128	3	GO:0010027	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the thylakoid membrane.
0.067	1	GO:0010343	Programmed cell death induced by singlet oxygen. Programmed cell death is the cell death resulting from activation of endogenous cellular processes.
0.067	1	GO:0016050	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.042 1 00196 Photosynthesis - antenna proteins
0.036 1 03060 Protein export
0.034 1 04712 Circadian rhythm - plant

SF	Genes	KEGG ID	Pathway name
0.042	1	00196	Photosynthesis - antenna proteins
0.036	1	03060	Protein export
0.034	1	04712	Circadian rhythm - plant

Inter-species module comparison

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

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Gene ID	At1g17990
Gene name	12-oxophytodienoate reductase, putative
Module size	29 genes
NF	0.20
%ile	19.0

Co-expression analysis

Gene ID At1g17990 Gene name 12-oxophytodienoate reductase, putative Module size 29 genes NF 0.20 %ile 19.0

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein: VF over 0.50, : over 0.25, : below 0.25

Co-expressed genes

Click More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Biological processes inferred to relate to the module

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG0.042100196Photosynthesis - antenna proteins0.036103060Protein export0.034104712Circadian rhythm - plant

Inter-species module comparison

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

Gene ID At1g17990

Gene name 12-oxophytodienoate reductase, putative

Module size 29 genes

NF 0.20

%ile 19.0

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

SF Genes KEGG ID Pathway name Link to KEGG
0.042 1 00196 Photosynthesis - antenna proteins
0.036 1 03060 Protein export
0.034 1 04712 Circadian rhythm - plant

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