CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g55840

Gene name -

Module size 33 genes

NF 0.55

%ile 76.4

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
0.82 90.9 1.00 At3g55840 824750 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.80 89.8 0.80 At4g30280 829151 XTH18 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 18) putative xyloglucan endotransglycosylase/hydrolase, expressed in the mature or basal regions of both the main and lateral roots, but not in the tip of these roots where cell division occurs. O.I. H.G. S.X.
0.65 79.6 0.76 At1g51620 841587 protein kinase family protein F:protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVA O.I. H.G. S.X.
0.65 79.6 0.77 At5g12340 831109 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. H.G. S.X.
0.64 78.9 0.76 At1g30135 839893 JAZ8 (JASMONATE-ZIM-DOMAIN PROTEIN 8) F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.63 78.1 0.73 At4g38420 829999 sks9 (SKU5 Similar 9) F:oxidoreductase activity, copper ion binding;P:unknown;C:plant-type cell wall;FBPMOA O.I. H.G. S.X.
0.62 77.3 0.72 At3g23250 821904 MYB15 (MYB DOMAIN PROTEIN 15) Member of the R2R3 factor gene family. O.I. H.G. S.X.
0.61 76.7 0.76 At1g56060 842057 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PF O.I. H.G. S.X.
0.60 75.7 0.77 At1g20310 838619 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P O.I. H.G. S.X.
0.59 74.7 0.77 At3g01830 820033 calmodulin-related protein, putative F:calcium ion binding;P:biological_process unknown;C:cellular_component unknown;MPFOB O.I. H.G. S.X.
0.59 74.7 0.72 At4g25810 828686 XTR6 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 6) xyloglucan endotransglycosylase-related protein (XTR6) O.I. H.G. S.X.
0.57 73.8 0.72 At2g34600 818025 JAZ7 (JASMONATE-ZIM-DOMAIN PROTEIN 7) F:molecular_function unknown;P:response to jasmonic acid stimulus, response to chitin;C:cellular_component unknown;P O.I. H.G. S.X.
0.57 73.8 0.74 At4g37770 829933 ACS8 Encodes an auxin inducible ACC synthase. O.I. H.G. S.X.
0.57 73.8 0.73 At1g14540 838016 anionic peroxidase, putative F:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:endomembrane system;PFOBM O.I. H.G. S.X.
0.56 73.0 0.74 At5g66620 836794 DAR6 (DA1-RELATED PROTEIN 6) F:zinc ion binding;P:unknown;C:unknown;MOBFPVA O.I. H.G. S.X.
0.55 70.6 0.73 At2g37430 818319 zinc finger (C2H2 type) family protein (ZAT11) F:transcription factor activity, zinc ion binding, nucleic acid binding;P:response to chitin, regulation of transcription;C:intracellular;MPOF O.I. H.G. S.X.
0.55 70.6 0.73 At2g20142 2745551 transmembrane receptor F:transmembrane receptor activity;P:signal transduction, innate immune response;C:intrinsic to membrane;P O.I. H.G. S.X.
0.54 69.5 0.73 At1g30370 839917 lipase class 3 family protein F:triacylglycerol lipase activity;P:lipid metabolic process;C:unknown;PBOFMV O.I. H.G. S.X.
0.53 68.6 0.73 At1g35210 840410 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PO O.I. H.G. S.X.
0.53 68.6 0.73 At5g56980 835800 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PM O.I. H.G. S.X.
0.51 66.3 0.72 At5g47220 834768 ERF2 (ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 2) Encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family (ATERF-2). The protein contains one AP2 domain. Functions as activator of GCC box�dependent transcription. Positive regulator of JA-responsive defense genes and resistance to F. oxysporum and enhances JA inhibition of root elongation. O.I. H.G. S.X.
0.51 66.3 0.73 At2g32030 817763 GCN5-related N-acetyltransferase (GNAT) family protein F:N-acetyltransferase activity;P:metabolic process;C:cellular_component unknown;BOFPAVM O.I. H.G. S.X.
0.50 65.3 0.73 At2g27310 817274 F-box family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.50 65.3 0.73 At5g42380 834244 CML37 (CALMODULIN LIKE 37) F:calcium ion binding;P:response to ozone;C:chloroplast;MPOFBV O.I. H.G. S.X.
0.49 63.5 0.76 At2g25735 817115 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. H.G. S.X.
0.49 63.5 0.71 At3g50930 824257 BCS1 (CYTOCHROME BC1 SYNTHESIS) F:nucleoside-triphosphatase activity, ATPase activity, nucleotide binding, ATP binding;P:unknown;C:mitochondrion, plastid;BOMFPAV O.I. H.G. S.X.
0.48 62.5 0.77 At1g72520 843584 lipoxygenase, putative F:electron carrier activity, oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen, lipoxygenase activity, iron ion binding, metal ion binding;P:growth, jasmonic acid biosynthetic process, response to wounding, defense response;C:chloroplast;PMBFO O.I. H.G. S.X.
0.47 61.2 0.71 At5g61900 836311 BON1 (BONZAI 1) Encodes a plasma-membrane localized, copine-like protein, which is a member of a newly identified class of calcium-dependent, phospholipid binding proteins that are present in a wide range of organisms. Mutants exhibit temperature-sensitive growth defects and increased hypersensitive response where permissive conditions are low temperature (22 degrees Celsius) and low humidity. Gene is expressed at 22 but not at 28 (restrictive condition) degrees. Lethality of double mutants with BON3 can be partially suppressed by SNC1. Double mutants show defects in development that are genetically separable from hypersensitive/cell death response. O.I. H.G. S.X.
0.47 61.2 0.77 At2g35930 818166 PUB23 (PLANT U-BOX 23) Encodes a cytoplasmically localized U-box domain containing E3 ubiquitin ligase that is involved in the response to water stress and acts as a negative regulator of PAMP-triggered immunity. O.I. H.G. S.X.
0.47 61.2 0.77 At2g41640 818762 transferase, transferring glycosyl groups F:transferase activity, transferring glycosyl groups;P:biological_process unknown;C:unknown;PMOBF O.I. H.G. S.X.
0.44 57.2 0.78 At4g31800 829308 WRKY18 Pathogen-induced transcription factor. Binds W-box sequences in vitro. Forms protein complexes with itself and with WRKY40 and WRKY60. Constitutive expression of WRKY18 enhanced resistance to P. syringae, but its coexpression with WRKY40 or WRKY60 made plants more susceptible to both P. syringae and B. cinerea. WRKY18, WRKY40, and WRKY60 have partially redundant roles in response to the hemibiotrophic bacterial pathogen Pseudomonas syringae and the necrotrophic fungal pathogen Botrytis cinerea, with WRKY18 playing a more important role than the other two. O.I. H.G. S.X.
0.38 46.7 0.71 At1g28480 839748 GRX480 Encodes GRX480, a member of the glutaredoxin family that regulates protein redox state. GRX480 interacts with TGA factors and suppresses JA-responsive PDF1.2 transcription. GRX480 transcription is SA-inducible and requires NPR1. Maybe involved in SA/JA cross-talk. O.I. H.G. S.X.
0.37 45.0 0.72 At2g35710 818140 glycogenin glucosyltransferase (glycogenin)-related F:transferase activity, transferring hexosyl groups, transferase activity, transferring glycosyl groups;P:carbohydrate biosynthetic process, biosynthetic process;C:endomembrane system;PMFOBV O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.82	90.9	1.00	At3g55840	824750	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.80	89.8	0.80	At4g30280	829151	XTH18 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 18)	putative xyloglucan endotransglycosylase/hydrolase, expressed in the mature or basal regions of both the main and lateral roots, but not in the tip of these roots where cell division occurs.	O.I.	H.G.	S.X.
0.65	79.6	0.76	At1g51620	841587	protein kinase family protein	F:protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVA	O.I.	H.G.	S.X.
0.65	79.6	0.77	At5g12340	831109	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	H.G.	S.X.
0.64	78.9	0.76	At1g30135	839893	JAZ8 (JASMONATE-ZIM-DOMAIN PROTEIN 8)	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.63	78.1	0.73	At4g38420	829999	sks9 (SKU5 Similar 9)	F:oxidoreductase activity, copper ion binding;P:unknown;C:plant-type cell wall;FBPMOA	O.I.	H.G.	S.X.
0.62	77.3	0.72	At3g23250	821904	MYB15 (MYB DOMAIN PROTEIN 15)	Member of the R2R3 factor gene family.	O.I.	H.G.	S.X.
0.61	76.7	0.76	At1g56060	842057	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PF	O.I.	H.G.	S.X.
0.60	75.7	0.77	At1g20310	838619	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	O.I.	H.G.	S.X.
0.59	74.7	0.77	At3g01830	820033	calmodulin-related protein, putative	F:calcium ion binding;P:biological_process unknown;C:cellular_component unknown;MPFOB	O.I.	H.G.	S.X.
0.59	74.7	0.72	At4g25810	828686	XTR6 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 6)	xyloglucan endotransglycosylase-related protein (XTR6)	O.I.	H.G.	S.X.
0.57	73.8	0.72	At2g34600	818025	JAZ7 (JASMONATE-ZIM-DOMAIN PROTEIN 7)	F:molecular_function unknown;P:response to jasmonic acid stimulus, response to chitin;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.57	73.8	0.74	At4g37770	829933	ACS8	Encodes an auxin inducible ACC synthase.	O.I.	H.G.	S.X.
0.57	73.8	0.73	At1g14540	838016	anionic peroxidase, putative	F:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:endomembrane system;PFOBM	O.I.	H.G.	S.X.
0.56	73.0	0.74	At5g66620	836794	DAR6 (DA1-RELATED PROTEIN 6)	F:zinc ion binding;P:unknown;C:unknown;MOBFPVA	O.I.	H.G.	S.X.
0.55	70.6	0.73	At2g37430	818319	zinc finger (C2H2 type) family protein (ZAT11)	F:transcription factor activity, zinc ion binding, nucleic acid binding;P:response to chitin, regulation of transcription;C:intracellular;MPOF	O.I.	H.G.	S.X.
0.55	70.6	0.73	At2g20142	2745551	transmembrane receptor	F:transmembrane receptor activity;P:signal transduction, innate immune response;C:intrinsic to membrane;P	O.I.	H.G.	S.X.
0.54	69.5	0.73	At1g30370	839917	lipase class 3 family protein	F:triacylglycerol lipase activity;P:lipid metabolic process;C:unknown;PBOFMV	O.I.	H.G.	S.X.
0.53	68.6	0.73	At1g35210	840410	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PO	O.I.	H.G.	S.X.
0.53	68.6	0.73	At5g56980	835800	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PM	O.I.	H.G.	S.X.
0.51	66.3	0.72	At5g47220	834768	ERF2 (ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 2)	Encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family (ATERF-2). The protein contains one AP2 domain. Functions as activator of GCC box�dependent transcription. Positive regulator of JA-responsive defense genes and resistance to F. oxysporum and enhances JA inhibition of root elongation.	O.I.	H.G.	S.X.
0.51	66.3	0.73	At2g32030	817763	GCN5-related N-acetyltransferase (GNAT) family protein	F:N-acetyltransferase activity;P:metabolic process;C:cellular_component unknown;BOFPAVM	O.I.	H.G.	S.X.
0.50	65.3	0.73	At2g27310	817274	F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.50	65.3	0.73	At5g42380	834244	CML37 (CALMODULIN LIKE 37)	F:calcium ion binding;P:response to ozone;C:chloroplast;MPOFBV	O.I.	H.G.	S.X.
0.49	63.5	0.76	At2g25735	817115	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	H.G.	S.X.
0.49	63.5	0.71	At3g50930	824257	BCS1 (CYTOCHROME BC1 SYNTHESIS)	F:nucleoside-triphosphatase activity, ATPase activity, nucleotide binding, ATP binding;P:unknown;C:mitochondrion, plastid;BOMFPAV	O.I.	H.G.	S.X.
0.48	62.5	0.77	At1g72520	843584	lipoxygenase, putative	F:electron carrier activity, oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen, lipoxygenase activity, iron ion binding, metal ion binding;P:growth, jasmonic acid biosynthetic process, response to wounding, defense response;C:chloroplast;PMBFO	O.I.	H.G.	S.X.
0.47	61.2	0.71	At5g61900	836311	BON1 (BONZAI 1)	Encodes a plasma-membrane localized, copine-like protein, which is a member of a newly identified class of calcium-dependent, phospholipid binding proteins that are present in a wide range of organisms. Mutants exhibit temperature-sensitive growth defects and increased hypersensitive response where permissive conditions are low temperature (22 degrees Celsius) and low humidity. Gene is expressed at 22 but not at 28 (restrictive condition) degrees. Lethality of double mutants with BON3 can be partially suppressed by SNC1. Double mutants show defects in development that are genetically separable from hypersensitive/cell death response.	O.I.	H.G.	S.X.
0.47	61.2	0.77	At2g35930	818166	PUB23 (PLANT U-BOX 23)	Encodes a cytoplasmically localized U-box domain containing E3 ubiquitin ligase that is involved in the response to water stress and acts as a negative regulator of PAMP-triggered immunity.	O.I.	H.G.	S.X.
0.47	61.2	0.77	At2g41640	818762	transferase, transferring glycosyl groups	F:transferase activity, transferring glycosyl groups;P:biological_process unknown;C:unknown;PMOBF	O.I.	H.G.	S.X.
0.44	57.2	0.78	At4g31800	829308	WRKY18	Pathogen-induced transcription factor. Binds W-box sequences in vitro. Forms protein complexes with itself and with WRKY40 and WRKY60. Constitutive expression of WRKY18 enhanced resistance to P. syringae, but its coexpression with WRKY40 or WRKY60 made plants more susceptible to both P. syringae and B. cinerea. WRKY18, WRKY40, and WRKY60 have partially redundant roles in response to the hemibiotrophic bacterial pathogen Pseudomonas syringae and the necrotrophic fungal pathogen Botrytis cinerea, with WRKY18 playing a more important role than the other two.	O.I.	H.G.	S.X.
0.38	46.7	0.71	At1g28480	839748	GRX480	Encodes GRX480, a member of the glutaredoxin family that regulates protein redox state. GRX480 interacts with TGA factors and suppresses JA-responsive PDF1.2 transcription. GRX480 transcription is SA-inducible and requires NPR1. Maybe involved in SA/JA cross-talk.	O.I.	H.G.	S.X.
0.37	45.0	0.72	At2g35710	818140	glycogenin glucosyltransferase (glycogenin)-related	F:transferase activity, transferring hexosyl groups, transferase activity, transferring glycosyl groups;P:carbohydrate biosynthetic process, biosynthetic process;C:endomembrane system;PMFOBV	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
103.8 99.9 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
98.0 99.9 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
95.4 99.9 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
85.4 99.9 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
63.4 99.8 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
62.9 99.8 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
59.6 99.8 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
48.9 99.8 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
48.4 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.0 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
47.9 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.0 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.9 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
46.5 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.6 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.4 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
45.2 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.3 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
42.5 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.1 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
41.6 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.0 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.0 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
38.5 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
38.0 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
35.3 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.8 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.6 99.7 GSM133755 Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
28.9 99.7 GSM133760 Lindsey_1-12_heart-stage-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
27.5 99.7 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
20.8 99.6 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.7 99.4 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.3 99.4 GSM142624 MC002_ATH1_A1.2-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
13.2 99.4 GSM142625 MC002_ATH1_A1.3-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.9 99.2 GSM142641 MC002_ATH1_A7.1-dubos-wLh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.8 99.2 GSM133756 Lindsey_1-10_heart-stage-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.6 99.1 GSM142643 MC002_ATH1_A7.3-dubos-wLh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.3 99.1 E-MEXP-807-raw-cel-1173273223
9.2 99.1 GSM133776 Lindsey_1-1_globular-apical_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.2 99.1 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
9.0 99.1 GSM142631 MC002_ATH1_A3.3-dubos-6kx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.8 99.0 E-MEXP-849-raw-cel-1181980982
8.8 99.0 E-MEXP-807-raw-cel-1173273196
8.7 99.0 GSM133303 RIKEN-NAKABAYASHI1A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
8.6 99.0 GSM142642 MC002_ATH1_A7.2-dubos-wLh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
103.8	99.9	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
98.0	99.9	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
95.4	99.9	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
85.4	99.9	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
63.4	99.8	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
62.9	99.8	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
59.6	99.8	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
48.9	99.8	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
48.4	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.0	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
47.9	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.0	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.9	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
46.5	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.6	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.4	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
45.2	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.3	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
42.5	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.1	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
41.6	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.0	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.0	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
38.5	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
38.0	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.3	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.8	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.6	99.7	GSM133755	Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
28.9	99.7	GSM133760	Lindsey_1-12_heart-stage-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
27.5	99.7	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
20.8	99.6	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.7	99.4	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.3	99.4	GSM142624	MC002_ATH1_A1.2-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
13.2	99.4	GSM142625	MC002_ATH1_A1.3-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.9	99.2	GSM142641	MC002_ATH1_A7.1-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.8	99.2	GSM133756	Lindsey_1-10_heart-stage-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.6	99.1	GSM142643	MC002_ATH1_A7.3-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.3	99.1	E-MEXP-807-raw-cel-1173273223
9.2	99.1	GSM133776	Lindsey_1-1_globular-apical_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.2	99.1	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
9.0	99.1	GSM142631	MC002_ATH1_A3.3-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.8	99.0	E-MEXP-849-raw-cel-1181980982
8.8	99.0	E-MEXP-807-raw-cel-1173273196
8.7	99.0	GSM133303	RIKEN-NAKABAYASHI1A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
8.6	99.0	GSM142642	MC002_ATH1_A7.2-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.075 6 GO:0010200 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 chitin stimulus.
0.073 2 GO:0006073 The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.
0.069 2 GO:0010193 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 ozone stimulus.

SF	Genes	GO ID	Process Name
0.075	6	GO:0010200	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 chitin stimulus.
0.073	2	GO:0006073	The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.
0.069	2	GO:0010193	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 ozone stimulus.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.032 1 00592 alpha-Linolenic acid metabolism
0.021 1 00270 Cysteine and methionine metabolism
0.018 1 00360 Phenylalanine metabolism

SF	Genes	KEGG ID	Pathway name
0.032	1	00592	alpha-Linolenic acid metabolism
0.021	1	00270	Cysteine and methionine metabolism
0.018	1	00360	Phenylalanine metabolism

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	At3g55840
Gene name	-
Module size	33 genes
NF	0.55
%ile	76.4

Co-expression analysis

Gene ID At3g55840 Gene name - Module size 33 genes NF 0.55 %ile 76.4

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 KEGG0.032100592alpha-Linolenic acid metabolism0.021100270Cysteine and methionine metabolism0.018100360Phenylalanine metabolism

Inter-species module comparison

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

Gene ID At3g55840

Gene name -

Module size 33 genes

NF 0.55

%ile 76.4

: 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
0.032 1 00592 alpha-Linolenic acid metabolism
0.021 1 00270 Cysteine and methionine metabolism
0.018 1 00360 Phenylalanine metabolism

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