CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At2g41260

Gene name M17

Module size 33 genes

NF 0.52

%ile 73.5

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
0.72 84.8 1.00 At2g41260 818725 M17 Late-embryogenesis-abundant gene. Involved in the acquisition of desiccation tolerance during late phase of embryogenesis. O.I. H.G. S.X.
0.78 88.6 0.80 At1g75830 843916 LCR67 Predicted to encode a PR (pathogenesis-related) protein. Belongs to the plant defensin (PDF) family with the following members: At1g75830/PDF1.1, At5g44420/PDF1.2a, At2g26020/PDF1.2b, At5g44430/PDF1.2c, At2g26010/PDF1.3, At1g19610/PDF1.4, At1g55010/PDF1.5, At2g02120/PDF2.1, At2g02100/PDF2.2, At2g02130/PDF2.3, At1g61070/PDF2.4, At5g63660/PDF2.5, At2g02140/PDF2.6, At5g38330/PDF3.1 and At4g30070/PDF3.2. O.I. H.G. S.X.
0.73 85.5 0.67 At3g19920 821530 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PB O.I. H.G. S.X.
0.69 82.9 0.62 At2g36640 818236 ATECP63 (EMBRYONIC CELL PROTEIN 63) Encodes putative phosphotyrosine protein belonging to late embryogenesis abundant (LEA) protein in group 3 that might be involved in maturation and desiccation tolerance of seeds. RFLP and CAPS mapping place it on chromosome 4 but the nucleotide sequence maps it to chromosome 2. O.I. H.G. S.X.
0.68 82.2 0.60 At1g22600 838866 - F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MPF O.I. H.G. S.X.
0.65 79.6 0.61 At5g44310 834454 late embryogenesis abundant domain-containing protein / LEA domain-containing protein F:unknown;P:embryonic development ending in seed dormancy;C:unknown;OMBFPAV O.I. H.G. S.X.
0.64 78.9 0.63 At5g62490 836369 ATHVA22B Part of the AtHVA22 family. Protein expression is ABA- and stress-inducible. O.I. H.G. S.X.
0.63 78.1 0.49 At1g52690 841701 late embryogenesis abundant protein, putative / LEA protein, putative F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;PBMOFVA O.I. H.G. S.X.
0.62 77.3 0.59 At5g66780 836811 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. H.G. S.X.
0.61 76.7 0.62 At3g53040 824470 late embryogenesis abundant protein, putative / LEA protein, putative F:unknown;P:embryonic development ending in seed dormancy;C:unknown;MBOFPAV O.I. H.G. S.X.
0.61 76.7 0.50 At1g32560 840150 late embryogenesis abundant group 1 domain-containing protein / LEA group 1 domain-containing protein F:molecular_function unknown;P:embryonic development ending in seed dormancy, embryonic development;C:cellular_component unknown;PMO O.I. H.G. S.X.
0.61 76.7 0.69 At2g41280 818727 M10 Encodes a hydrophilic protein similar to Late Embryogenesis Activated (LEA) proteins expressed during embryogenesis, which are thought to be involved in the acquisition of dessication tolerance. O.I. H.G. S.X.
0.59 74.7 0.66 At1g16730 838244 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO O.I. H.G. S.X.
0.59 74.7 0.63 At2g40170 818608 GEA6 (LATE EMBRYOGENESIS ABUNDANT 6) Encodes a group 1 LEA gene that is activated by direct binding of ABI5 to its promoter and is involved in response to ABA. Is required for normal seed development. Involved in regulating the timing of dessication tolerance and rate of water loss during seed maturation. O.I. H.G. S.X.
0.57 73.8 0.52 At5g07330 830624 unknown protein F:molecular_function unknown;P:biological_process unknown;C:mitochondrion;P O.I. H.G. S.X.
0.51 66.3 0.53 At1g03790 839408 SOM (SOMNUS) Encodes SOMNUS (SOM), a nucleus-localized CCCH-type zinc finger protein. SOM negatively regulates light-dependent seed germination downstream of PIL5 (AT2G20180). O.I. H.G. S.X.
0.51 66.3 0.51 At5g04000 830279 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.50 65.3 0.56 At3g54940 824659 - - O.I. H.G. S.X.
0.49 63.5 0.55 At1g62710 842569 BETA-VPE (BETA VACUOLAR PROCESSING ENZYME) Encodes a vacuolar processing enzyme belonging to a novel group of cysteine proteases that is expressed specifically in seeds and is essential for the proper processing of storage proteins. O.I. H.G. S.X.
0.48 62.5 0.52 At1g72100 843541 late embryogenesis abundant domain-containing protein / LEA domain-containing protein F:unknown;P:embryonic development ending in seed dormancy;C:endomembrane system;BPOMFAV O.I. H.G. S.X.
0.48 62.5 0.51 At2g28420 817390 lactoylglutathione lyase family protein / glyoxalase I family protein F:lactoylglutathione lyase activity;P:carbohydrate metabolic process;C:cellular_component unknown;BOPMFA O.I. H.G. S.X.
0.48 62.5 0.54 At5g24130 832478 unknown protein F:molecular_function unknown;P:biological_process unknown;C:mitochondrion;PM O.I. H.G. S.X.
0.47 61.2 0.64 At2g23240 816856 plant EC metallothionein-like family 15 protein F:zinc ion binding;P:biological_process unknown;C:unknown;POMB O.I. H.G. S.X.
0.47 61.2 0.53 At2g21820 816718 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.46 59.8 0.46 At2g25890 817130 glycine-rich protein / oleosin F:molecular_function unknown;P:lipid storage;C:monolayer-surrounded lipid storage body, integral to membrane, membrane;PB O.I. H.G. S.X.
0.45 58.3 0.47 At5g51760 835250 AHG1 (ABA-hypersensitive germination 1) Encodes AHG1 (ABA-hypersensitive germination 1), a putative protein phosphatase 2C (PP2C). Expressed in seeds. AHG1 functions in seed development and germination. O.I. H.G. S.X.
0.45 58.3 0.45 At3g24650 822061 ABI3 (ABA INSENSITIVE 3) Homologous to the maize transcription factor Viviparous-1. Full length ABI3 protein binds to the highly conserved RY motif [DNA motif CATGCA(TG)], present in many seed-specific promoters, and the B3 domains of this transcription factor is necessary for the specific interaction with the RY element. Transcriptional activity of ABI3 requires the B3 DNA-binding domain and an activation domain. In addition to the known N-terminal-located activation domain, a second transcription activation domain was found in the B1 region of ABI3. ABI3 is essential for seed maturation. Regulator of the transition between embryo maturation and early seedling development. Putative seed-specific transcriptional activator. Mutants exhibit decreased responsiveness to ABA suggesting that ABI3 protein participates in the ABA perception/transduction cascade. Based on double mutant analyses, ABI3 interacts genetically with both FUS3 and LEC1 and is involved in controlling accumulation of chlorophyll and anthocyanins, sensitivity to abscisic acid, and expression of the members of the 12S storage protein gene family. In addition, both FUS3 and LEC1 regulate positively the abundance of the ABI3 protein in the seed. O.I. H.G. S.X.
0.43 55.3 0.45 At3g58450 825014 universal stress protein (USP) family protein F:molecular_function unknown;P:response to stress;C:cellular_component unknown;BPAOFM O.I. H.G. S.X.
0.42 53.9 0.53 At1g04560 839491 AWPM-19-like membrane family protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. H.G. S.X.
0.41 52.4 0.44 At5g01300 830983 phosphatidylethanolamine-binding family protein F:phosphatidylethanolamine binding;P:biological_process unknown;C:cellular_component unknown;BOAPF O.I. H.G. S.X.
0.40 50.8 0.55 At1g23070 838915 unknown protein F:unknown;P:biological_process unknown;C:unknown;MPFO O.I. H.G. S.X.
0.39 48.4 0.47 At1g54870 841926 binding / catalytic/ oxidoreductase F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:chloroplast;BOMFPAV O.I. H.G. S.X.
0.36 43.6 0.50 At1g48130 841231 ATPER1 encodes a protein similar to the 1-cysteine (1-Cys) peroxiredoxin family of antioxidants. Expression is limited to seed (aleurone and embryo) and is not induced by ABA or drought. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.72	84.8	1.00	At2g41260	818725	M17	Late-embryogenesis-abundant gene. Involved in the acquisition of desiccation tolerance during late phase of embryogenesis.	O.I.	H.G.	S.X.
0.78	88.6	0.80	At1g75830	843916	LCR67	Predicted to encode a PR (pathogenesis-related) protein. Belongs to the plant defensin (PDF) family with the following members: At1g75830/PDF1.1, At5g44420/PDF1.2a, At2g26020/PDF1.2b, At5g44430/PDF1.2c, At2g26010/PDF1.3, At1g19610/PDF1.4, At1g55010/PDF1.5, At2g02120/PDF2.1, At2g02100/PDF2.2, At2g02130/PDF2.3, At1g61070/PDF2.4, At5g63660/PDF2.5, At2g02140/PDF2.6, At5g38330/PDF3.1 and At4g30070/PDF3.2.	O.I.	H.G.	S.X.
0.73	85.5	0.67	At3g19920	821530	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PB	O.I.	H.G.	S.X.
0.69	82.9	0.62	At2g36640	818236	ATECP63 (EMBRYONIC CELL PROTEIN 63)	Encodes putative phosphotyrosine protein belonging to late embryogenesis abundant (LEA) protein in group 3 that might be involved in maturation and desiccation tolerance of seeds. RFLP and CAPS mapping place it on chromosome 4 but the nucleotide sequence maps it to chromosome 2.	O.I.	H.G.	S.X.
0.68	82.2	0.60	At1g22600	838866	-	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MPF	O.I.	H.G.	S.X.
0.65	79.6	0.61	At5g44310	834454	late embryogenesis abundant domain-containing protein / LEA domain-containing protein	F:unknown;P:embryonic development ending in seed dormancy;C:unknown;OMBFPAV	O.I.	H.G.	S.X.
0.64	78.9	0.63	At5g62490	836369	ATHVA22B	Part of the AtHVA22 family. Protein expression is ABA- and stress-inducible.	O.I.	H.G.	S.X.
0.63	78.1	0.49	At1g52690	841701	late embryogenesis abundant protein, putative / LEA protein, putative	F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;PBMOFVA	O.I.	H.G.	S.X.
0.62	77.3	0.59	At5g66780	836811	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	H.G.	S.X.
0.61	76.7	0.62	At3g53040	824470	late embryogenesis abundant protein, putative / LEA protein, putative	F:unknown;P:embryonic development ending in seed dormancy;C:unknown;MBOFPAV	O.I.	H.G.	S.X.
0.61	76.7	0.50	At1g32560	840150	late embryogenesis abundant group 1 domain-containing protein / LEA group 1 domain-containing protein	F:molecular_function unknown;P:embryonic development ending in seed dormancy, embryonic development;C:cellular_component unknown;PMO	O.I.	H.G.	S.X.
0.61	76.7	0.69	At2g41280	818727	M10	Encodes a hydrophilic protein similar to Late Embryogenesis Activated (LEA) proteins expressed during embryogenesis, which are thought to be involved in the acquisition of dessication tolerance.	O.I.	H.G.	S.X.
0.59	74.7	0.66	At1g16730	838244	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO	O.I.	H.G.	S.X.
0.59	74.7	0.63	At2g40170	818608	GEA6 (LATE EMBRYOGENESIS ABUNDANT 6)	Encodes a group 1 LEA gene that is activated by direct binding of ABI5 to its promoter and is involved in response to ABA. Is required for normal seed development. Involved in regulating the timing of dessication tolerance and rate of water loss during seed maturation.	O.I.	H.G.	S.X.
0.57	73.8	0.52	At5g07330	830624	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:mitochondrion;P	O.I.	H.G.	S.X.
0.51	66.3	0.53	At1g03790	839408	SOM (SOMNUS)	Encodes SOMNUS (SOM), a nucleus-localized CCCH-type zinc finger protein. SOM negatively regulates light-dependent seed germination downstream of PIL5 (AT2G20180).	O.I.	H.G.	S.X.
0.51	66.3	0.51	At5g04000	830279	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.50	65.3	0.56	At3g54940	824659	-	-	O.I.	H.G.	S.X.
0.49	63.5	0.55	At1g62710	842569	BETA-VPE (BETA VACUOLAR PROCESSING ENZYME)	Encodes a vacuolar processing enzyme belonging to a novel group of cysteine proteases that is expressed specifically in seeds and is essential for the proper processing of storage proteins.	O.I.	H.G.	S.X.
0.48	62.5	0.52	At1g72100	843541	late embryogenesis abundant domain-containing protein / LEA domain-containing protein	F:unknown;P:embryonic development ending in seed dormancy;C:endomembrane system;BPOMFAV	O.I.	H.G.	S.X.
0.48	62.5	0.51	At2g28420	817390	lactoylglutathione lyase family protein / glyoxalase I family protein	F:lactoylglutathione lyase activity;P:carbohydrate metabolic process;C:cellular_component unknown;BOPMFA	O.I.	H.G.	S.X.
0.48	62.5	0.54	At5g24130	832478	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:mitochondrion;PM	O.I.	H.G.	S.X.
0.47	61.2	0.64	At2g23240	816856	plant EC metallothionein-like family 15 protein	F:zinc ion binding;P:biological_process unknown;C:unknown;POMB	O.I.	H.G.	S.X.
0.47	61.2	0.53	At2g21820	816718	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.46	59.8	0.46	At2g25890	817130	glycine-rich protein / oleosin	F:molecular_function unknown;P:lipid storage;C:monolayer-surrounded lipid storage body, integral to membrane, membrane;PB	O.I.	H.G.	S.X.
0.45	58.3	0.47	At5g51760	835250	AHG1 (ABA-hypersensitive germination 1)	Encodes AHG1 (ABA-hypersensitive germination 1), a putative protein phosphatase 2C (PP2C). Expressed in seeds. AHG1 functions in seed development and germination.	O.I.	H.G.	S.X.
0.45	58.3	0.45	At3g24650	822061	ABI3 (ABA INSENSITIVE 3)	Homologous to the maize transcription factor Viviparous-1. Full length ABI3 protein binds to the highly conserved RY motif [DNA motif CATGCA(TG)], present in many seed-specific promoters, and the B3 domains of this transcription factor is necessary for the specific interaction with the RY element. Transcriptional activity of ABI3 requires the B3 DNA-binding domain and an activation domain. In addition to the known N-terminal-located activation domain, a second transcription activation domain was found in the B1 region of ABI3. ABI3 is essential for seed maturation. Regulator of the transition between embryo maturation and early seedling development. Putative seed-specific transcriptional activator. Mutants exhibit decreased responsiveness to ABA suggesting that ABI3 protein participates in the ABA perception/transduction cascade. Based on double mutant analyses, ABI3 interacts genetically with both FUS3 and LEC1 and is involved in controlling accumulation of chlorophyll and anthocyanins, sensitivity to abscisic acid, and expression of the members of the 12S storage protein gene family. In addition, both FUS3 and LEC1 regulate positively the abundance of the ABI3 protein in the seed.	O.I.	H.G.	S.X.
0.43	55.3	0.45	At3g58450	825014	universal stress protein (USP) family protein	F:molecular_function unknown;P:response to stress;C:cellular_component unknown;BPAOFM	O.I.	H.G.	S.X.
0.42	53.9	0.53	At1g04560	839491	AWPM-19-like membrane family protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	H.G.	S.X.
0.41	52.4	0.44	At5g01300	830983	phosphatidylethanolamine-binding family protein	F:phosphatidylethanolamine binding;P:biological_process unknown;C:cellular_component unknown;BOAPF	O.I.	H.G.	S.X.
0.40	50.8	0.55	At1g23070	838915	unknown protein	F:unknown;P:biological_process unknown;C:unknown;MPFO	O.I.	H.G.	S.X.
0.39	48.4	0.47	At1g54870	841926	binding / catalytic/ oxidoreductase	F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:chloroplast;BOMFPAV	O.I.	H.G.	S.X.
0.36	43.6	0.50	At1g48130	841231	ATPER1	encodes a protein similar to the 1-cysteine (1-Cys) peroxiredoxin family of antioxidants. Expression is limited to seed (aleurone and embryo) and is not induced by ABA or drought.	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
124.2 99.9 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
112.9 99.9 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
109.9 99.9 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
108.1 99.9 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
55.5 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.0 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
52.5 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.4 99.8 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
50.5 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.4 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.9 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.3 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.8 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.7 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
46.0 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
43.0 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
42.2 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.1 99.8 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
37.8 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.8 99.7 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.1 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
27.9 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
27.3 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.3 99.6 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
24.1 99.6 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
21.5 99.6 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
19.0 99.5 GSM284398 Arabidopsis GGSc2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
18.2 99.5 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
16.8 99.5 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.0 99.4 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
14.9 99.4 GSM284397 Arabidopsis GGSc1 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
12.0 99.3 GSM311284 Laser capture microdissected (LCM) general seed coat at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
11.1 99.2 GSM142735 DH001_ATH1_A2-BCP1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
10.7 99.2 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.7 99.1 GSM142740 DH001_ATH1_A7-MPG1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
9.2 99.1 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
8.7 99.0 GSM142734 DH001_ATH1_A1-UNM1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
124.2	99.9	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
112.9	99.9	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
109.9	99.9	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
108.1	99.9	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
55.5	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.0	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
52.5	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.4	99.8	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
50.5	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.4	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.9	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.3	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.8	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.7	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
46.0	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
43.0	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
42.2	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.1	99.8	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
37.8	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.8	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.1	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
27.9	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
27.3	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.3	99.6	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
24.1	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.5	99.6	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
19.0	99.5	GSM284398	Arabidopsis GGSc2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
18.2	99.5	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
16.8	99.5	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.0	99.4	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
14.9	99.4	GSM284397	Arabidopsis GGSc1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
12.0	99.3	GSM311284	Laser capture microdissected (LCM) general seed coat at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
11.1	99.2	GSM142735	DH001_ATH1_A2-BCP1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
10.7	99.2	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.7	99.1	GSM142740	DH001_ATH1_A7-MPG1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
9.2	99.1	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
8.7	99.0	GSM142734	DH001_ATH1_A1-UNM1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.076 3 GO:0009790 The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
0.057 1 GO:0048700 The process by which a seed acquires tolerance to severe drying, before entering into a dry, either dormant or quiescent state.
0.056 1 GO:0031930 A series of molecular signals that forms a pathway of communication from the mitochondria to the nucleus and initiates cellular changes in response to changes in mitochondrial function.

SF	Genes	GO ID	Process Name
0.076	3	GO:0009790	The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
0.057	1	GO:0048700	The process by which a seed acquires tolerance to severe drying, before entering into a dry, either dormant or quiescent state.
0.056	1	GO:0031930	A series of molecular signals that forms a pathway of communication from the mitochondria to the nucleus and initiates cellular changes in response to changes in mitochondrial function.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG

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	At2g41260
Gene name	M17
Module size	33 genes
NF	0.52
%ile	73.5

Co-expression analysis

Gene ID At2g41260 Gene name M17 Module size 33 genes NF 0.52 %ile 73.5

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 KEGG

Inter-species module comparison

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

Gene ID At2g41260

Gene name M17

Module size 33 genes

NF 0.52

%ile 73.5

: 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

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