CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g59680

Gene name EDA1 (embryo sac development arrest 1)

Module size 5 genes

NF 0.52

%ile 73.3

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 At1g59680 842259 EDA1 (embryo sac development arrest 1) F:molecular_function unknown;P:megagametogenesis;C:cellular_component unknown;P O.I. H.G. S.X.
0.86 93.1 0.87 At1g35610 840457 DC1 domain-containing protein F:protein binding, zinc ion binding;P:unknown;C:unknown;POM O.I. H.G. S.X.
0.67 81.6 0.88 At5g04400 830319 anac077 (Arabidopsis NAC domain containing protein 77) F:DNA binding;P:multicellular organismal development, regulation of transcription;C:cellular_component unknown;POBM O.I. H.G. S.X.
0.35 41.6 0.88 At1g50350 841457 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.32 35.7 0.88 At5g40050 834002 F-box family protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P 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	At1g59680	842259	EDA1 (embryo sac development arrest 1)	F:molecular_function unknown;P:megagametogenesis;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.86	93.1	0.87	At1g35610	840457	DC1 domain-containing protein	F:protein binding, zinc ion binding;P:unknown;C:unknown;POM	O.I.	H.G.	S.X.
0.67	81.6	0.88	At5g04400	830319	anac077 (Arabidopsis NAC domain containing protein 77)	F:DNA binding;P:multicellular organismal development, regulation of transcription;C:cellular_component unknown;POBM	O.I.	H.G.	S.X.
0.35	41.6	0.88	At1g50350	841457	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.32	35.7	0.88	At5g40050	834002	F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	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
365.5 100.0 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
261.2 100.0 E-ATMX-33-raw-cel-1562596241
260.5 100.0 GSM133773 Lindsey_1-25_torpedo-meristem_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
204.4 100.0 E-ATMX-33-raw-cel-1562596174
164.0 99.9 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
97.5 99.9 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
72.4 99.9 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
27.6 99.7 E-ATMX-33-raw-cel-1562596197
26.2 99.7 GSM133761 Lindsey_1-13_torpedo-cotyledon_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
23.3 99.6 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.8 99.6 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
19.0 99.5 GSM133768 Lindsey_1-20_torpedo-basal_Rep5_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
18.8 99.5 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.3 99.5 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.4 99.5 GSM184555 Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
15.1 99.4 E-ATMX-33-raw-cel-1562596219
14.8 99.4 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.1 99.4 GSM133774 Lindsey_1-26_torpedo-meristem_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
14.0 99.4 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.2 99.4 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.2 99.3 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.6 99.3 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.5 99.3 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.4 99.3 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.8 99.1 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.3 99.1 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.2 99.1 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.8 99.0 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
365.5	100.0	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
261.2	100.0	E-ATMX-33-raw-cel-1562596241
260.5	100.0	GSM133773	Lindsey_1-25_torpedo-meristem_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
204.4	100.0	E-ATMX-33-raw-cel-1562596174
164.0	99.9	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
97.5	99.9	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
72.4	99.9	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
27.6	99.7	E-ATMX-33-raw-cel-1562596197
26.2	99.7	GSM133761	Lindsey_1-13_torpedo-cotyledon_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
23.3	99.6	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.8	99.6	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
19.0	99.5	GSM133768	Lindsey_1-20_torpedo-basal_Rep5_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
18.8	99.5	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.3	99.5	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.4	99.5	GSM184555	Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
15.1	99.4	E-ATMX-33-raw-cel-1562596219
14.8	99.4	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.1	99.4	GSM133774	Lindsey_1-26_torpedo-meristem_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
14.0	99.4	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.2	99.4	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.2	99.3	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.6	99.3	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.5	99.3	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.4	99.3	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.8	99.1	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.3	99.1	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.2	99.1	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.8	99.0	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.087 1 GO:0009561 The process whose specific outcome is the progression of the embryo sac over time, from its formation as the megaspore to the mature structure. The process begins when three of the four haploid megaspores disintegrate, and the fourth undergoes mitosis giving rise to a binucleate syncytial embryo sac. The two haploid nuclei migrate to the opposite poles of the embryo sac and then undergo two rounds of mitosis generating four haploid nuclei at each pole. One nucleus from each set of four migrates to the center of the cell. Cellularization occurs, resulting in an eight-nucleate seven-celled structure. This structure contains two synergid cells and an egg cell at the micropylar end, and three antipodal cells at the other end. A binucleate endosperm mother cell is formed at the center.
0.013 1 GO:0007275 The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).

SF	Genes	GO ID	Process Name	Link to AmiGO
0.087	1	GO:0009561	The process whose specific outcome is the progression of the embryo sac over time, from its formation as the megaspore to the mature structure. The process begins when three of the four haploid megaspores disintegrate, and the fourth undergoes mitosis giving rise to a binucleate syncytial embryo sac. The two haploid nuclei migrate to the opposite poles of the embryo sac and then undergo two rounds of mitosis generating four haploid nuclei at each pole. One nucleus from each set of four migrates to the center of the cell. Cellularization occurs, resulting in an eight-nucleate seven-celled structure. This structure contains two synergid cells and an egg cell at the micropylar end, and three antipodal cells at the other end. A binucleate endosperm mother cell is formed at the center.
0.013	1	GO:0007275	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).

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

Back to the CoP portal site

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Gene ID	At1g59680
Gene name	EDA1 (embryo sac development arrest 1)
Module size	5 genes
NF	0.52
%ile	73.3

Co-expression analysis

Gene ID At1g59680 Gene name EDA1 (embryo sac development arrest 1) Module size 5 genes NF 0.52 %ile 73.3

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 At1g59680

Gene name EDA1 (embryo sac development arrest 1)

Module size 5 genes

NF 0.52

%ile 73.3

: 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