CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g43530

Gene name transposable element gene

Module size 21 genes

NF 0.57

%ile 78.8

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
0.66 80.1 1.00 At3g43530 823445 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.76 87.4 0.93 At3g30660 822783 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.70 83.5 0.94 At2g07770 815424 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.68 82.2 0.92 At2g07730 3768192 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.68 82.2 0.92 At3g30845 822868 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.68 82.2 0.92 At1g43745 3767315 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.68 82.2 0.94 At1g29620 839839 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.65 79.6 0.94 At1g36035 3766971 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.61 76.7 0.91 At1g35110 840395 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.61 76.7 0.92 At2g05660 3768558 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.61 76.7 0.92 At2g29610 817511 - pseudogene of the F-box protein family, contains Pfam profile PF00646: F-box domain O.I. H.G. S.X.
0.56 73.0 0.91 At2g14420 3768298 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.55 70.6 0.92 At2g12710 3768564 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.50 65.3 0.92 At3g29640 822637 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.50 65.3 0.92 At3g32120 822975 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 0.92 At4g04440 3769954 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.49 63.5 0.92 At1g43740 3767314 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.44 57.2 0.92 At1g43050 3767286 - F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.44 57.2 0.91 At5g35140 3771250 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.44 57.2 0.95 At3g43060 3769525 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.33 38.1 0.93 At2g11590 3768652 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.66	80.1	1.00	At3g43530	823445	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.76	87.4	0.93	At3g30660	822783	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.70	83.5	0.94	At2g07770	815424	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.68	82.2	0.92	At2g07730	3768192	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.68	82.2	0.92	At3g30845	822868	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.68	82.2	0.92	At1g43745	3767315	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.68	82.2	0.94	At1g29620	839839	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.65	79.6	0.94	At1g36035	3766971	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.61	76.7	0.91	At1g35110	840395	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.61	76.7	0.92	At2g05660	3768558	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.61	76.7	0.92	At2g29610	817511	-	pseudogene of the F-box protein family, contains Pfam profile PF00646: F-box domain	O.I.	H.G.	S.X.
0.56	73.0	0.91	At2g14420	3768298	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.55	70.6	0.92	At2g12710	3768564	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.50	65.3	0.92	At3g29640	822637	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.50	65.3	0.92	At3g32120	822975	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	0.92	At4g04440	3769954	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.49	63.5	0.92	At1g43740	3767314	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.44	57.2	0.92	At1g43050	3767286	-	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.44	57.2	0.91	At5g35140	3771250	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.44	57.2	0.95	At3g43060	3769525	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.33	38.1	0.93	At2g11590	3768652	transposable element gene	F:unknown;P:unknown;C:unknown	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
78.8 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
55.1 99.8 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
44.2 99.8 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
41.9 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.9 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.8 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.8 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.3 99.7 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.0 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.6 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.8 99.7 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
30.9 99.7 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
30.8 99.7 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
30.3 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.7 99.7 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
28.0 99.7 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
27.6 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.4 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.2 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
25.8 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.9 99.6 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.6 99.6 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.2 99.6 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.0 99.6 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.6 99.6 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.6 99.6 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
22.2 99.6 GSM133756 Lindsey_1-10_heart-stage-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
21.9 99.6 GSM142738 DH001_ATH1_A5-BCP2 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
21.2 99.6 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
20.7 99.6 GSM142735 DH001_ATH1_A2-BCP1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
19.5 99.6 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.9 99.3 GSM131593 ATGE_36_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
11.7 99.3 GSM142736 DH001_ATH1_A3-TCP1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
10.1 99.2 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
10.0 99.2 GSM131591 ATGE_36_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
9.7 99.1 GSM106825 opr3_0 hr_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.7 99.1 E-MEXP-1797-raw-cel-1669767940
9.6 99.1 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
9.4 99.1 E-MEXP-1797-raw-cel-1669768030
9.2 99.1 GSM133768 Lindsey_1-20_torpedo-basal_Rep5_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.1 99.1 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
9.1 99.1 GSM142739 DH001_ATH1_A6-TCP2 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
8.9 99.0 GSM142734 DH001_ATH1_A1-UNM1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
78.8	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
55.1	99.8	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
44.2	99.8	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
41.9	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.9	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.8	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.8	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.3	99.7	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.0	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.6	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.8	99.7	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
30.9	99.7	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
30.8	99.7	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
30.3	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.7	99.7	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
28.0	99.7	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
27.6	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.4	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.2	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
25.8	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.9	99.6	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.6	99.6	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.2	99.6	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.0	99.6	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.6	99.6	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.6	99.6	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
22.2	99.6	GSM133756	Lindsey_1-10_heart-stage-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
21.9	99.6	GSM142738	DH001_ATH1_A5-BCP2	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
21.2	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
20.7	99.6	GSM142735	DH001_ATH1_A2-BCP1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
19.5	99.6	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.9	99.3	GSM131593	ATGE_36_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
11.7	99.3	GSM142736	DH001_ATH1_A3-TCP1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
10.1	99.2	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.0	99.2	GSM131591	ATGE_36_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.7	99.1	GSM106825	opr3_0 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.7	99.1	E-MEXP-1797-raw-cel-1669767940
9.6	99.1	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
9.4	99.1	E-MEXP-1797-raw-cel-1669768030
9.2	99.1	GSM133768	Lindsey_1-20_torpedo-basal_Rep5_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.1	99.1	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
9.1	99.1	GSM142739	DH001_ATH1_A6-TCP2	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
8.9	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

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

Back to the KAGIANA project homepage

Gene ID	At3g43530
Gene name	transposable element gene
Module size	21 genes
NF	0.57
%ile	78.8

Co-expression analysis

Gene ID At3g43530 Gene name transposable element gene Module size 21 genes NF 0.57 %ile 78.8

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

SFGenesGO IDProcess NameLink to AmiGO

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 At3g43530

Gene name transposable element gene

Module size 21 genes

NF 0.57

%ile 78.8

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

SF Genes GO ID Process Name Link to AmiGO

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