CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g43920

Gene name transposable element gene

Module size 22 genes

NF 0.44

%ile 61.5

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
0.51 66.3 1.00 At1g43920 840991 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.69 82.9 0.83 At3g42070 823176 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.60 75.7 0.83 At1g31100 3766864 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.54 69.5 0.82 At2g15540 3768274 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.53 68.6 0.82 At1g24640 3766791 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.50 65.3 0.80 At2g20460 3767852 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.50 65.3 0.79 At4g03870 3770320 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.49 63.5 0.83 At2g07240 815294 cysteine-type peptidase F:cysteine-type peptidase activity;P:proteolysis;C:cellular_component unknown;POFMBV O.I. H.G. S.X.
0.49 63.5 0.80 At5g28860 833005 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.48 62.5 0.80 At2g16000 3768393 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.48 62.5 0.80 At2g16110 3768127 - F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.47 61.2 0.80 At2g13940 3768461 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.43 55.3 0.80 At3g31920 3769214 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.42 53.9 0.79 At2g05200 3768310 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.42 53.9 0.82 At3g26614 3768945 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.40 50.8 0.84 At3g22870 821859 F-box family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO O.I. H.G. S.X.
0.37 45.0 0.79 At4g08730 826442 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMF O.I. H.G. S.X.
0.36 43.6 0.86 At3g46360 823782 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.34 39.8 0.85 At4g14820 827139 pentatricopeptide (PPR) repeat-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFMB O.I. H.G. S.X.
0.33 38.1 0.82 At2g07070 815276 transposable element gene pseudogene of unknown protein O.I. H.G. S.X.
0.28 30.3 0.82 At1g19930 838582 kelch repeat-containing F-box family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMBOVA O.I. H.G. S.X.
0.25 22.6 0.82 At4g17450 3770187 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.
0.51	66.3	1.00	At1g43920	840991	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.69	82.9	0.83	At3g42070	823176	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.60	75.7	0.83	At1g31100	3766864	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.54	69.5	0.82	At2g15540	3768274	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.53	68.6	0.82	At1g24640	3766791	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.50	65.3	0.80	At2g20460	3767852	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.50	65.3	0.79	At4g03870	3770320	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.49	63.5	0.83	At2g07240	815294	cysteine-type peptidase	F:cysteine-type peptidase activity;P:proteolysis;C:cellular_component unknown;POFMBV	O.I.	H.G.	S.X.
0.49	63.5	0.80	At5g28860	833005	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.48	62.5	0.80	At2g16000	3768393	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.48	62.5	0.80	At2g16110	3768127	-	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.47	61.2	0.80	At2g13940	3768461	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.43	55.3	0.80	At3g31920	3769214	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.42	53.9	0.79	At2g05200	3768310	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.42	53.9	0.82	At3g26614	3768945	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.40	50.8	0.84	At3g22870	821859	F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO	O.I.	H.G.	S.X.
0.37	45.0	0.79	At4g08730	826442	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMF	O.I.	H.G.	S.X.
0.36	43.6	0.86	At3g46360	823782	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.34	39.8	0.85	At4g14820	827139	pentatricopeptide (PPR) repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFMB	O.I.	H.G.	S.X.
0.33	38.1	0.82	At2g07070	815276	transposable element gene	pseudogene of unknown protein	O.I.	H.G.	S.X.
0.28	30.3	0.82	At1g19930	838582	kelch repeat-containing F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMBOVA	O.I.	H.G.	S.X.
0.25	22.6	0.82	At4g17450	3770187	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
76.1 99.9 GSM184905 Arabidopsis, root cells, protophloem, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
73.1 99.9 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
70.4 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
69.7 99.9 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
67.8 99.9 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
67.1 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
64.1 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
63.9 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.7 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
62.9 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
62.7 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
62.6 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
60.6 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
59.6 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
59.1 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
58.7 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.8 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.2 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.8 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.3 99.8 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
49.2 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
47.6 99.8 GSM184904 Arabidopsis, root cells, protophloem, standard conditions, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
45.5 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
45.1 99.8 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
42.1 99.8 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
41.0 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
40.1 99.8 E-MEXP-1443-raw-cel-1581869515
39.6 99.8 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
39.4 99.8 GSM184906 Arabidopsis, root cells, protophloem, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
34.5 99.7 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
31.2 99.7 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.7 99.6 GSM184923 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
24.2 99.6 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
23.4 99.6 E-MEXP-1443-raw-cel-1581869573
15.8 99.5 GSM142751 MJ001_ATH1_A2-jones-WT2 GSE6165 The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
15.3 99.4 GSM142750 MJ001_ATH1_A1-jones-WT1 GSE6165 The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
13.1 99.4 GSM184924 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
11.5 99.3 GSM142754 MJ001_ATH1_A5-jones-WT-Rep3 GSE6165 The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
11.4 99.3 GSM184922 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
10.5 99.2 GSM131589 ATGE_35_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
10.5 99.2 GSM131588 ATGE_35_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
9.7 99.1 GSM131590 ATGE_35_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
9.2 99.1 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.0 99.1 GSM226538 L8SB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
76.1	99.9	GSM184905	Arabidopsis, root cells, protophloem, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
73.1	99.9	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
70.4	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
69.7	99.9	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
67.8	99.9	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
67.1	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
64.1	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
63.9	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.7	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
62.9	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
62.7	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
62.6	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
60.6	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
59.6	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
59.1	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
58.7	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.8	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.2	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.8	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.3	99.8	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
49.2	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
47.6	99.8	GSM184904	Arabidopsis, root cells, protophloem, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
45.5	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
45.1	99.8	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
42.1	99.8	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
41.0	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
40.1	99.8	E-MEXP-1443-raw-cel-1581869515
39.6	99.8	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
39.4	99.8	GSM184906	Arabidopsis, root cells, protophloem, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
34.5	99.7	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
31.2	99.7	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.7	99.6	GSM184923	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
24.2	99.6	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
23.4	99.6	E-MEXP-1443-raw-cel-1581869573
15.8	99.5	GSM142751	MJ001_ATH1_A2-jones-WT2	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
15.3	99.4	GSM142750	MJ001_ATH1_A1-jones-WT1	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
13.1	99.4	GSM184924	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
11.5	99.3	GSM142754	MJ001_ATH1_A5-jones-WT-Rep3	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
11.4	99.3	GSM184922	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
10.5	99.2	GSM131589	ATGE_35_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
10.5	99.2	GSM131588	ATGE_35_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.7	99.1	GSM131590	ATGE_35_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.2	99.1	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.0	99.1	GSM226538	L8SB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function

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	At1g43920
Gene name	transposable element gene
Module size	22 genes
NF	0.44
%ile	61.5

Co-expression analysis

Gene ID At1g43920 Gene name transposable element gene Module size 22 genes NF 0.44 %ile 61.5

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

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 At1g43920

Gene name transposable element gene

Module size 22 genes

NF 0.44

%ile 61.5

: 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