CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At2g10050

Gene name transposable element gene

Module size 34 genes

NF 0.70

%ile 89.1

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
0.78 88.6 1.00 At2g10050 815462 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.85 92.4 0.97 At1g43970 840996 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;PO O.I. H.G. S.X.
0.81 90.4 0.97 At4g04560 3769781 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.81 90.4 0.96 At2g19840 3768331 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.80 89.8 0.97 At3g42120 823184 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.79 89.1 0.97 At1g32590 3766881 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.79 89.1 0.96 At4g07750 3769978 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.79 89.1 0.97 At2g14570 815944 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.78 88.6 0.98 At2g13930 3768460 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.77 88.0 0.96 At3g28870 822521 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOFB O.I. H.G. S.X.
0.77 88.0 0.97 At1g36600 3767017 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.76 87.4 0.96 At2g21460 3768354 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.76 87.4 0.96 At2g07510 3768270 transposable element gene pseudogene of Ulp1 protease family protein O.I. H.G. S.X.
0.76 87.4 0.97 At2g14590 815946 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.75 86.9 0.98 At1g47816 3767392 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.73 85.5 0.97 At5g35820 3771306 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.72 84.8 0.96 At1g67240 3767657 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.70 83.5 0.96 At4g04590 3770515 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.69 82.9 0.97 At2g10900 3768617 transposable element gene similarity to non-LTR retroelement protein O.I. H.G. S.X.
0.69 82.9 0.96 At2g14350 3768589 transposable element gene pseudogene of unknown protein O.I. H.G. S.X.
0.68 82.2 0.96 At3g45520 3769652 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.67 81.6 0.96 At3g27980 822422 pectinesterase family protein F:pectinesterase activity;P:cell wall modification;C:membrane, plant-type cell wall;PBFM O.I. H.G. S.X.
0.66 80.1 0.97 At2g07740 815421 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.65 79.6 0.97 At3g27800 822400 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.64 78.9 0.97 At3g44270 3769630 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.64 78.9 0.96 At4g08970 3769794 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.64 78.9 0.97 At1g37080 840625 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.64 78.9 0.96 At2g13270 815813 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.63 78.1 0.97 At2g14950 3768119 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.62 77.3 0.96 At1g35995 3766969 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.61 76.7 0.96 At2g07330 3767907 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.59 74.7 0.97 At2g07505 815323 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.55 70.6 0.96 At2g14930 3768116 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.55 70.6 0.96 At2g05960 3768174 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.
0.78	88.6	1.00	At2g10050	815462	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.85	92.4	0.97	At1g43970	840996	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;PO	O.I.	H.G.	S.X.
0.81	90.4	0.97	At4g04560	3769781	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.81	90.4	0.96	At2g19840	3768331	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.80	89.8	0.97	At3g42120	823184	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.79	89.1	0.97	At1g32590	3766881	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.79	89.1	0.96	At4g07750	3769978	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.79	89.1	0.97	At2g14570	815944	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.78	88.6	0.98	At2g13930	3768460	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.77	88.0	0.96	At3g28870	822521	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOFB	O.I.	H.G.	S.X.
0.77	88.0	0.97	At1g36600	3767017	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.76	87.4	0.96	At2g21460	3768354	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.76	87.4	0.96	At2g07510	3768270	transposable element gene	pseudogene of Ulp1 protease family protein	O.I.	H.G.	S.X.
0.76	87.4	0.97	At2g14590	815946	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.75	86.9	0.98	At1g47816	3767392	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.73	85.5	0.97	At5g35820	3771306	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.72	84.8	0.96	At1g67240	3767657	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.70	83.5	0.96	At4g04590	3770515	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.69	82.9	0.97	At2g10900	3768617	transposable element gene	similarity to non-LTR retroelement protein	O.I.	H.G.	S.X.
0.69	82.9	0.96	At2g14350	3768589	transposable element gene	pseudogene of unknown protein	O.I.	H.G.	S.X.
0.68	82.2	0.96	At3g45520	3769652	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.67	81.6	0.96	At3g27980	822422	pectinesterase family protein	F:pectinesterase activity;P:cell wall modification;C:membrane, plant-type cell wall;PBFM	O.I.	H.G.	S.X.
0.66	80.1	0.97	At2g07740	815421	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.65	79.6	0.97	At3g27800	822400	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.64	78.9	0.97	At3g44270	3769630	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.64	78.9	0.96	At4g08970	3769794	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.64	78.9	0.97	At1g37080	840625	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.64	78.9	0.96	At2g13270	815813	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.63	78.1	0.97	At2g14950	3768119	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.62	77.3	0.96	At1g35995	3766969	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.61	76.7	0.96	At2g07330	3767907	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.59	74.7	0.97	At2g07505	815323	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.55	70.6	0.96	At2g14930	3768116	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.55	70.6	0.96	At2g05960	3768174	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
75.6 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
44.1 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.3 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.0 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.9 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.7 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.3 99.7 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.9 99.7 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
35.9 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.2 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.5 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
34.4 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.8 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.3 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.3 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.5 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
29.8 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
29.3 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
29.0 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
28.4 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
21.4 99.6 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
21.1 99.6 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
20.9 99.6 GSM184906 Arabidopsis, root cells, protophloem, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
19.0 99.5 GSM184905 Arabidopsis, root cells, protophloem, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
18.5 99.5 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.5 99.4 GSM184520 Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
14.4 99.4 GSM184904 Arabidopsis, root cells, protophloem, standard conditions, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
14.1 99.4 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
13.5 99.4 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
10.3 99.2 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.2 99.2 GSM67087 Arabidopsis_Stigma03 GSE3056 Arabidopsis Pollination Study
10.1 99.2 GSM133303 RIKEN-NAKABAYASHI1A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
9.1 99.1 GSM184923 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
75.6	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
44.1	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.3	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.0	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.9	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.7	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.3	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.9	99.7	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.9	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.2	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.5	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
34.4	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.8	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.3	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.3	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.5	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
29.8	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
29.3	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
29.0	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
28.4	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.4	99.6	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
21.1	99.6	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
20.9	99.6	GSM184906	Arabidopsis, root cells, protophloem, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
19.0	99.5	GSM184905	Arabidopsis, root cells, protophloem, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
18.5	99.5	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.5	99.4	GSM184520	Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
14.4	99.4	GSM184904	Arabidopsis, root cells, protophloem, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
14.1	99.4	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
13.5	99.4	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
10.3	99.2	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.2	99.2	GSM67087	Arabidopsis_Stigma03	GSE3056	Arabidopsis Pollination Study
10.1	99.2	GSM133303	RIKEN-NAKABAYASHI1A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
9.1	99.1	GSM184923	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.021 1 GO:0042545 The series of events leading to chemical and structural alterations of an existing cell wall that can result in loosening, increased extensibility or disassembly.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.021	1	GO:0042545	The series of events leading to chemical and structural alterations of an existing cell wall that can result in loosening, increased extensibility or disassembly.

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	At2g10050
Gene name	transposable element gene
Module size	34 genes
NF	0.70
%ile	89.1

Co-expression analysis

Gene ID At2g10050 Gene name transposable element gene Module size 34 genes NF 0.70 %ile 89.1

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 AmiGO0.0211GO:0042545The series of events leading to chemical and structural alterations of an existing cell wall that can result in loosening, increased extensibility or disassembly.

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 At2g10050

Gene name transposable element gene

Module size 34 genes

NF 0.70

%ile 89.1

: 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
0.021 1 GO:0042545 The series of events leading to chemical and structural alterations of an existing cell wall that can result in loosening, increased extensibility or disassembly.

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