CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At2g11165

Gene name transposable element gene

Module size 7 genes

NF 0.69

%ile 88.4

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
0.71 84.2 1.00 At2g11165 3768074 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.92 96.0 0.90 At3g30846 3769163 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.83 91.4 0.89 At5g28950 833021 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMF O.I. H.G. S.X.
0.67 81.6 0.88 At1g29480 839825 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OBP O.I. H.G. S.X.
0.63 78.1 0.93 At5g34895 833430 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.59 74.7 0.89 At1g36670 840575 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.55 70.6 0.90 At3g47270 823880 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.
0.71	84.2	1.00	At2g11165	3768074	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.92	96.0	0.90	At3g30846	3769163	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.83	91.4	0.89	At5g28950	833021	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMF	O.I.	H.G.	S.X.
0.67	81.6	0.88	At1g29480	839825	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OBP	O.I.	H.G.	S.X.
0.63	78.1	0.93	At5g34895	833430	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.59	74.7	0.89	At1g36670	840575	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.55	70.6	0.90	At3g47270	823880	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.
0.61	76.7	0.84	At4g07450	826178	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.61	76.7	0.86	At2g28755	817425	UDP-D-glucuronate carboxy-lyase-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BOPMFA	O.I.	H.G.	S.X.
0.59	74.7	0.80	At2g04063	814941	glycine-rich protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PMBO	O.I.	H.G.	S.X.
0.57	73.8	0.82	At2g15450	816037	glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein	F:polygalacturonase activity;P:carbohydrate metabolic process;C:endomembrane system;FPBOMA	O.I.	H.G.	S.X.
0.56	73.0	0.78	At2g02210	3767940	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.53	68.6	0.85	At5g46440	834687	-	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	H.G.	S.X.
0.50	65.3	0.88	At2g02200	3768149	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.50	65.3	0.84	At1g66790	842997	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	0.79	At2g13890	3768362	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.50	65.3	0.78	At5g37420	833718	AGL105	F:transcription factor activity;P:biological_process unknown;C:cellular_component unknown;OMFBPVA	O.I.	H.G.	S.X.
0.47	61.2	0.80	At2g11150	3768073	transposable element gene	pseudogene of putative replication protein A1	O.I.	H.G.	S.X.
0.46	59.8	0.85	At1g48800	841302	terpene synthase/cyclase family protein	F:lyase activity, magnesium ion binding;P:metabolic process;C:unknown;PO	O.I.	H.G.	S.X.
0.44	57.2	0.75	At2g06390	815197	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.44	57.2	0.67	At2g16040	816101	hAT dimerisation domain-containing protein / transposase-related	F:protein dimerization activity;P:biological_process unknown;C:cellular_component unknown;MPO	O.I.	H.G.	S.X.
0.44	57.2	0.78	At1g32840	840178	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.43	55.3	0.88	At3g31910	822931	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBOMF	O.I.	H.G.	S.X.
0.41	52.4	0.88	At1g54430	841885	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.40	50.8	0.89	At3g30450	822756	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.40	50.8	0.85	At3g30200	822713	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.40	50.8	0.83	At3g04390	819594	xanthine dehydrogenase family protein	F:electron carrier activity, oxidoreductase activity, catalytic activity;P:biological_process unknown;C:endomembrane system;MOBFP	O.I.	H.G.	S.X.
0.38	46.7	0.85	At3g30730	822811	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.38	46.7	0.78	At4g11745	826780	kelch repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOBA	O.I.	H.G.	S.X.
0.37	45.0	0.76	At3g32900	823050	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.36	43.6	0.82	At3g61720	825345	C2 domain-containing protein	F:unknown;P:tryptophan biosynthetic process;C:unknown;PMOF	O.I.	H.G.	S.X.
0.36	43.6	0.73	At2g14130	815899	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.35	41.6	0.82	At5g30440	3770957	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.35	41.6	0.79	At1g68420	843171	asparaginyl-tRNA synthetase-related	F:nucleotide binding, aminoacyl-tRNA ligase activity, ATP binding;P:translation, tRNA aminoacylation for protein translation;C:cytoplasm;BOMFAP	O.I.	H.G.	S.X.
0.33	38.1	0.86	At4g05580	825912	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.33	38.1	0.83	At4g15710	827248	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.31	33.8	0.81	At1g35663	840469	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.29	30.3	0.80	At5g49640	835026	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.29	30.3	0.79	At4g15870	827268	ATTS1	encodes a putative terpene synthase	O.I.	H.G.	S.X.
0.29	30.3	0.76	At1g17390	838311	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.27	26.2	0.81	At2g13960	815880	myb family transcription factor	F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent, regulation of transcription;C:chloroplast;OMPFV	O.I.	H.G.	S.X.
0.27	26.2	0.74	At5g34900	833431	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.27	26.2	0.71	At1g10420		-	-	O.I.	H.G.	S.X.
0.27	26.2	0.70	At4g08190	826369	Ras-related GTP-binding protein, putative	F:GTP binding;P:small GTPase mediated signal transduction;C:cellular_component unknown;MPOF	O.I.	H.G.	S.X.
0.26	24.4	0.84	At5g35240	3771259	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.26	24.4	0.74	At5g35880	833574	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.25	22.6	0.85	At5g26890	832747	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown	O.I.	H.G.	S.X.
0.25	22.6	0.75	At3g43160	823389	MEE38 (maternal effect embryo arrest 38)	F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;OPF	O.I.	H.G.	S.X.
0.25	22.6	0.74	At3g20760	821624	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;FMPOB	O.I.	H.G.	S.X.
0.25	22.6	0.84	At4g08140	826362	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOP	O.I.	H.G.	S.X.

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
66.7 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
56.4 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
42.8 99.8 E-MEXP-1443-raw-cel-1581869515
41.7 99.8 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
27.4 99.7 E-MEXP-1443-raw-cel-1581869745
27.3 99.7 E-MEXP-1443-raw-cel-1581869803
20.5 99.6 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
20.1 99.6 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
19.8 99.6 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.7 99.6 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.9 99.5 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.9 99.5 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.6 99.5 E-MEXP-449-raw-cel-676423362
18.2 99.5 E-MEXP-98-raw-cel-320188914
17.9 99.5 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.6 99.5 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.4 99.5 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.3 99.5 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.0 99.5 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.3 99.5 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
16.1 99.5 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
15.5 99.5 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
15.2 99.4 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.2 99.4 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.0 99.4 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
14.4 99.4 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.4 99.4 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
13.2 99.4 GSM184910 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
13.2 99.4 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.4 99.3 GSM134316 Penfield_1-18_embryo-PAC_Rep3_ATH1 GSE5751 The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
11.0 99.2 GSM184911 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
10.9 99.2 GSM133303 RIKEN-NAKABAYASHI1A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
10.1 99.2 E-MEXP-1725-raw-cel-1669614634
10.0 99.2 GSM74904 ice1_3H Cold_Rep1 GSE3326 ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome
8.9 99.0 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
66.7	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
56.4	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
42.8	99.8	E-MEXP-1443-raw-cel-1581869515
41.7	99.8	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
27.4	99.7	E-MEXP-1443-raw-cel-1581869745
27.3	99.7	E-MEXP-1443-raw-cel-1581869803
20.5	99.6	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
20.1	99.6	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
19.8	99.6	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.7	99.6	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.9	99.5	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.9	99.5	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.6	99.5	E-MEXP-449-raw-cel-676423362
18.2	99.5	E-MEXP-98-raw-cel-320188914
17.9	99.5	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.6	99.5	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.4	99.5	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.3	99.5	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.0	99.5	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.3	99.5	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.1	99.5	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.5	99.5	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.2	99.4	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.2	99.4	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.0	99.4	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
14.4	99.4	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.4	99.4	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
13.2	99.4	GSM184910	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
13.2	99.4	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.4	99.3	GSM134316	Penfield_1-18_embryo-PAC_Rep3_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
11.0	99.2	GSM184911	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
10.9	99.2	GSM133303	RIKEN-NAKABAYASHI1A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
10.1	99.2	E-MEXP-1725-raw-cel-1669614634
10.0	99.2	GSM74904	ice1_3H Cold_Rep1	GSE3326	ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome
8.9	99.0	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition

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	At2g11165
Gene name	transposable element gene
Module size	7 genes
NF	0.69
%ile	88.4

Co-expression analysis

Gene ID At2g11165 Gene name transposable element gene Module size 7 genes NF 0.69 %ile 88.4

Co-expression network

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

Co-expressed 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 At2g11165

Gene name transposable element gene

Module size 7 genes

NF 0.69

%ile 88.4

: 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