CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g24460

Gene name TMS membrane family protein / tumour differentially expressed (TDE) family protein

Module size 6 genes

NF 0.02

%ile 1.0

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 At3g24460 822036 TMS membrane family protein / tumour differentially expressed (TDE) family protein F:unknown;P:unknown;C:membrane;MFPO O.I. H.G. S.X.
0.29 30.3 0.70 At3g16175 820863 thioesterase family protein F:hydrolase activity, acting on ester bonds, acyl-CoA thioesterase activity;P:biological_process unknown;C:cellular_component unknown;PMBFO O.I. H.G. S.X.
0.04 0.9 0.67 At1g66840 843002 - F:unknown;P:biological_process unknown;C:unknown;MOBFPAV O.I. H.G. S.X.
0.04 0.9 0.69 At5g01260 831794 glycoside hydrolase starch-binding domain-containing protein F:carbohydrate binding, catalytic activity;P:carbohydrate metabolic process;C:cellular_component unknown;BPFOM O.I. H.G. S.X.
0.02 0.4 0.68 At1g05690 837076 BT3 (BTB AND TAZ DOMAIN PROTEIN 3) BTB and TAZ domain protein. Acts redunantly with BT1 and BT2 during female gametophyte development. Acts with BT2 during male gametophyte development. O.I. H.G. S.X.
- 0.0 0.68 At2g19280 816445 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:biological_process unknown;C:unknown;POMFBA 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	At3g24460	822036	TMS membrane family protein / tumour differentially expressed (TDE) family protein	F:unknown;P:unknown;C:membrane;MFPO	O.I.	H.G.	S.X.
0.29	30.3	0.70	At3g16175	820863	thioesterase family protein	F:hydrolase activity, acting on ester bonds, acyl-CoA thioesterase activity;P:biological_process unknown;C:cellular_component unknown;PMBFO	O.I.	H.G.	S.X.
0.04	0.9	0.67	At1g66840	843002	-	F:unknown;P:biological_process unknown;C:unknown;MOBFPAV	O.I.	H.G.	S.X.
0.04	0.9	0.69	At5g01260	831794	glycoside hydrolase starch-binding domain-containing protein	F:carbohydrate binding, catalytic activity;P:carbohydrate metabolic process;C:cellular_component unknown;BPFOM	O.I.	H.G.	S.X.
0.02	0.4	0.68	At1g05690	837076	BT3 (BTB AND TAZ DOMAIN PROTEIN 3)	BTB and TAZ domain protein. Acts redunantly with BT1 and BT2 during female gametophyte development. Acts with BT2 during male gametophyte development.	O.I.	H.G.	S.X.
-	0.0	0.68	At2g19280	816445	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:biological_process unknown;C:unknown;POMFBA	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
63.8 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
60.1 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.0 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
55.6 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
54.5 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
51.9 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.2 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.9 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.6 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.3 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.1 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.1 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
41.9 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
38.3 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.1 99.7 GSM133774 Lindsey_1-26_torpedo-meristem_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
34.0 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.8 99.7 GSM13784 Cycloheximide - replicate GSE911 Identification of LEAFY targets during reproductive transition
31.1 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
30.4 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.5 99.6 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
21.3 99.6 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
20.1 99.6 GSM13779 Dexamethasone plus cycloheximide GSE911 Identification of LEAFY targets during reproductive transition
19.0 99.5 E-MEXP-546-raw-cel-863289532
19.0 99.5 GSM142839 MG001_ATH1_A18-Torres-6N6 GSE6176 Impact of Type III effectors on plant defense responses
16.0 99.5 GSM133773 Lindsey_1-25_torpedo-meristem_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.6 99.5 E-ATMX-35-raw-cel-1574334832
15.4 99.5 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
15.3 99.4 E-MEXP-546-raw-cel-863289424
15.1 99.4 GSM13783 Dexamethasone plus cycloheximide - replicate GSE911 Identification of LEAFY targets during reproductive transition
14.1 99.4 GSM142837 MG001_ATH1_A16-Torres-6N1 GSE6176 Impact of Type III effectors on plant defense responses
14.0 99.4 GSM311282 Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
13.6 99.4 GSM133117 RIKEN-YAMAUCHI1A GSE5687 AtGenExpress: Different temperature treatment of seeds
13.2 99.4 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.4 99.3 E-MEXP-807-raw-cel-1173273252
11.1 99.2 E-MEXP-807-raw-cel-1173273144
11.0 99.2 GSM13780 Cycloheximide GSE911 Identification of LEAFY targets during reproductive transition
10.9 99.2 GSM173442 wild-type Arabidopsis, biological rep1 GSE7211 A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana
10.3 99.2 GSM284387 Arabidopsis GSUS4b GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
10.2 99.2 GSM133765 Lindsey_1-17_torpedo-cotyledon_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.0 99.2 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
9.8 99.1 GSM173447 oxt6 mutant, biological rep3 GSE7211 A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana
9.5 99.1 GSM173446 oxt6 mutant, biological rep2 GSE7211 A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana
8.8 99.0 GSM173445 oxt6 mutant, biological rep1 GSE7211 A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
63.8	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
60.1	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.0	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
55.6	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
54.5	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
51.9	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.2	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.9	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.6	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.3	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.1	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.1	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
41.9	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
38.3	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.1	99.7	GSM133774	Lindsey_1-26_torpedo-meristem_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
34.0	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.8	99.7	GSM13784	Cycloheximide - replicate	GSE911	Identification of LEAFY targets during reproductive transition
31.1	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
30.4	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.5	99.6	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
21.3	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
20.1	99.6	GSM13779	Dexamethasone plus cycloheximide	GSE911	Identification of LEAFY targets during reproductive transition
19.0	99.5	E-MEXP-546-raw-cel-863289532
19.0	99.5	GSM142839	MG001_ATH1_A18-Torres-6N6	GSE6176	Impact of Type III effectors on plant defense responses
16.0	99.5	GSM133773	Lindsey_1-25_torpedo-meristem_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.6	99.5	E-ATMX-35-raw-cel-1574334832
15.4	99.5	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
15.3	99.4	E-MEXP-546-raw-cel-863289424
15.1	99.4	GSM13783	Dexamethasone plus cycloheximide - replicate	GSE911	Identification of LEAFY targets during reproductive transition
14.1	99.4	GSM142837	MG001_ATH1_A16-Torres-6N1	GSE6176	Impact of Type III effectors on plant defense responses
14.0	99.4	GSM311282	Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
13.6	99.4	GSM133117	RIKEN-YAMAUCHI1A	GSE5687	AtGenExpress: Different temperature treatment of seeds
13.2	99.4	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.4	99.3	E-MEXP-807-raw-cel-1173273252
11.1	99.2	E-MEXP-807-raw-cel-1173273144
11.0	99.2	GSM13780	Cycloheximide	GSE911	Identification of LEAFY targets during reproductive transition
10.9	99.2	GSM173442	wild-type Arabidopsis, biological rep1	GSE7211	A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana
10.3	99.2	GSM284387	Arabidopsis GSUS4b	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
10.2	99.2	GSM133765	Lindsey_1-17_torpedo-cotyledon_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.0	99.2	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
9.8	99.1	GSM173447	oxt6 mutant, biological rep3	GSE7211	A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana
9.5	99.1	GSM173446	oxt6 mutant, biological rep2	GSE7211	A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana
8.8	99.0	GSM173445	oxt6 mutant, biological rep1	GSE7211	A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.048 1 GO:0009553 The process whose specific outcome is the progression of the embryo sac over time, from its formation to the mature structure. The process begins with the meiosis of the megasporocyte to form four haploid megaspores. Three of the 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. The two polar nuclei fuse resulting in a mononucleate diploid endosperm mother cell. The three antipodal cells degenerate.
0.025 1 GO:0009555 The process whose specific outcome is the progression of the pollen grain over time, from its formation to the mature structure. The process begins with the meiosis of the microsporocyte to form four haploid microspores. The nucleus of each microspore then divides by mitosis to form a two-celled organism, the pollen grain, that contains a tube cell as well as a smaller generative cell. The pollen grain is surrounded by an elaborate cell wall. In some species, the generative cell immediately divides again to give a pair of sperm cells. In most flowering plants, however this division takes place later, in the tube that develops when a pollen grain germinates.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.048	1	GO:0009553	The process whose specific outcome is the progression of the embryo sac over time, from its formation to the mature structure. The process begins with the meiosis of the megasporocyte to form four haploid megaspores. Three of the 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. The two polar nuclei fuse resulting in a mononucleate diploid endosperm mother cell. The three antipodal cells degenerate.
0.025	1	GO:0009555	The process whose specific outcome is the progression of the pollen grain over time, from its formation to the mature structure. The process begins with the meiosis of the microsporocyte to form four haploid microspores. The nucleus of each microspore then divides by mitosis to form a two-celled organism, the pollen grain, that contains a tube cell as well as a smaller generative cell. The pollen grain is surrounded by an elaborate cell wall. In some species, the generative cell immediately divides again to give a pair of sperm cells. In most flowering plants, however this division takes place later, in the tube that develops when a pollen grain germinates.

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	At3g24460
Gene name	TMS membrane family protein / tumour differentially expressed (TDE) family protein
Module size	6 genes
NF	0.02
%ile	1.0

Co-expression analysis

Gene ID At3g24460 Gene name TMS membrane family protein / tumour differentially expressed (TDE) family protein Module size 6 genes NF 0.02 %ile 1.0

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 At3g24460

Gene name TMS membrane family protein / tumour differentially expressed (TDE) family protein

Module size 6 genes

NF 0.02

%ile 1.0

: 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