CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At2g16990

Gene name tetracycline transporter

Module size 5 genes

NF 0.12

%ile 8.4

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
0.22 17.5 1.00 At2g16990 816202 tetracycline transporter F:tetracycline transporter activity;P:unknown;C:endomembrane system;BOMPFA O.I. H.G. S.X.
0.46 59.8 0.69 At5g15190 831371 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P O.I. H.G. S.X.
0.33 38.1 0.72 At4g16750 827379 DRE-binding transcription factor, putative encodes a member of the DREB subfamily A-4 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 17 members in this subfamily including TINY. O.I. H.G. S.X.
0.07 1.9 0.67 At4g24010 828501 ATCSLG1 encodes a protein similar to cellulose synthase O.I. H.G. S.X.
0.07 1.9 0.67 At5g01520 831747 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:unknown;MOPVF O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.22	17.5	1.00	At2g16990	816202	tetracycline transporter	F:tetracycline transporter activity;P:unknown;C:endomembrane system;BOMPFA	O.I.	H.G.	S.X.
0.46	59.8	0.69	At5g15190	831371	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	O.I.	H.G.	S.X.
0.33	38.1	0.72	At4g16750	827379	DRE-binding transcription factor, putative	encodes a member of the DREB subfamily A-4 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 17 members in this subfamily including TINY.	O.I.	H.G.	S.X.
0.07	1.9	0.67	At4g24010	828501	ATCSLG1	encodes a protein similar to cellulose synthase	O.I.	H.G.	S.X.
0.07	1.9	0.67	At5g01520	831747	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:unknown;MOPVF	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
161.6 99.9 GSM106914 opr3_JA_8 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
128.3 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
121.7 99.9 GSM106912 opr3_JA 8hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
109.3 99.9 GSM106913 opr3_JA_8 hrs_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
75.0 99.9 GSM311295 Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
55.5 99.8 GSM131591 ATGE_36_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
54.2 99.8 GSM184922 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
53.0 99.8 GSM131593 ATGE_36_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
52.3 99.8 GSM311296 Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 2 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
47.2 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
40.0 99.8 GSM10480 lec1-1 Cotyledon Stage Seed 2 GSE1051 Seed development in LEAFY COTYLEDON1 mutants
36.2 99.7 GSM131689 ATGE_77_E GSE5634 AtGenExpress: Developmental series (siliques and seeds)
33.1 99.7 GSM67087 Arabidopsis_Stigma03 GSE3056 Arabidopsis Pollination Study
32.7 99.7 GSM10479 lec1-1 Cotyledon Stage Seed 1 GSE1051 Seed development in LEAFY COTYLEDON1 mutants
32.1 99.7 GSM67086 Arabidopsis_Stigma02 GSE3056 Arabidopsis Pollination Study
31.5 99.7 GSM147966 lec1-1 Globular Stage Seed 2 GSE1051 Seed development in LEAFY COTYLEDON1 mutants
31.1 99.7 GSM131592 ATGE_36_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
30.9 99.7 GSM131690 ATGE_77_F GSE5634 AtGenExpress: Developmental series (siliques and seeds)
30.2 99.7 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
29.6 99.7 E-MEXP-285-raw-cel-440783152
28.6 99.7 GSM131688 ATGE_77_D GSE5634 AtGenExpress: Developmental series (siliques and seeds)
28.3 99.7 GSM147963 WT Globular Stage Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
27.1 99.7 GSM10448 WT Cotyledon Stage Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
27.1 99.7 GSM10449 WT Cotyledon Stage Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
26.8 99.7 GSM147965 lec1-1 Globular Stage Seed 1 GSE1051 Seed development in LEAFY COTYLEDON1 mutants
26.4 99.7 GSM147964 WT Globular Stage Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
24.1 99.6 GSM106915 opr3_JA_22 hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
23.9 99.6 E-MEXP-285-raw-cel-440783213
23.4 99.6 E-ATMX-33-raw-cel-1562596197
21.9 99.6 E-ATMX-33-raw-cel-1562596241
21.4 99.6 GSM106917 opr3_JA_22 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
21.2 99.6 GSM284398 Arabidopsis GGSc2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
20.1 99.6 GSM311293 Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
18.9 99.5 GSM142736 DH001_ATH1_A3-TCP1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
18.7 99.5 GSM142739 DH001_ATH1_A6-TCP2 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
18.2 99.5 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.3 99.5 GSM106911 opr2_JA_2 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
16.7 99.5 GSM131691 ATGE_78_D GSE5634 AtGenExpress: Developmental series (siliques and seeds)
15.3 99.4 GSM106973 ws_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
13.2 99.4 GSM131692 ATGE_78_E GSE5634 AtGenExpress: Developmental series (siliques and seeds)
12.1 99.3 GSM131693 ATGE_78_F GSE5634 AtGenExpress: Developmental series (siliques and seeds)
10.5 99.2 E-MEXP-1592-raw-cel-1617526832
10.5 99.2 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.5 99.2 GSM239252 Columbia glabrous (C24) wild type stamen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
10.0 99.2 E-ATMX-33-raw-cel-1562596103
10.0 99.2 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.9 99.1 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.7 99.1 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.4 99.1 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.3 99.1 GSM106910 opr3_JA_2 hrs_rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.2 99.1 E-MEXP-1138-raw-cel-1432773258
9.2 99.1 GSM131299 AtGen_6-2511_Osmoticstress-Shoots-12.0h_Rep1 GSE5622 AtGenExpress: Stress Treatments (Osmotic stress)
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
161.6	99.9	GSM106914	opr3_JA_8 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
128.3	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
121.7	99.9	GSM106912	opr3_JA 8hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
109.3	99.9	GSM106913	opr3_JA_8 hrs_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
75.0	99.9	GSM311295	Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
55.5	99.8	GSM131591	ATGE_36_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
54.2	99.8	GSM184922	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
53.0	99.8	GSM131593	ATGE_36_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
52.3	99.8	GSM311296	Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
47.2	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
40.0	99.8	GSM10480	lec1-1 Cotyledon Stage Seed 2	GSE1051	Seed development in LEAFY COTYLEDON1 mutants
36.2	99.7	GSM131689	ATGE_77_E	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
33.1	99.7	GSM67087	Arabidopsis_Stigma03	GSE3056	Arabidopsis Pollination Study
32.7	99.7	GSM10479	lec1-1 Cotyledon Stage Seed 1	GSE1051	Seed development in LEAFY COTYLEDON1 mutants
32.1	99.7	GSM67086	Arabidopsis_Stigma02	GSE3056	Arabidopsis Pollination Study
31.5	99.7	GSM147966	lec1-1 Globular Stage Seed 2	GSE1051	Seed development in LEAFY COTYLEDON1 mutants
31.1	99.7	GSM131592	ATGE_36_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
30.9	99.7	GSM131690	ATGE_77_F	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
30.2	99.7	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
29.6	99.7	E-MEXP-285-raw-cel-440783152
28.6	99.7	GSM131688	ATGE_77_D	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
28.3	99.7	GSM147963	WT Globular Stage Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
27.1	99.7	GSM10448	WT Cotyledon Stage Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
27.1	99.7	GSM10449	WT Cotyledon Stage Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
26.8	99.7	GSM147965	lec1-1 Globular Stage Seed 1	GSE1051	Seed development in LEAFY COTYLEDON1 mutants
26.4	99.7	GSM147964	WT Globular Stage Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
24.1	99.6	GSM106915	opr3_JA_22 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
23.9	99.6	E-MEXP-285-raw-cel-440783213
23.4	99.6	E-ATMX-33-raw-cel-1562596197
21.9	99.6	E-ATMX-33-raw-cel-1562596241
21.4	99.6	GSM106917	opr3_JA_22 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
21.2	99.6	GSM284398	Arabidopsis GGSc2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
20.1	99.6	GSM311293	Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
18.9	99.5	GSM142736	DH001_ATH1_A3-TCP1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
18.7	99.5	GSM142739	DH001_ATH1_A6-TCP2	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
18.2	99.5	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.3	99.5	GSM106911	opr2_JA_2 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
16.7	99.5	GSM131691	ATGE_78_D	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
15.3	99.4	GSM106973	ws_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
13.2	99.4	GSM131692	ATGE_78_E	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
12.1	99.3	GSM131693	ATGE_78_F	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
10.5	99.2	E-MEXP-1592-raw-cel-1617526832
10.5	99.2	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.5	99.2	GSM239252	Columbia glabrous (C24) wild type stamen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
10.0	99.2	E-ATMX-33-raw-cel-1562596103
10.0	99.2	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.9	99.1	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.7	99.1	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.4	99.1	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.3	99.1	GSM106910	opr3_JA_2 hrs_rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.2	99.1	E-MEXP-1138-raw-cel-1432773258
9.2	99.1	GSM131299	AtGen_6-2511_Osmoticstress-Shoots-12.0h_Rep1	GSE5622	AtGenExpress: Stress Treatments (Osmotic stress)
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
0.083 1 GO:0000271 The chemical reactions and pathways resulting in the formation of polysaccharides, polymers of more than 10 monosaccharide residues joined by glycosidic linkages.
0.061 1 GO:0030244 The chemical reactions and pathways resulting in the formation of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
0.013 1 GO:0007275 The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).

SF	Genes	GO ID	Process Name
0.083	1	GO:0000271	The chemical reactions and pathways resulting in the formation of polysaccharides, polymers of more than 10 monosaccharide residues joined by glycosidic linkages.
0.061	1	GO:0030244	The chemical reactions and pathways resulting in the formation of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
0.013	1	GO:0007275	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).

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

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Gene ID	At2g16990
Gene name	tetracycline transporter
Module size	5 genes
NF	0.12
%ile	8.4

Co-expression analysis

Gene ID At2g16990 Gene name tetracycline transporter Module size 5 genes NF 0.12 %ile 8.4

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 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 At2g16990

Gene name tetracycline transporter

Module size 5 genes

NF 0.12

%ile 8.4

: 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