CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g15520

Gene name PDR12 (PLEIOTROPIC DRUG RESISTANCE 12)

Module size 7 genes

NF 0.39

%ile 54.6

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 At1g15520 838122 PDR12 (PLEIOTROPIC DRUG RESISTANCE 12) ABC transporter family involved in resistant to lead. Localizes to plasma membrane. Upregulated by lead. Expressed in leaves, flowers. Not expressed in roots. O.I. H.G. S.X.
0.55 70.6 0.71 At2g30770 817628 CYP71A13 (cytochrome P450, family 71, subfamily A, polypeptide 13) putative cytochrome P450 O.I. H.G. S.X.
0.55 70.6 0.77 At3g26830 822298 PAD3 (PHYTOALEXIN DEFICIENT 3) Mutations in pad3 are defective in biosynthesis of the indole derived phytoalexin camalexin. Encodes a cytochrome P450 enzyme that catalyzes the conversion of dihydrocamalexic acid to camalexin. O.I. H.G. S.X.
0.38 46.7 0.70 At1g32960 840190 SBT3.3 F:identical protein binding, serine-type endopeptidase activity;P:proteolysis, negative regulation of catalytic activity;C:apoplast, plant-type cell wall;BPOAFM O.I. H.G. S.X.
0.35 41.6 0.72 At2g24850 817022 TAT3 (TYROSINE AMINOTRANSFERASE 3) Encodes a tyrosine aminotransferase that is responsive to treatment with jasmonic acid. O.I. H.G. S.X.
0.31 33.8 0.70 At2g29460 817495 ATGSTU4 (ARABIDOPSIS THALIANA GLUTATHIONE S-TRANSFERASE TAU 4) Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002). O.I. H.G. S.X.
0.23 19.3 0.67 At1g32940 840188 SBT3.5 F:identical protein binding, serine-type endopeptidase activity;P:proteolysis, negative regulation of catalytic activity;C:apoplast;BPOAFM 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	At1g15520	838122	PDR12 (PLEIOTROPIC DRUG RESISTANCE 12)	ABC transporter family involved in resistant to lead. Localizes to plasma membrane. Upregulated by lead. Expressed in leaves, flowers. Not expressed in roots.	O.I.	H.G.	S.X.
0.55	70.6	0.71	At2g30770	817628	CYP71A13 (cytochrome P450, family 71, subfamily A, polypeptide 13)	putative cytochrome P450	O.I.	H.G.	S.X.
0.55	70.6	0.77	At3g26830	822298	PAD3 (PHYTOALEXIN DEFICIENT 3)	Mutations in pad3 are defective in biosynthesis of the indole derived phytoalexin camalexin. Encodes a cytochrome P450 enzyme that catalyzes the conversion of dihydrocamalexic acid to camalexin.	O.I.	H.G.	S.X.
0.38	46.7	0.70	At1g32960	840190	SBT3.3	F:identical protein binding, serine-type endopeptidase activity;P:proteolysis, negative regulation of catalytic activity;C:apoplast, plant-type cell wall;BPOAFM	O.I.	H.G.	S.X.
0.35	41.6	0.72	At2g24850	817022	TAT3 (TYROSINE AMINOTRANSFERASE 3)	Encodes a tyrosine aminotransferase that is responsive to treatment with jasmonic acid.	O.I.	H.G.	S.X.
0.31	33.8	0.70	At2g29460	817495	ATGSTU4 (ARABIDOPSIS THALIANA GLUTATHIONE S-TRANSFERASE TAU 4)	Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002).	O.I.	H.G.	S.X.
0.23	19.3	0.67	At1g32940	840188	SBT3.5	F:identical protein binding, serine-type endopeptidase activity;P:proteolysis, negative regulation of catalytic activity;C:apoplast;BPOAFM	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
389.1 100.0 GSM133773 Lindsey_1-25_torpedo-meristem_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
168.4 100.0 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
154.5 99.9 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
133.0 99.9 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
122.5 99.9 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
92.2 99.9 E-ATMX-1-raw-cel-1112746209
79.0 99.9 E-ATMX-1-raw-cel-1112746267
76.7 99.9 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
72.9 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
72.3 99.9 E-ATMX-1-raw-cel-1112746154
70.1 99.9 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
69.4 99.9 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
69.3 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
69.3 99.9 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
67.5 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
66.8 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
66.7 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
66.1 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
65.8 99.8 GSM133768 Lindsey_1-20_torpedo-basal_Rep5_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
65.1 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.9 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.7 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.2 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
59.8 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.8 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
55.2 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
44.9 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
43.9 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
43.0 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
39.5 99.8 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
36.8 99.7 GSM131699 ATGE_81_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
36.4 99.7 GSM131698 ATGE_81_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
35.6 99.7 GSM131697 ATGE_81_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
27.4 99.7 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
26.6 99.7 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
19.4 99.6 GSM131700 ATGE_82_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
19.2 99.6 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
18.2 99.5 GSM131701 ATGE_82_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
17.1 99.5 GSM131702 ATGE_82_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
16.5 99.5 GSM131705 ATGE_83_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
16.4 99.5 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
16.3 99.5 GSM131707 ATGE_84_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
16.0 99.5 GSM131703 ATGE_83_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
15.6 99.5 GSM131706 ATGE_84_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
15.3 99.4 GSM265431 Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2 GSE10497 Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
14.5 99.4 GSM131704 ATGE_83_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
14.4 99.4 GSM131708 ATGE_84_D GSE5634 AtGenExpress: Developmental series (siliques and seeds)
13.4 99.4 GSM311291 Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
11.8 99.3 GSM184524 Stele root cells 2hr KCl control treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
11.4 99.3 GSM10451 WT Mature Green Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
389.1	100.0	GSM133773	Lindsey_1-25_torpedo-meristem_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
168.4	100.0	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
154.5	99.9	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
133.0	99.9	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
122.5	99.9	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
92.2	99.9	E-ATMX-1-raw-cel-1112746209
79.0	99.9	E-ATMX-1-raw-cel-1112746267
76.7	99.9	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
72.9	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
72.3	99.9	E-ATMX-1-raw-cel-1112746154
70.1	99.9	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
69.4	99.9	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
69.3	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
69.3	99.9	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
67.5	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
66.8	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
66.7	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
66.1	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
65.8	99.8	GSM133768	Lindsey_1-20_torpedo-basal_Rep5_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
65.1	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.9	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.7	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.2	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
59.8	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.8	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
55.2	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
44.9	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
43.9	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
43.0	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
39.5	99.8	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
36.8	99.7	GSM131699	ATGE_81_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
36.4	99.7	GSM131698	ATGE_81_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
35.6	99.7	GSM131697	ATGE_81_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
27.4	99.7	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
26.6	99.7	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
19.4	99.6	GSM131700	ATGE_82_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
19.2	99.6	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
18.2	99.5	GSM131701	ATGE_82_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
17.1	99.5	GSM131702	ATGE_82_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
16.5	99.5	GSM131705	ATGE_83_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
16.4	99.5	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
16.3	99.5	GSM131707	ATGE_84_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
16.0	99.5	GSM131703	ATGE_83_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
15.6	99.5	GSM131706	ATGE_84_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
15.3	99.4	GSM265431	Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
14.5	99.4	GSM131704	ATGE_83_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
14.4	99.4	GSM131708	ATGE_84_D	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
13.4	99.4	GSM311291	Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
11.8	99.3	GSM184524	Stele root cells 2hr KCl control treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
11.4	99.3	GSM10451	WT Mature Green Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.267 2 GO:0010120 The chemical reactions and pathways resulting in the formation of camalexin, an indole phytoalexin.
0.222 1 GO:0009700 The chemical reactions and pathways resulting in the formation of indole phytoalexins, any indole compound produced by plants as part of their defense response.
0.182 1 GO:0015692 The directed movement of lead (Pb) ions into, out of, within or between cells.

SF	Genes	GO ID	Process Name
0.267	2	GO:0010120	The chemical reactions and pathways resulting in the formation of camalexin, an indole phytoalexin.
0.222	1	GO:0009700	The chemical reactions and pathways resulting in the formation of indole phytoalexins, any indole compound produced by plants as part of their defense response.
0.182	1	GO:0015692	The directed movement of lead (Pb) ions into, out of, within or between cells.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.074 1 00980 Metabolism of xenobiotics by cytochrome P450
0.045 1 00380 Tryptophan metabolism
0.033 1 00480 Glutathione metabolism

SF	Genes	KEGG ID	Pathway name
0.074	1	00980	Metabolism of xenobiotics by cytochrome P450
0.045	1	00380	Tryptophan metabolism
0.033	1	00480	Glutathione metabolism

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	At1g15520
Gene name	PDR12 (PLEIOTROPIC DRUG RESISTANCE 12)
Module size	7 genes
NF	0.39
%ile	54.6

Co-expression analysis

Gene ID At1g15520 Gene name PDR12 (PLEIOTROPIC DRUG RESISTANCE 12) Module size 7 genes NF 0.39 %ile 54.6

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 KEGG0.074100980Metabolism of xenobiotics by cytochrome P4500.045100380Tryptophan metabolism0.033100480Glutathione metabolism

Inter-species module comparison

Select a plant to compare co-expressed genes between species.Glycine_maxHordeum_vulgareOryza_sativaPopulus_trichocarpaTriticum_aestivumVitis_viniferaZea_mays

Gene ID At1g15520

Gene name PDR12 (PLEIOTROPIC DRUG RESISTANCE 12)

Module size 7 genes

NF 0.39

%ile 54.6

: 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
0.074 1 00980 Metabolism of xenobiotics by cytochrome P450
0.045 1 00380 Tryptophan metabolism
0.033 1 00480 Glutathione metabolism

Select a plant to compare co-expressed genes between species.
Glycine_max
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays