CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g05670

Gene name PHD finger family protein

Module size 5 genes

NF 0.49

%ile 69.2

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
0.44 57.2 1.00 At3g05670 819734 PHD finger family protein F:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:unknown;MOFBPVA O.I. H.G. S.X.
0.57 73.8 0.92 At1g04300 839551 - F:molecular_function unknown;P:biological_process unknown;C:unknown;OMFBPVA O.I. H.G. S.X.
0.50 65.3 0.90 At1g11480 837691 eukaryotic translation initiation factor-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPB O.I. H.G. S.X.
0.50 65.3 0.91 At3g15290 820760 3-hydroxybutyryl-CoA dehydrogenase, putative F:coenzyme binding, oxidoreductase activity, 3-hydroxybutyryl-CoA dehydrogenase activity, binding, catalytic activity;P:fatty acid metabolic process, metabolic process;C:peroxisome;BOMAFP O.I. H.G. S.X.
0.40 50.8 0.91 At5g43930 834415 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:biological_process unknown;C:chloroplast;MBFOPA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.44	57.2	1.00	At3g05670	819734	PHD finger family protein	F:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:unknown;MOFBPVA	O.I.	H.G.	S.X.
0.57	73.8	0.92	At1g04300	839551	-	F:molecular_function unknown;P:biological_process unknown;C:unknown;OMFBPVA	O.I.	H.G.	S.X.
0.50	65.3	0.90	At1g11480	837691	eukaryotic translation initiation factor-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPB	O.I.	H.G.	S.X.
0.50	65.3	0.91	At3g15290	820760	3-hydroxybutyryl-CoA dehydrogenase, putative	F:coenzyme binding, oxidoreductase activity, 3-hydroxybutyryl-CoA dehydrogenase activity, binding, catalytic activity;P:fatty acid metabolic process, metabolic process;C:peroxisome;BOMAFP	O.I.	H.G.	S.X.
0.40	50.8	0.91	At5g43930	834415	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:biological_process unknown;C:chloroplast;MBFOPA	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
28.0 99.7 GSM142904 WW002_ATH1_A1-willa-CON-REP2 GSE6181 Assembly of the cell wall pectic matrix.
23.9 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
22.6 99.6 GSM184918 Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
22.4 99.6 GSM184895 Arabidopsis, root cells, cortex, standard conditions, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
22.1 99.6 GSM184896 Arabidopsis, root cells, cortex, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
21.5 99.6 GSM184913 Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
20.8 99.6 GSM142902 WW001_ATH1_A1-WILLA-CON GSE6181 Assembly of the cell wall pectic matrix.
20.2 99.6 GSM184897 Arabidopsis, root cells, cortex, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
19.2 99.6 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.6 99.5 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
16.4 99.5 GSM184914 Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
15.8 99.5 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.3 99.4 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.2 99.4 GSM143300 Ts_genomic_hyb_3 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
15.1 99.4 GSM184844 Arabidopsis, root, longitudinal zone 3, standard conditions, NaCl, replicate 2 GSE7639 Expression analysis of root developmental zones after treatment with salt
15.1 99.4 GSM184921 Arabidopsis, root cells, stele, 140 mM NaCls, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
14.9 99.4 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.7 99.4 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.6 99.4 GSM184915 Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
14.2 99.4 GSM184633 Arabidopsis, whole roots, 140 mM NaCl, replicate 2 GSE7636 Expression analysis of the effect of protoplasting and FACS sorting in roots
14.0 99.4 GSM184843 Arabidopsis, root, longitudinal zone 3, standard conditions, NaCl, replicate 1 GSE7639 Expression analysis of root developmental zones after treatment with salt
12.9 99.3 GSM75517 slr-1 2h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
12.6 99.3 GSM265422 Arabidopsis, root, longitudinal zone 3, standard conditions, rep1 GSE10497 Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
12.5 99.3 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.5 99.3 GSM266671 Arabidopsis, root cells, cortex, -Fe, replicate 3 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
12.2 99.3 GSM265433 Arabidopsis, root, longitudinal zone 4, -Fe conditions, rep 2 GSE10497 Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
12.1 99.3 GSM266669 Arabidopsis, root cells, cortex, -Fe, replicate 1 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
11.9 99.3 GSM184934 Arabidopsis, whole roots, 140 mM NaCl, 16 hour, replicate 2 GSE7642 Time course expression analysis of the salt stress response in Arabidopsis roots
11.3 99.3 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.8 99.2 GSM265425 Arabidopsis, root, longitudinal zone 4, standard conditions, rep 2 GSE10497 Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
10.7 99.2 GSM265424 Arabidopsis, root, longitudinal zone 4, standard conditions, rep 1 GSE10497 Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
10.5 99.2 GSM184846 Arabidopsis, root, longitudinal zone 4, standard conditions, NaCl, replicate 2 GSE7639 Expression analysis of root developmental zones after treatment with salt
10.4 99.2 GSM265432 Arabidopsis, root, longitudinal zone 4, -Fe conditions, rep 1 GSE10497 Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
10.4 99.2 GSM184909 Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
9.8 99.1 GSM75509 Col-0 2h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
9.8 99.1 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.8 99.1 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.7 99.1 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.4 99.1 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4 99.1 GSM128662 Underwood_1-15_Cor-5x10e7-10h_Rep3_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
9.3 99.1 GSM265423 Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2 GSE10497 Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
9.3 99.1 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
8.9 99.0 GSM184924 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
8.9 99.0 GSM128661 Underwood_1-14_Cor-5x10e7-10h_Rep2_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
8.8 99.0 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
8.7 99.0 GSM265431 Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2 GSE10497 Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
8.7 99.0 GSM184935 Arabidopsis, whole roots, 140 mM NaCl, 32 hour, replicate 1 GSE7642 Time course expression analysis of the salt stress response in Arabidopsis roots
8.7 99.0 GSM184933 Arabidopsis, whole roots, 140 mM NaCl, 16 hour, replicate 1 GSE7642 Time course expression analysis of the salt stress response in Arabidopsis roots
8.6 99.0 GSM184920 Arabidopsis, root cells, stele, 140 mM NaCls, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
28.0	99.7	GSM142904	WW002_ATH1_A1-willa-CON-REP2	GSE6181	Assembly of the cell wall pectic matrix.
23.9	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
22.6	99.6	GSM184918	Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
22.4	99.6	GSM184895	Arabidopsis, root cells, cortex, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
22.1	99.6	GSM184896	Arabidopsis, root cells, cortex, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
21.5	99.6	GSM184913	Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
20.8	99.6	GSM142902	WW001_ATH1_A1-WILLA-CON	GSE6181	Assembly of the cell wall pectic matrix.
20.2	99.6	GSM184897	Arabidopsis, root cells, cortex, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
19.2	99.6	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.6	99.5	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.4	99.5	GSM184914	Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
15.8	99.5	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.3	99.4	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.2	99.4	GSM143300	Ts_genomic_hyb_3	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
15.1	99.4	GSM184844	Arabidopsis, root, longitudinal zone 3, standard conditions, NaCl, replicate 2	GSE7639	Expression analysis of root developmental zones after treatment with salt
15.1	99.4	GSM184921	Arabidopsis, root cells, stele, 140 mM NaCls, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
14.9	99.4	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.7	99.4	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.6	99.4	GSM184915	Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
14.2	99.4	GSM184633	Arabidopsis, whole roots, 140 mM NaCl, replicate 2	GSE7636	Expression analysis of the effect of protoplasting and FACS sorting in roots
14.0	99.4	GSM184843	Arabidopsis, root, longitudinal zone 3, standard conditions, NaCl, replicate 1	GSE7639	Expression analysis of root developmental zones after treatment with salt
12.9	99.3	GSM75517	slr-1 2h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
12.6	99.3	GSM265422	Arabidopsis, root, longitudinal zone 3, standard conditions, rep1	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
12.5	99.3	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.5	99.3	GSM266671	Arabidopsis, root cells, cortex, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
12.2	99.3	GSM265433	Arabidopsis, root, longitudinal zone 4, -Fe conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
12.1	99.3	GSM266669	Arabidopsis, root cells, cortex, -Fe, replicate 1	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
11.9	99.3	GSM184934	Arabidopsis, whole roots, 140 mM NaCl, 16 hour, replicate 2	GSE7642	Time course expression analysis of the salt stress response in Arabidopsis roots
11.3	99.3	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.8	99.2	GSM265425	Arabidopsis, root, longitudinal zone 4, standard conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
10.7	99.2	GSM265424	Arabidopsis, root, longitudinal zone 4, standard conditions, rep 1	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
10.5	99.2	GSM184846	Arabidopsis, root, longitudinal zone 4, standard conditions, NaCl, replicate 2	GSE7639	Expression analysis of root developmental zones after treatment with salt
10.4	99.2	GSM265432	Arabidopsis, root, longitudinal zone 4, -Fe conditions, rep 1	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
10.4	99.2	GSM184909	Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
9.8	99.1	GSM75509	Col-0 2h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
9.8	99.1	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.8	99.1	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.7	99.1	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.4	99.1	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4	99.1	GSM128662	Underwood_1-15_Cor-5x10e7-10h_Rep3_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
9.3	99.1	GSM265423	Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
9.3	99.1	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
8.9	99.0	GSM184924	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
8.9	99.0	GSM128661	Underwood_1-14_Cor-5x10e7-10h_Rep2_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
8.8	99.0	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
8.7	99.0	GSM265431	Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
8.7	99.0	GSM184935	Arabidopsis, whole roots, 140 mM NaCl, 32 hour, replicate 1	GSE7642	Time course expression analysis of the salt stress response in Arabidopsis roots
8.7	99.0	GSM184933	Arabidopsis, whole roots, 140 mM NaCl, 16 hour, replicate 1	GSE7642	Time course expression analysis of the salt stress response in Arabidopsis roots
8.6	99.0	GSM184920	Arabidopsis, root cells, stele, 140 mM NaCls, 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
0.071 1 GO:0006631 The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.071	1	GO:0006631	The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.074 1 00650 Butanoate metabolism
0.002 1 01100 Metabolic pathways

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.074	1	00650	Butanoate metabolism
0.002	1	01100	Metabolic pathways

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	At3g05670
Gene name	PHD finger family protein
Module size	5 genes
NF	0.49
%ile	69.2

Co-expression analysis

Gene ID At3g05670 Gene name PHD finger family protein Module size 5 genes NF 0.49 %ile 69.2

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 AmiGO0.0711GO:0006631The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG0.074100650Butanoate metabolism0.002101100Metabolic pathways

Inter-species module comparison

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

Gene ID At3g05670

Gene name PHD finger family protein

Module size 5 genes

NF 0.49

%ile 69.2

: 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
0.071 1 GO:0006631 The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.

SF Genes KEGG ID Pathway name Link to KEGG
0.074 1 00650 Butanoate metabolism
0.002 1 01100 Metabolic pathways

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