CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g10390

Gene name histone H3

Module size 5 genes

NF 0.59

%ile 80.8

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
0.47 61.2 1.00 At5g10390 830903 histone H3 F:DNA binding;P:nucleosome assembly;C:nucleus, chloroplast, nucleosome;MFPO O.I. H.G. S.X.
0.86 93.1 0.92 At5g65360 836661 histone H3 F:DNA binding;P:nucleosome assembly;C:nucleus, chloroplast, nucleosome;MFPO O.I. H.G. S.X.
0.67 81.6 0.87 At1g09200 837440 histone H3 F:DNA binding;P:nucleosome assembly;C:nucleus, chloroplast, nucleosome;MFPO O.I. H.G. S.X.
0.60 75.7 0.89 At1g51060 841528 HTA10 Encodes HTA10, a histone H2A protein. O.I. H.G. S.X.
0.50 65.3 0.88 At3g20670 821614 HTA13 Encodes HTA13, a histone H2A protein. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.47	61.2	1.00	At5g10390	830903	histone H3	F:DNA binding;P:nucleosome assembly;C:nucleus, chloroplast, nucleosome;MFPO	O.I.	H.G.	S.X.
0.86	93.1	0.92	At5g65360	836661	histone H3	F:DNA binding;P:nucleosome assembly;C:nucleus, chloroplast, nucleosome;MFPO	O.I.	H.G.	S.X.
0.67	81.6	0.87	At1g09200	837440	histone H3	F:DNA binding;P:nucleosome assembly;C:nucleus, chloroplast, nucleosome;MFPO	O.I.	H.G.	S.X.
0.60	75.7	0.89	At1g51060	841528	HTA10	Encodes HTA10, a histone H2A protein.	O.I.	H.G.	S.X.
0.50	65.3	0.88	At3g20670	821614	HTA13	Encodes HTA13, a histone H2A protein.	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
46.2 99.8 GSM184516 Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
36.5 99.7 GSM184539 Whole roots 2hr KCl control treated then frozen, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
35.2 99.7 GSM184545 Whole roots 2hr KNO3 treated then frozen, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
31.2 99.7 GSM184520 Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
30.4 99.7 GSM184533 Protoplasted root cells 2hr KCl control treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
30.4 99.7 GSM184509 Pericycle root cells 2hr continuous KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
30.1 99.7 GSM142846 MG001_ATH1_A27-Torres-9N1 GSE6176 Impact of Type III effectors on plant defense responses
28.8 99.7 GSM284391 Arabidopsis GPE3 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
26.8 99.7 GSM184519 Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
26.4 99.7 GSM131603 ATGE_41_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
24.8 99.6 GSM142845 MG001_ATH1_A26-Torres-8N3 GSE6176 Impact of Type III effectors on plant defense responses
24.6 99.6 GSM184517 Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
24.6 99.6 GSM131605 ATGE_41_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
23.3 99.6 GSM131604 ATGE_41_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
22.7 99.6 GSM184538 Whole roots 2hr KCl control treated then frozen, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
21.9 99.6 GSM184493 Epidermis&Cortex root cells 2hr continuous KNO3 treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
21.1 99.6 GSM184521 Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
20.8 99.6 GSM184506 Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
19.9 99.6 GSM184518 Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
18.8 99.5 GSM184487 Epidermis&Cortex root cells 2hr KCl control treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
18.1 99.5 GSM133731 Buchanan-Wollaston_A-3-bwoll-C0S_SLD GSE5727 The effects of mutants in stress response pathways on gene expression during senescence
16.3 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
15.2 99.4 GSM142650 MC002_ATH1_A10.1-dubos-wth GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
14.3 99.4 GSM142651 MC002_ATH1_A10.2-dubos-wth GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
13.4 99.4 GSM218591 Whole roots 3.5hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
12.0 99.3 GSM184508 Pericycle root cells 2hr transitory KNO3 treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
10.8 99.2 GSM284390 Arabidopsis GPE2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
10.8 99.2 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.8 99.2 GSM142652 MC002_ATH1_A10.3-dubos-wth GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.8 99.2 GSM133720 Deeken_A-2-Deeke-Inf_SLD_REP1 GSE5725 Agrobacterium tumefaciens-induced tumour development of Arabidopsis thaliana
10.3 99.2 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.3 99.2 GSM218594 Whole roots 3.5hr KNO3 treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
10.2 99.2 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.2 99.2 GSM268245 dor-drought-1, biological rep 1 GSE10643 Transcription profiling of Arabidopsis dor mutant and wild-type plants in response to drought stress.
10.1 99.2 GSM218586 Pericycle root cells 2hr continuous KNO3 and MSX and Gln treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
10.0 99.2 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.9 99.1 GSM318330 EL_14DAS_1 GSE12676 Arabidopsis thaliana Ler developmental series
9.8 99.1 GSM184507 Pericycle root cells 2hr transitory KNO3 treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.7 99.1 GSM142844 MG001_ATH1_A25-Torres-8N1 GSE6176 Impact of Type III effectors on plant defense responses
9.6 99.1 GSM184559 Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes with KNO3, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.6 99.1 GSM133722 Deeken_A-2-Deeke-Inf_SLD_REP2 GSE5725 Agrobacterium tumefaciens-induced tumour development of Arabidopsis thaliana
9.5 99.1 GSM184504 Pericycle root cells 2hr KCl control treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.3 99.1 GSM218587 Pericycle root cells 2hr continuous KNO3 and MSX and Gln treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.2 99.1 E-TABM-62-raw-cel-720984390
9.1 99.1 GSM184488 Epidermis&Cortex root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
8.8 99.0 GSM133025 BC181-1 GSE5684 AtGenExpress: Pathogen Series: Response to Botrytis cinerea infection
8.6 99.0 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
46.2	99.8	GSM184516	Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
36.5	99.7	GSM184539	Whole roots 2hr KCl control treated then frozen, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
35.2	99.7	GSM184545	Whole roots 2hr KNO3 treated then frozen, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
31.2	99.7	GSM184520	Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
30.4	99.7	GSM184533	Protoplasted root cells 2hr KCl control treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
30.4	99.7	GSM184509	Pericycle root cells 2hr continuous KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
30.1	99.7	GSM142846	MG001_ATH1_A27-Torres-9N1	GSE6176	Impact of Type III effectors on plant defense responses
28.8	99.7	GSM284391	Arabidopsis GPE3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
26.8	99.7	GSM184519	Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
26.4	99.7	GSM131603	ATGE_41_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
24.8	99.6	GSM142845	MG001_ATH1_A26-Torres-8N3	GSE6176	Impact of Type III effectors on plant defense responses
24.6	99.6	GSM184517	Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
24.6	99.6	GSM131605	ATGE_41_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
23.3	99.6	GSM131604	ATGE_41_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
22.7	99.6	GSM184538	Whole roots 2hr KCl control treated then frozen, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
21.9	99.6	GSM184493	Epidermis&Cortex root cells 2hr continuous KNO3 treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
21.1	99.6	GSM184521	Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
20.8	99.6	GSM184506	Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
19.9	99.6	GSM184518	Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
18.8	99.5	GSM184487	Epidermis&Cortex root cells 2hr KCl control treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
18.1	99.5	GSM133731	Buchanan-Wollaston_A-3-bwoll-C0S_SLD	GSE5727	The effects of mutants in stress response pathways on gene expression during senescence
16.3	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
15.2	99.4	GSM142650	MC002_ATH1_A10.1-dubos-wth	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
14.3	99.4	GSM142651	MC002_ATH1_A10.2-dubos-wth	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
13.4	99.4	GSM218591	Whole roots 3.5hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
12.0	99.3	GSM184508	Pericycle root cells 2hr transitory KNO3 treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.8	99.2	GSM284390	Arabidopsis GPE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
10.8	99.2	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.8	99.2	GSM142652	MC002_ATH1_A10.3-dubos-wth	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.8	99.2	GSM133720	Deeken_A-2-Deeke-Inf_SLD_REP1	GSE5725	Agrobacterium tumefaciens-induced tumour development of Arabidopsis thaliana
10.3	99.2	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.3	99.2	GSM218594	Whole roots 3.5hr KNO3 treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.2	99.2	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.2	99.2	GSM268245	dor-drought-1, biological rep 1	GSE10643	Transcription profiling of Arabidopsis dor mutant and wild-type plants in response to drought stress.
10.1	99.2	GSM218586	Pericycle root cells 2hr continuous KNO3 and MSX and Gln treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.0	99.2	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.9	99.1	GSM318330	EL_14DAS_1	GSE12676	Arabidopsis thaliana Ler developmental series
9.8	99.1	GSM184507	Pericycle root cells 2hr transitory KNO3 treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.7	99.1	GSM142844	MG001_ATH1_A25-Torres-8N1	GSE6176	Impact of Type III effectors on plant defense responses
9.6	99.1	GSM184559	Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes with KNO3, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.6	99.1	GSM133722	Deeken_A-2-Deeke-Inf_SLD_REP2	GSE5725	Agrobacterium tumefaciens-induced tumour development of Arabidopsis thaliana
9.5	99.1	GSM184504	Pericycle root cells 2hr KCl control treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.3	99.1	GSM218587	Pericycle root cells 2hr continuous KNO3 and MSX and Gln treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.2	99.1	E-TABM-62-raw-cel-720984390
9.1	99.1	GSM184488	Epidermis&Cortex root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
8.8	99.0	GSM133025	BC181-1	GSE5684	AtGenExpress: Pathogen Series: Response to Botrytis cinerea infection
8.6	99.0	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.159 5 GO:0006334 The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.159	5	GO:0006334	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.

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	At5g10390
Gene name	histone H3
Module size	5 genes
NF	0.59
%ile	80.8

Co-expression analysis

Gene ID At5g10390 Gene name histone H3 Module size 5 genes NF 0.59 %ile 80.8

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 AmiGO0.1595GO:0006334The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.

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 At5g10390

Gene name histone H3

Module size 5 genes

NF 0.59

%ile 80.8

: 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
0.159 5 GO:0006334 The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.

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