CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g10400

Gene name histone H3

Module size 5 genes

NF 0.53

%ile 74.3

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 At5g10400 830904 histone H3 F:DNA binding;P:nucleosome assembly;C:nucleus, chloroplast, nucleosome;MFPO O.I. H.G. S.X.
0.86 93.1 0.86 At5g22880 832352 HTB2 Encodes a histone 2B (H2B) protein. This protein can be ubiquitinated in planta, and this modification depends on the HUB1 and HUB2 E3 ubiquitin ligases. O.I. H.G. S.X.
0.75 86.9 0.87 At3g27360 822357 histone H3 F:DNA binding;P:nucleosome assembly;C:nucleus, chloroplast, nucleosome;MFPO O.I. H.G. S.X.
0.50 65.3 0.83 At3g45930 823736 histone H4 F:DNA binding;P:nucleosome assembly;C:nucleus, nucleosome;MOPFV O.I. H.G. S.X.
0.35 41.6 0.84 At5g23420 832408 HMGB6 Encodes HMGB6, a protein belonging to the subgroup of HMGB (high mobility group B) proteins. Localized in the nucleus. Binds to supercoiled DNA in vitro. HMGB6 is phosphorylated by protein kinase CK2alpha within its acidic C-terminal domain. 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	At5g10400	830904	histone H3	F:DNA binding;P:nucleosome assembly;C:nucleus, chloroplast, nucleosome;MFPO	O.I.	H.G.	S.X.
0.86	93.1	0.86	At5g22880	832352	HTB2	Encodes a histone 2B (H2B) protein. This protein can be ubiquitinated in planta, and this modification depends on the HUB1 and HUB2 E3 ubiquitin ligases.	O.I.	H.G.	S.X.
0.75	86.9	0.87	At3g27360	822357	histone H3	F:DNA binding;P:nucleosome assembly;C:nucleus, chloroplast, nucleosome;MFPO	O.I.	H.G.	S.X.
0.50	65.3	0.83	At3g45930	823736	histone H4	F:DNA binding;P:nucleosome assembly;C:nucleus, nucleosome;MOPFV	O.I.	H.G.	S.X.
0.35	41.6	0.84	At5g23420	832408	HMGB6	Encodes HMGB6, a protein belonging to the subgroup of HMGB (high mobility group B) proteins. Localized in the nucleus. Binds to supercoiled DNA in vitro. HMGB6 is phosphorylated by protein kinase CK2alpha within its acidic C-terminal domain.	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
500.1 100.0 GSM184905 Arabidopsis, root cells, protophloem, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
184.4 100.0 GSM184904 Arabidopsis, root cells, protophloem, standard conditions, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
171.9 100.0 GSM184906 Arabidopsis, root cells, protophloem, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
88.4 99.9 GSM184923 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
54.8 99.8 GSM131321 AtGen_6-3421_Saltstress-Roots-6.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
44.9 99.8 GSM184918 Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
43.6 99.8 GSM131322 AtGen_6-3422_Saltstress-Roots-6.0h_Rep2 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
38.4 99.8 GSM131325 AtGen_6-3521_Saltstress-Roots-12.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
38.1 99.8 GSM184919 Arabidopsis, root cells, stele, 140 mM NaCls, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
35.4 99.7 GSM184924 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
28.1 99.7 GSM131317 AtGen_6-3321_Saltstress-Roots-3.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
26.9 99.7 GSM184922 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
25.5 99.7 GSM131274 AtGen_6-1422_Cold(4°C)-Roots-6.0h_Rep2 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
25.0 99.6 GSM184921 Arabidopsis, root cells, stele, 140 mM NaCls, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
23.4 99.6 GSM184920 Arabidopsis, root cells, stele, 140 mM NaCls, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
23.3 99.6 GSM184898 Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
22.4 99.6 GSM184912 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
21.6 99.6 GSM131329 AtGen_6-3621_Saltstress-Roots-24.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
20.8 99.6 GSM131273 AtGen_6-1421_Cold(4°C)-Roots-6.0h_Rep1 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
18.3 99.5 GSM131318 AtGen_6-3322_Saltstress-Roots-3.0h_Rep2 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
17.9 99.5 GSM184633 Arabidopsis, whole roots, 140 mM NaCl, replicate 2 GSE7636 Expression analysis of the effect of protoplasting and FACS sorting in roots
16.9 99.5 GSM184915 Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
16.1 99.5 GSM131330 AtGen_6-3622_Saltstress-Roots-24.0h_Rep2 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
15.8 99.5 GSM184899 Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
15.3 99.4 GSM184634 Arabidopsis, root cells, 140 mM NaCl, replicate 1 GSE7636 Expression analysis of the effect of protoplasting and FACS sorting in roots
15.2 99.4 GSM184914 Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
13.7 99.4 GSM184632 Arabidopsis, whole roots, 140 mM NaCl, replicate 1 GSE7636 Expression analysis of the effect of protoplasting and FACS sorting in roots
13.5 99.4 GSM131277 AtGen_6-1521_Cold(4°C)-Roots-12.0h_Rep1 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
13.3 99.4 GSM184900 Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
13.2 99.4 GSM184916 Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
12.7 99.3 GSM75516 slr-1 0h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
12.2 99.3 GSM184917 Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
11.4 99.3 GSM266676 Arabidopsis, root cells, stele, -Fe, replicate 2 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
10.9 99.2 GSM184845 Arabidopsis, root, longitudinal zone 4, standard conditions, NaCl, replicate 1 GSE7639 Expression analysis of root developmental zones after treatment with salt
10.8 99.2 GSM265414 Arabidopsis, root cells, -Fe, replicate 1 GSE10496 Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)
10.4 99.2 GSM131326 AtGen_6-3522_Saltstress-Roots-12.0h_Rep2 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
10.2 99.2 GSM184913 Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
10.1 99.2 GSM75519 slr-1 0h NAA replicate 2 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
10.1 99.2 GSM75520 slr-1 2h NAA replicate 2 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
10.0 99.2 GSM75518 slr-1 6h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
9.7 99.1 GSM266677 Arabidopsis, root cells, stele, -Fe, replicate 3 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
9.3 99.1 GSM266672 Arabidopsis, root cells, endodermis and quiescent center, -Fe, replicate 1 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
9.3 99.1 GSM75521 slr-1 6h NAA replicate 2 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
8.9 99.0 GSM266675 Arabidopsis, root cells, stele, -Fe, replicate 1 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
8.7 99.0 GSM184894 Arabidopsis, root cells, columella root cap, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
8.7 99.0 GSM179974 Arabidopsis roots, IAA treatment, replica 2 GSE7432 Ethylene and auxin interactions in the roots of Arabidopsis seedlings
8.7 99.0 GSM184910 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
500.1	100.0	GSM184905	Arabidopsis, root cells, protophloem, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
184.4	100.0	GSM184904	Arabidopsis, root cells, protophloem, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
171.9	100.0	GSM184906	Arabidopsis, root cells, protophloem, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
88.4	99.9	GSM184923	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
54.8	99.8	GSM131321	AtGen_6-3421_Saltstress-Roots-6.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
44.9	99.8	GSM184918	Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
43.6	99.8	GSM131322	AtGen_6-3422_Saltstress-Roots-6.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
38.4	99.8	GSM131325	AtGen_6-3521_Saltstress-Roots-12.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
38.1	99.8	GSM184919	Arabidopsis, root cells, stele, 140 mM NaCls, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
35.4	99.7	GSM184924	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
28.1	99.7	GSM131317	AtGen_6-3321_Saltstress-Roots-3.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
26.9	99.7	GSM184922	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
25.5	99.7	GSM131274	AtGen_6-1422_Cold(4°C)-Roots-6.0h_Rep2	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
25.0	99.6	GSM184921	Arabidopsis, root cells, stele, 140 mM NaCls, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
23.4	99.6	GSM184920	Arabidopsis, root cells, stele, 140 mM NaCls, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
23.3	99.6	GSM184898	Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
22.4	99.6	GSM184912	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
21.6	99.6	GSM131329	AtGen_6-3621_Saltstress-Roots-24.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
20.8	99.6	GSM131273	AtGen_6-1421_Cold(4°C)-Roots-6.0h_Rep1	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
18.3	99.5	GSM131318	AtGen_6-3322_Saltstress-Roots-3.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
17.9	99.5	GSM184633	Arabidopsis, whole roots, 140 mM NaCl, replicate 2	GSE7636	Expression analysis of the effect of protoplasting and FACS sorting in roots
16.9	99.5	GSM184915	Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
16.1	99.5	GSM131330	AtGen_6-3622_Saltstress-Roots-24.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
15.8	99.5	GSM184899	Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
15.3	99.4	GSM184634	Arabidopsis, root cells, 140 mM NaCl, replicate 1	GSE7636	Expression analysis of the effect of protoplasting and FACS sorting in roots
15.2	99.4	GSM184914	Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
13.7	99.4	GSM184632	Arabidopsis, whole roots, 140 mM NaCl, replicate 1	GSE7636	Expression analysis of the effect of protoplasting and FACS sorting in roots
13.5	99.4	GSM131277	AtGen_6-1521_Cold(4°C)-Roots-12.0h_Rep1	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
13.3	99.4	GSM184900	Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
13.2	99.4	GSM184916	Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
12.7	99.3	GSM75516	slr-1 0h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
12.2	99.3	GSM184917	Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
11.4	99.3	GSM266676	Arabidopsis, root cells, stele, -Fe, replicate 2	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
10.9	99.2	GSM184845	Arabidopsis, root, longitudinal zone 4, standard conditions, NaCl, replicate 1	GSE7639	Expression analysis of root developmental zones after treatment with salt
10.8	99.2	GSM265414	Arabidopsis, root cells, -Fe, replicate 1	GSE10496	Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)
10.4	99.2	GSM131326	AtGen_6-3522_Saltstress-Roots-12.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
10.2	99.2	GSM184913	Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
10.1	99.2	GSM75519	slr-1 0h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
10.1	99.2	GSM75520	slr-1 2h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
10.0	99.2	GSM75518	slr-1 6h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
9.7	99.1	GSM266677	Arabidopsis, root cells, stele, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
9.3	99.1	GSM266672	Arabidopsis, root cells, endodermis and quiescent center, -Fe, replicate 1	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
9.3	99.1	GSM75521	slr-1 6h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
8.9	99.0	GSM266675	Arabidopsis, root cells, stele, -Fe, replicate 1	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
8.7	99.0	GSM184894	Arabidopsis, root cells, columella root cap, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
8.7	99.0	GSM179974	Arabidopsis roots, IAA treatment, replica 2	GSE7432	Ethylene and auxin interactions in the roots of Arabidopsis seedlings
8.7	99.0	GSM184910	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1	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
0.127 4 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
0.127	4	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	At5g10400
Gene name	histone H3
Module size	5 genes
NF	0.53
%ile	74.3

Co-expression analysis

Gene ID At5g10400 Gene name histone H3 Module size 5 genes NF 0.53 %ile 74.3

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 AmiGO0.1274GO: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 At5g10400

Gene name histone H3

Module size 5 genes

NF 0.53

%ile 74.3

: 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
0.127 4 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