CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At4g10930

Gene name unknown protein

Module size 5 genes

NF 0.23

%ile 23.2

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
0.50 65.3 1.00 At4g10930 826692 unknown protein F:unknown;P:unknown;C:cellular_component unknown;MOFBP O.I. H.G. S.X.
0.44 57.2 0.89 At5g42400 834246 SDG25 (SET DOMAIN PROTEIN 25) F:unknown;P:unknown;C:unknown;MOPFBAV O.I. H.G. S.X.
0.40 50.8 0.89 At1g76320 843965 FRS4 (FAR1-related sequence 4) F:zinc ion binding;P:response to red or far red light;C:cellular_component unknown;PFM O.I. H.G. S.X.
0.14 6.8 0.89 At5g13540 - - O.I. H.G. S.X.
0.13 5.8 0.89 At4g02560 827904 LD (luminidependens) Encodes a nuclear localized protein with similarity to transcriptional regulators. Recessive mutants are late flowering. Expression of LFY is reduced in LD mutants. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.50	65.3	1.00	At4g10930	826692	unknown protein	F:unknown;P:unknown;C:cellular_component unknown;MOFBP	O.I.	H.G.	S.X.
0.44	57.2	0.89	At5g42400	834246	SDG25 (SET DOMAIN PROTEIN 25)	F:unknown;P:unknown;C:unknown;MOPFBAV	O.I.	H.G.	S.X.
0.40	50.8	0.89	At1g76320	843965	FRS4 (FAR1-related sequence 4)	F:zinc ion binding;P:response to red or far red light;C:cellular_component unknown;PFM	O.I.	H.G.	S.X.
0.14	6.8	0.89	At5g13540		-	-	O.I.	H.G.	S.X.
0.13	5.8	0.89	At4g02560	827904	LD (luminidependens)	Encodes a nuclear localized protein with similarity to transcriptional regulators. Recessive mutants are late flowering. Expression of LFY is reduced in LD mutants.	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
246.6 100.0 GSM284389 Arabidopsis GMPE2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
225.0 100.0 GSM311275 Laser capture microdissected (LCM) micropylar endosperm at the pre-globular stage, biological replicate 1 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
156.8 99.9 GSM311276 Laser capture microdissected (LCM) micropylar endospermr at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
113.2 99.9 GSM284388 Arabidopsis GMPE1 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
96.6 99.9 E-MEXP-265-raw-cel-414618693
65.7 99.8 E-MEXP-265-raw-cel-414618585
48.8 99.8 E-MEXP-265-raw-cel-414618796
47.0 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
45.7 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.4 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.7 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.7 99.8 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
42.7 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.0 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.9 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.5 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.4 99.8 E-MEXP-265-raw-cel-414617783
39.4 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.0 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.0 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
35.7 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.6 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.5 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.4 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
31.8 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
31.6 99.7 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
30.4 99.7 E-MEXP-265-raw-cel-414617695
28.2 99.7 GSM284386 Arabidopsis GSUS3 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
27.4 99.7 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
27.3 99.7 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
26.5 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
21.7 99.6 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
21.4 99.6 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
20.5 99.6 E-MEXP-265-raw-cel-414617890
19.9 99.6 GSM184911 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
19.8 99.6 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
18.5 99.5 E-MEXP-265-raw-cel-414618394
18.2 99.5 GSM284387 Arabidopsis GSUS4b GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
17.5 99.5 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
16.5 99.5 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
15.2 99.4 E-MEXP-265-raw-cel-414618491
13.2 99.4 E-MEXP-265-raw-cel-414619001
12.2 99.3 GSM131660 ATGE_28_C2 GSE5633 AtGenExpress: Developmental series (shoots and stems)
11.8 99.3 GSM131655 ATGE_27_A GSE5633 AtGenExpress: Developmental series (shoots and stems)
11.6 99.3 GSM184910 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
11.4 99.3 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.2 99.2 GSM131658 ATGE_28_A2 GSE5633 AtGenExpress: Developmental series (shoots and stems)
11.1 99.2 GSM131656 ATGE_27_B GSE5633 AtGenExpress: Developmental series (shoots and stems)
11.0 99.2 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.2 99.2 GSM131659 ATGE_28_B2 GSE5633 AtGenExpress: Developmental series (shoots and stems)
9.9 99.1 E-MEXP-265-raw-cel-414619106

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
246.6	100.0	GSM284389	Arabidopsis GMPE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
225.0	100.0	GSM311275	Laser capture microdissected (LCM) micropylar endosperm at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
156.8	99.9	GSM311276	Laser capture microdissected (LCM) micropylar endospermr at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
113.2	99.9	GSM284388	Arabidopsis GMPE1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
96.6	99.9	E-MEXP-265-raw-cel-414618693
65.7	99.8	E-MEXP-265-raw-cel-414618585
48.8	99.8	E-MEXP-265-raw-cel-414618796
47.0	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
45.7	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.4	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.7	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.7	99.8	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
42.7	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.0	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.9	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.5	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.4	99.8	E-MEXP-265-raw-cel-414617783
39.4	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.0	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.0	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.7	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.6	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.5	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.4	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
31.8	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
31.6	99.7	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
30.4	99.7	E-MEXP-265-raw-cel-414617695
28.2	99.7	GSM284386	Arabidopsis GSUS3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
27.4	99.7	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
27.3	99.7	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
26.5	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.7	99.6	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.4	99.6	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
20.5	99.6	E-MEXP-265-raw-cel-414617890
19.9	99.6	GSM184911	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
19.8	99.6	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
18.5	99.5	E-MEXP-265-raw-cel-414618394
18.2	99.5	GSM284387	Arabidopsis GSUS4b	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
17.5	99.5	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
16.5	99.5	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
15.2	99.4	E-MEXP-265-raw-cel-414618491
13.2	99.4	E-MEXP-265-raw-cel-414619001
12.2	99.3	GSM131660	ATGE_28_C2	GSE5633	AtGenExpress: Developmental series (shoots and stems)
11.8	99.3	GSM131655	ATGE_27_A	GSE5633	AtGenExpress: Developmental series (shoots and stems)
11.6	99.3	GSM184910	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
11.4	99.3	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.2	99.2	GSM131658	ATGE_28_A2	GSE5633	AtGenExpress: Developmental series (shoots and stems)
11.1	99.2	GSM131656	ATGE_27_B	GSE5633	AtGenExpress: Developmental series (shoots and stems)
11.0	99.2	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.2	99.2	GSM131659	ATGE_28_B2	GSE5633	AtGenExpress: Developmental series (shoots and stems)
9.9	99.1	E-MEXP-265-raw-cel-414619106

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.057 1 GO:0009911 Any process that activates or increases the frequency, rate or extent of flower development.
0.053 1 GO:0009639 A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a red or far red light stimulus. Red light is electromagnetic radiation of wavelength of 580-700nm. Far red light is electromagnetic radiation of wavelength 700-800nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.057	1	GO:0009911	Any process that activates or increases the frequency, rate or extent of flower development.
0.053	1	GO:0009639	A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a red or far red light stimulus. Red light is electromagnetic radiation of wavelength of 580-700nm. Far red light is electromagnetic radiation of wavelength 700-800nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.100 1 00310 Lysine degradation

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.100	1	00310	Lysine degradation

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	At4g10930
Gene name	unknown protein
Module size	5 genes
NF	0.23
%ile	23.2

Co-expression analysis

Gene ID At4g10930 Gene name unknown protein Module size 5 genes NF 0.23 %ile 23.2

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

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG0.100100310Lysine degradation

Inter-species module comparison

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

Gene ID At4g10930

Gene name unknown protein

Module size 5 genes

NF 0.23

%ile 23.2

: 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
0.100 1 00310 Lysine degradation

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