CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At4g09960

Gene name STK (SEEDSTICK)

Module size 5 genes

NF 0.25

%ile 27.1

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
0.19 12.7 1.00 At4g09960 826586 STK (SEEDSTICK) a MADS box transcription factor expressed in the carpel and ovules O.I. H.G. S.X.
0.33 38.1 0.70 At1g24010 839013 - F:molecular_function unknown;P:response to biotic stimulus, defense response;C:cellular_component unknown;P O.I. H.G. S.X.
0.33 38.1 0.72 At4g22050 828294 aspartyl protease family protein F:aspartic-type endopeptidase activity;P:proteolysis;C:endomembrane system;MFOP O.I. H.G. S.X.
0.27 26.2 0.58 At1g12180 837771 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.22 17.5 0.61 At4g29570 829078 cytidine deaminase, putative / cytidine aminohydrolase, putative F:hydrolase activity, cytidine deaminase activity, catalytic activity, zinc ion binding;P:cytidine deamination, cytidine metabolic process;C:cellular_component unknown;BPO O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.19	12.7	1.00	At4g09960	826586	STK (SEEDSTICK)	a MADS box transcription factor expressed in the carpel and ovules	O.I.	H.G.	S.X.
0.33	38.1	0.70	At1g24010	839013	-	F:molecular_function unknown;P:response to biotic stimulus, defense response;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.33	38.1	0.72	At4g22050	828294	aspartyl protease family protein	F:aspartic-type endopeptidase activity;P:proteolysis;C:endomembrane system;MFOP	O.I.	H.G.	S.X.
0.27	26.2	0.58	At1g12180	837771	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.22	17.5	0.61	At4g29570	829078	cytidine deaminase, putative / cytidine aminohydrolase, putative	F:hydrolase activity, cytidine deaminase activity, catalytic activity, zinc ion binding;P:cytidine deamination, cytidine metabolic process;C:cellular_component unknown;BPO	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
71.1 99.9 GSM142655 MC002_ATH1_A11.3-dubos-mxh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
67.0 99.8 GSM142653 MC002_ATH1_A11.1-dubos-mxh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
59.2 99.8 GSM142654 MC002_ATH1_A11.2-dubos-mxh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
51.0 99.8 GSM142624 MC002_ATH1_A1.2-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
50.0 99.8 E-MEXP-1474-raw-cel-1593932705
43.0 99.8 GSM142625 MC002_ATH1_A1.3-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
36.4 99.7 GSM142631 MC002_ATH1_A3.3-dubos-6kx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
35.9 99.7 E-MEXP-1474-raw-cel-1593932609
29.7 99.7 GSM131608 ATGE_42_D GSE5632 AtGenExpress: Developmental series (flowers and pollen)
28.2 99.7 E-MEXP-1474-raw-cel-1593932513
27.3 99.7 GSM131606 ATGE_42_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
22.5 99.6 GSM142623 MC002_ATH1_A1.1-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
20.4 99.6 E-MEXP-1474-raw-cel-1593932737
18.9 99.5 GSM131607 ATGE_42_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
18.6 99.5 GSM142642 MC002_ATH1_A7.2-dubos-wLh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
17.5 99.5 GSM142641 MC002_ATH1_A7.1-dubos-wLh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
16.4 99.5 GSM142643 MC002_ATH1_A7.3-dubos-wLh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
15.3 99.4 GSM142630 MC002_ATH1_A3.2-dubos-6kx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
13.6 99.4 E-MEXP-1474-raw-cel-1593932897
12.9 99.3 E-MEXP-1474-raw-cel-1593932641
12.8 99.3 E-ATMX-33-raw-cel-1562596310
12.5 99.3 E-MEXP-828-raw-cel-1156922634
10.3 99.2 GSM142644 MC002_ATH1_A8.1-dubos-aih GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.1 99.2 GSM142629 MC002_ATH1_A3.1-dubos-6kx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.6 99.1 GSM62700 arf6/arf6 ARF8/arf8 flowers_stage 13-14 GSE2848 Auxin Response Factor mediated flower gene expression
9.5 99.1 E-MEXP-828-raw-cel-1156922296
9.3 99.1 E-MEXP-828-raw-cel-1156922684
9.2 99.1 GSM142646 MC002_ATH1_A8.3-dubos-aih GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.0 99.1 E-MEXP-1474-raw-cel-1593932769
8.9 99.0 E-MEXP-285-raw-cel-440783335
8.8 99.0 GSM291098 root - 08% oxygen - 48h - F GSE11558 transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
8.7 99.0 E-MEXP-285-raw-cel-440783273

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
71.1	99.9	GSM142655	MC002_ATH1_A11.3-dubos-mxh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
67.0	99.8	GSM142653	MC002_ATH1_A11.1-dubos-mxh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
59.2	99.8	GSM142654	MC002_ATH1_A11.2-dubos-mxh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
51.0	99.8	GSM142624	MC002_ATH1_A1.2-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
50.0	99.8	E-MEXP-1474-raw-cel-1593932705
43.0	99.8	GSM142625	MC002_ATH1_A1.3-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
36.4	99.7	GSM142631	MC002_ATH1_A3.3-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
35.9	99.7	E-MEXP-1474-raw-cel-1593932609
29.7	99.7	GSM131608	ATGE_42_D	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
28.2	99.7	E-MEXP-1474-raw-cel-1593932513
27.3	99.7	GSM131606	ATGE_42_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
22.5	99.6	GSM142623	MC002_ATH1_A1.1-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
20.4	99.6	E-MEXP-1474-raw-cel-1593932737
18.9	99.5	GSM131607	ATGE_42_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
18.6	99.5	GSM142642	MC002_ATH1_A7.2-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
17.5	99.5	GSM142641	MC002_ATH1_A7.1-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
16.4	99.5	GSM142643	MC002_ATH1_A7.3-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
15.3	99.4	GSM142630	MC002_ATH1_A3.2-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
13.6	99.4	E-MEXP-1474-raw-cel-1593932897
12.9	99.3	E-MEXP-1474-raw-cel-1593932641
12.8	99.3	E-ATMX-33-raw-cel-1562596310
12.5	99.3	E-MEXP-828-raw-cel-1156922634
10.3	99.2	GSM142644	MC002_ATH1_A8.1-dubos-aih	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.1	99.2	GSM142629	MC002_ATH1_A3.1-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.6	99.1	GSM62700	arf6/arf6 ARF8/arf8 flowers_stage 13-14	GSE2848	Auxin Response Factor mediated flower gene expression
9.5	99.1	E-MEXP-828-raw-cel-1156922296
9.3	99.1	E-MEXP-828-raw-cel-1156922684
9.2	99.1	GSM142646	MC002_ATH1_A8.3-dubos-aih	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.0	99.1	E-MEXP-1474-raw-cel-1593932769
8.9	99.0	E-MEXP-285-raw-cel-440783335
8.8	99.0	GSM291098	root - 08% oxygen - 48h - F	GSE11558	transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
8.7	99.0	E-MEXP-285-raw-cel-440783273

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.167 1 GO:0046087 The chemical reactions and pathways involving cytidine, cytosine riboside, a widely distributed nucleoside.
0.154 1 GO:0009972 The removal of amino group in the presence of water.
0.100 1 GO:0048440 The process whose specific outcome is the progression of the carpel over time, from its formation to the mature structure. A carpel is an organ (generally believed to be a modified foliar unit) at the centre of a flower, bearing one or more ovules and having its margins fused together or with other carpels to enclose the ovule in an ovary, and consisting also of a stigma and usually a style.

SF	Genes	GO ID	Process Name
0.167	1	GO:0046087	The chemical reactions and pathways involving cytidine, cytosine riboside, a widely distributed nucleoside.
0.154	1	GO:0009972	The removal of amino group in the presence of water.
0.100	1	GO:0048440	The process whose specific outcome is the progression of the carpel over time, from its formation to the mature structure. A carpel is an organ (generally believed to be a modified foliar unit) at the centre of a flower, bearing one or more ovules and having its margins fused together or with other carpels to enclose the ovule in an ovary, and consisting also of a stigma and usually a style.

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	At4g09960
Gene name	STK (SEEDSTICK)
Module size	5 genes
NF	0.25
%ile	27.1

Co-expression analysis

Gene ID At4g09960 Gene name STK (SEEDSTICK) Module size 5 genes NF 0.25 %ile 27.1

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 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 At4g09960

Gene name STK (SEEDSTICK)

Module size 5 genes

NF 0.25

%ile 27.1

: 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

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