CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g71692

Gene name AGL12 (AGAMOUS-LIKE 12)

Module size 6 genes

NF 0.41

%ile 56.9

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
0.38 46.7 1.00 At1g71692 843497 AGL12 (AGAMOUS-LIKE 12) Encodes a member of the MADS box family of transcription factors. Involved in root cell differentiation and flowering time. Loss of function mutations have abnormal cellular differentiation in the roots and are late flowering. AGL12 along with AGL14, and AGL17 is preferentially expressed in root tissues and represent the only characterized MADS box genes expressed in roots. O.I. H.G. S.X.
0.83 91.4 0.77 At4g31100 829237 wall-associated kinase, putative F:kinase activity;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVA O.I. H.G. S.X.
0.55 70.6 0.78 At5g44160 834439 NUC (nutcracker) F:transcription factor activity, zinc ion binding, nucleic acid binding;P:regulation of transcription;C:intracellular;MOPF O.I. H.G. S.X.
0.42 53.9 0.76 At5g65790 836708 MYB68 (MYB DOMAIN PROTEIN 68) Encodes a putative MYB transcription factor. O.I. H.G. S.X.
0.35 41.6 0.76 At2g31020 817653 ORP1A (OSBP(OXYSTEROL BINDING PROTEIN)-RELATED PROTEIN 1A) F:oxysterol binding;P:steroid metabolic process;C:unknown;MFOPBV O.I. H.G. S.X.
0.26 24.4 0.77 At4g37340 829889 CYP81D3 member of CYP81D O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.38	46.7	1.00	At1g71692	843497	AGL12 (AGAMOUS-LIKE 12)	Encodes a member of the MADS box family of transcription factors. Involved in root cell differentiation and flowering time. Loss of function mutations have abnormal cellular differentiation in the roots and are late flowering. AGL12 along with AGL14, and AGL17 is preferentially expressed in root tissues and represent the only characterized MADS box genes expressed in roots.	O.I.	H.G.	S.X.
0.83	91.4	0.77	At4g31100	829237	wall-associated kinase, putative	F:kinase activity;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVA	O.I.	H.G.	S.X.
0.55	70.6	0.78	At5g44160	834439	NUC (nutcracker)	F:transcription factor activity, zinc ion binding, nucleic acid binding;P:regulation of transcription;C:intracellular;MOPF	O.I.	H.G.	S.X.
0.42	53.9	0.76	At5g65790	836708	MYB68 (MYB DOMAIN PROTEIN 68)	Encodes a putative MYB transcription factor.	O.I.	H.G.	S.X.
0.35	41.6	0.76	At2g31020	817653	ORP1A (OSBP(OXYSTEROL BINDING PROTEIN)-RELATED PROTEIN 1A)	F:oxysterol binding;P:steroid metabolic process;C:unknown;MFOPBV	O.I.	H.G.	S.X.
0.26	24.4	0.77	At4g37340	829889	CYP81D3	member of CYP81D	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
87.1 99.9 E-MEXP-1451-raw-cel-1585200170
83.8 99.9 E-MEXP-1451-raw-cel-1585200202
73.5 99.9 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
73.1 99.9 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
65.3 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
64.7 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.7 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.3 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.1 99.8 E-MEXP-1451-raw-cel-1585200234
58.2 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
57.5 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.3 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
56.8 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
54.5 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
54.2 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.3 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
52.3 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
51.3 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
50.2 99.8 E-MEXP-1451-raw-cel-1585200266
50.0 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
48.7 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
48.4 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.9 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
38.4 99.8 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
29.5 99.7 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
23.4 99.6 GSM131687 ATGE_76_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
23.2 99.6 GSM131686 ATGE_76_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
21.1 99.6 GSM131685 ATGE_76_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
16.1 99.5 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.4 99.5 GSM62705 arf6 arf8_stem GSE2848 Auxin Response Factor mediated flower gene expression
14.6 99.4 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
13.0 99.4 GSM128731 Hennig_1-3_siliques-CK_021114_3_A_Rep1_ATH1 GSE5526 Transcriptional Programs of Early Reproductive Stages in Arabidopsis
11.9 99.3 GSM133721 Deeken_A-1-Deeke-Tum_SLD_REP2 GSE5725 Agrobacterium tumefaciens-induced tumour development of Arabidopsis thaliana
11.6 99.3 GSM75510 Col-0 6h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
11.5 99.3 E-MEXP-715-raw-cel-1121836221
10.7 99.2 GSM75514 Col-0 6h NAA replicate 2 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
10.7 99.2 E-MEXP-715-raw-cel-1121836087
10.7 99.2 E-MEXP-1474-raw-cel-1593932897
10.5 99.2 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.5 99.1 E-MEXP-715-raw-cel-1121836361
9.4 99.1 E-MEXP-1474-raw-cel-1593932865
9.1 99.1 E-MEXP-1474-raw-cel-1593932609
8.9 99.0 E-MEXP-715-raw-cel-1121836113
8.9 99.0 E-MEXP-1474-raw-cel-1593932705
8.8 99.0 E-MEXP-1474-raw-cel-1593932929
8.7 99.0 E-MEXP-1474-raw-cel-1593932513

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
87.1	99.9	E-MEXP-1451-raw-cel-1585200170
83.8	99.9	E-MEXP-1451-raw-cel-1585200202
73.5	99.9	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
73.1	99.9	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
65.3	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
64.7	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.7	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.3	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.1	99.8	E-MEXP-1451-raw-cel-1585200234
58.2	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
57.5	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.3	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
56.8	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
54.5	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
54.2	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.3	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
52.3	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
51.3	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
50.2	99.8	E-MEXP-1451-raw-cel-1585200266
50.0	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
48.7	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
48.4	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.9	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
38.4	99.8	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
29.5	99.7	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
23.4	99.6	GSM131687	ATGE_76_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
23.2	99.6	GSM131686	ATGE_76_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
21.1	99.6	GSM131685	ATGE_76_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
16.1	99.5	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.4	99.5	GSM62705	arf6 arf8_stem	GSE2848	Auxin Response Factor mediated flower gene expression
14.6	99.4	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
13.0	99.4	GSM128731	Hennig_1-3_siliques-CK_021114_3_A_Rep1_ATH1	GSE5526	Transcriptional Programs of Early Reproductive Stages in Arabidopsis
11.9	99.3	GSM133721	Deeken_A-1-Deeke-Tum_SLD_REP2	GSE5725	Agrobacterium tumefaciens-induced tumour development of Arabidopsis thaliana
11.6	99.3	GSM75510	Col-0 6h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
11.5	99.3	E-MEXP-715-raw-cel-1121836221
10.7	99.2	GSM75514	Col-0 6h NAA replicate 2	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
10.7	99.2	E-MEXP-715-raw-cel-1121836087
10.7	99.2	E-MEXP-1474-raw-cel-1593932897
10.5	99.2	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.5	99.1	E-MEXP-715-raw-cel-1121836361
9.4	99.1	E-MEXP-1474-raw-cel-1593932865
9.1	99.1	E-MEXP-1474-raw-cel-1593932609
8.9	99.0	E-MEXP-715-raw-cel-1121836113
8.9	99.0	E-MEXP-1474-raw-cel-1593932705
8.8	99.0	E-MEXP-1474-raw-cel-1593932929
8.7	99.0	E-MEXP-1474-raw-cel-1593932513

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.111 1 GO:0008202 The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
0.048 1 GO:0010228 The process involved in transforming a meristem that produces vegetative structures, such as leaves, into a meristem that produces reproductive structures, such as a flower or an inflorescence.
0.023 1 GO:0048364 The process whose specific outcome is the progression of the root over time, from its formation to the mature structure. The root is the water- and mineral-absorbing part of a plant which is usually underground, does not bear leaves, tends to grow downwards and is typically derived from the radicle of the embryo.

SF	Genes	GO ID	Process Name
0.111	1	GO:0008202	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
0.048	1	GO:0010228	The process involved in transforming a meristem that produces vegetative structures, such as leaves, into a meristem that produces reproductive structures, such as a flower or an inflorescence.
0.023	1	GO:0048364	The process whose specific outcome is the progression of the root over time, from its formation to the mature structure. The root is the water- and mineral-absorbing part of a plant which is usually underground, does not bear leaves, tends to grow downwards and is typically derived from the radicle of the embryo.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.028 1 00945 Stilbenoid, diarylheptanoid and gingerol biosynthesis
0.027 1 00903 Limonene and pinene degradation

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.028	1	00945	Stilbenoid, diarylheptanoid and gingerol biosynthesis
0.027	1	00903	Limonene and pinene 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	At1g71692
Gene name	AGL12 (AGAMOUS-LIKE 12)
Module size	6 genes
NF	0.41
%ile	56.9

Co-expression analysis

Gene ID At1g71692 Gene name AGL12 (AGAMOUS-LIKE 12) Module size 6 genes NF 0.41 %ile 56.9

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 KEGG0.028100945Stilbenoid, diarylheptanoid and gingerol biosynthesis0.027100903Limonene and pinene 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 At1g71692

Gene name AGL12 (AGAMOUS-LIKE 12)

Module size 6 genes

NF 0.41

%ile 56.9

: 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
0.028 1 00945 Stilbenoid, diarylheptanoid and gingerol biosynthesis
0.027 1 00903 Limonene and pinene 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