Co-expression analysis

Gene ID	At4g21470
Gene name	ATFMN/FHY (riboflavin kinase/FMN hydrolase)
Module size	5 genes
NF	0.03
%ile	1.8

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
1.00	100.0	1.00	At4g21470	828232	ATFMN/FHY (riboflavin kinase/FMN hydrolase)	Bifunctional enzyme that catalyzes hydrolysis of FMN to riboflavin, and phosphorylation of riboflavin to FMN.	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.60	75.7	0.88	At2g38740	818456	haloacid dehalogenase-like hydrolase family protein	F:hydrolase activity, catalytic activity;P:metabolic process;C:plasma membrane;BOFPMAV	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.40	50.8	0.90	At2g26660	817207	SPX2 (SPX DOMAIN GENE 2)	F:molecular_function unknown;P:cellular response to phosphate starvation;C:nucleus;FMPOB	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.29	30.3	0.89	At2g01350	814663	QPT (QUINOLINATE PHOSHORIBOSYLTRANSFERASE)	At2g01350 encodes quinolinate phosphoribosyl transferase involved in NAD biosynthesis as shown by heterologous expression in E. coli.	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
-	0.0	0.88	At1g16010	838171	magnesium transporter CorA-like family protein (MRS2-1)	F:metal ion transmembrane transporter activity;P:metal ion transport;C:vacuole, membrane;PFOMBA	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)

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
124.4	99.9	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
109.4	99.9	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
87.8	99.9	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
85.4	99.9	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
81.1	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
76.7	99.9	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
74.9	99.9	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
74.4	99.9	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
73.9	99.9	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.7	99.9	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
68.7	99.9	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.2	99.9	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.1	99.9	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
62.2	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
61.4	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
60.3	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
52.6	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.0	99.8	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
51.7	99.8	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
51.0	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.0	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
49.5	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
48.2	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.9	99.8	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
43.1	99.8	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
36.9	99.7	GSM131704	ATGE_83_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
34.4	99.7	GSM142643	MC002_ATH1_A7.3-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
34.0	99.7	GSM10456	WT Post-Mature Green Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
32.8	99.7	GSM131700	ATGE_82_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
32.5	99.7	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
31.3	99.7	GSM131708	ATGE_84_D	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
31.3	99.7	GSM131707	ATGE_84_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
29.4	99.7	GSM131705	ATGE_83_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
29.1	99.7	GSM142641	MC002_ATH1_A7.1-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
28.9	99.7	E-MEXP-509-raw-cel-829148561
28.8	99.7	GSM131703	ATGE_83_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
28.8	99.7	GSM134313	Penfield_1-15_embryo-ABA_Rep3_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
27.9	99.7	GSM134312	Penfield_1-14_embryo-ABA_Rep2_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
27.5	99.7	GSM131706	ATGE_84_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
26.7	99.7	E-MEXP-849-raw-cel-1181980982
26.7	99.7	GSM10454	WT Post-Mature Green Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
26.1	99.7	GSM134311	Penfield_1-13_embryo-ABA_Rep1_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
25.9	99.7	GSM131702	ATGE_82_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
24.9	99.6	GSM142642	MC002_ATH1_A7.2-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
24.8	99.6	GSM131701	ATGE_82_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
24.6	99.6	GSM10451	WT Mature Green Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
24.6	99.6	E-ATMX-1-raw-cel-1112746267
24.1	99.6	E-ATMX-1-raw-cel-1112746209
22.9	99.6	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
22.3	99.6	GSM134316	Penfield_1-18_embryo-PAC_Rep3_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
21.6	99.6	GSM134304	Penfield_1-6_endosperm-ABA_Rep3_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
21.4	99.6	GSM142629	MC002_ATH1_A3.1-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
21.1	99.6	GSM106912	opr3_JA 8hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
20.6	99.6	GSM10453	WT Mature Green Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
20.2	99.6	GSM134302	Penfield_1-4_endosperm-ABA_Rep1_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
19.5	99.6	GSM242958	Mock day 3 (day3E2)	GSE9605	Target genes of AGAMOUS during early flower development in Arabidopsis
19.5	99.6	GSM142644	MC002_ATH1_A8.1-dubos-aih	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
19.2	99.6	GSM242956	Steroid day 1 (day1D2)	GSE9605	Target genes of AGAMOUS during early flower development in Arabidopsis
18.6	99.5	GSM134314	Penfield_1-16_embryo-PAC_Rep1_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
17.6	99.5	E-ATMX-1-raw-cel-1112746154
17.4	99.5	E-MEXP-509-raw-cel-829148456
17.3	99.5	GSM134303	Penfield_1-5_endosperm-ABA_Rep2_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
16.5	99.5	GSM242960	Steroid day 3 (day3D2)	GSE9605	Target genes of AGAMOUS during early flower development in Arabidopsis
15.4	99.5	GSM131697	ATGE_81_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
15.4	99.5	GSM134315	Penfield_1-17_embryo-PAC_Rep2_ATH1	GSE5751	The early post-germinative embryo and endosperm transcriptomes in Arabidopsis
14.6	99.4	GSM131698	ATGE_81_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
14.6	99.4	E-MEXP-849-raw-cel-1181980998
14.1	99.4	E-MEXP-509-raw-cel-829148348
13.8	99.4	GSM305282	estradiol induced, biological replicate 1	GSE12137	LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis thaliana
13.5	99.4	GSM153927	ahg1-1 rep2	GSE6638	Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA
13.5	99.4	GSM131699	ATGE_81_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
13.0	99.4	GSM142645	MC002_ATH1_A8.2-dubos-aih	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
12.9	99.3	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
12.8	99.3	E-MEXP-509-raw-cel-829148525
12.3	99.3	GSM142623	MC002_ATH1_A1.1-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
12.1	99.3	GSM142631	MC002_ATH1_A3.3-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.8	99.3	E-MEXP-509-raw-cel-829148129
11.6	99.3	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
11.6	99.3	GSM153926	ahg1-1 rep1	GSE6638	Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA
11.0	99.2	GSM242954	Mock day 1 (day1E2)	GSE9605	Target genes of AGAMOUS during early flower development in Arabidopsis
11.0	99.2	GSM133817	Yang_1-2_old-pod_Rep1_ATH1	GSE5736	To identify changes in gene expression during silique senescence in Arabidopsis thaliana
10.9	99.2	E-MEXP-849-raw-cel-1181980990
10.9	99.2	E-MEXP-509-raw-cel-829148420
10.9	99.2	GSM133720	Deeken_A-2-Deeke-Inf_SLD_REP1	GSE5725	Agrobacterium tumefaciens-induced tumour development of Arabidopsis thaliana
10.4	99.2	GSM153928	ahg3-1 rep1	GSE6638	Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA
10.4	99.2	E-MEXP-849-raw-cel-1181981006
10.4	99.2	GSM131696	ATGE_79_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
10.2	99.2	E-MEXP-509-raw-cel-829148597
9.8	99.1	GSM131694	ATGE_79_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
9.8	99.1	GSM142624	MC002_ATH1_A1.2-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.8	99.1	GSM10483	lec1-1 Post-Mature Green Seed 1	GSE1051	Seed development in LEAFY COTYLEDON1 mutants
9.7	99.1	GSM131695	ATGE_79_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
9.7	99.1	E-MEXP-849-raw-cel-1181981030
9.6	99.1	GSM106914	opr3_JA_8 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.6	99.1	GSM67080	Arabidopsis_Ovary03	GSE3056	Arabidopsis Pollination Study
9.0	99.1	GSM133117	RIKEN-YAMAUCHI1A	GSE5687	AtGenExpress: Different temperature treatment of seeds
8.9	99.0	E-MEXP-509-raw-cel-829148632
8.7	99.0	GSM10479	lec1-1 Cotyledon Stage Seed 1	GSE1051	Seed development in LEAFY COTYLEDON1 mutants
8.6	99.0	GSM142646	MC002_ATH1_A8.3-dubos-aih	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis

Biological processes inferred to relate to the module

SF	Genes	GO ID	Process Name	Link to AmiGO
0.200	1	GO:0009435	The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
0.133	1	GO:0009231	The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).
0.048	1	GO:0016036	A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of phosphate.

KEGG PATHWAY inferred to related to the module

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.154	1	00740	Riboflavin metabolism
0.154	1	00760	Nicotinate and nicotinamide metabolism
0.012	1	01064	Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
0.003	2	01100	Metabolic pathways

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

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