Other supporting information

Gene Model

Correlation Plot

Expression profile (Values are plotted in Log(2) values.)

Genes with related expresssion profiles.

Positively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
OMAT1P021825	0.84893	-	-	-	AT1G74840	myb family transcription factor
OMAT5P006940	0.843452	-	AT5G20050	protein kinase family protein	-	-
OMAT2P110170	0.830208	-	AT2G40860	protein kinase family protein / protein phosphatase 2C ( PP2C) family protein	-	-
OMAT2P013370	0.82823	-	AT2G46790	APRR9 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9)	-	-
OMAT5P115250	0.826414	-	AT5G57890	anthranilate synthase beta subunit, putative	-	-
OMAT3P009480	0.824705	-	AT3G25250	AGC2-1 (OXIDATIVE SIGNAL-INDUCIBLE1)	-	-
OMAT1P110510	0.822346	-	AT1G33475	INVOLVED IN: transport, vesicle-mediated transport	-	-
OMAT4P104540	0.81806	-	AT4G18230	FUNCTIONS IN: molecular_function unknown	-	-
OMAT3P114675	0.817773	-	AT3G59060	PIL6 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 6)	-	-
OMAT4P106140	0.805918	-	AT4G23190	CRK11 (CYSTEINE-RICH RLK11)	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
OMAT1P002090	-0.768613	-	AT1G06500	unknown protein	-	-
OMAT1P012920	-0.73925	-	AT1G47250	PAF2	-	-
OMAT2P007060	-0.734951	-	AT2G30100	ubiquitin family protein	-	-
OMAT3P001670	-0.732025	-	AT3G04830	binding	-	-
OMAT2P010100	-0.717854	-	AT2G38550	unknown protein	-	-
OMAT4P010370	-0.710323	-	AT4G31300	PBA1	-	-
OMAT4P009520	-0.706691	-	AT4G29040	RPT2a (regulatory particle AAA-ATPase 2a)	-	-
OMAT1P012250	-0.701625	-	AT1G35620	ATPDIL5-2 (PDI-LIKE 5-2)	-	-
OMAT5P020150	-0.698411	-	AT5G65270	AtRABA4a (Arabidopsis Rab GTPase homolog A4a)	-	-
OMAT3P104160	-0.695594	-	AT3G12650	unknown protein	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 3.07e-16	:20 terms with high significance
3.07e-16 <	p-value	<= 8.76e-06	:With considering multiple testing correction; p <= 1.00e-02 / 1142
8.76e-06 <	p-value	<= 1.00e-02

Type of term (*1)	Depth of the term in ontology tree	ID/Term	Description	Number of genes	Over-Representative rate (*2)	p-value (*3)	PosMed p-value (*4) (Link to PosMed)	Found on gene annotation
B	3	GO:0042221	response to chemical stimulus	32/200	2.81	3.68e-08	-	no
B	3	GO:0050794	regulation of cellular process	38/200	2.49	4.96e-08	-	no
B	3	GO:0006950	response to stress	33/200	2.66	8.11e-08	-	no
B	3	GO:0050789	regulation of biological process	40/200	2.31	1.65e-07	-	no
B	3	GO:0009628	response to abiotic stimulus	23/200	3.10	4.55e-07	-	no
B	5	GO:0010556	regulation of macromolecule biosynthetic process	27/200	2.74	6.47e-07	-	no
B	5	GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	27/200	2.69	9.13e-07	-	no
B	4	GO:0009889	regulation of biosynthetic process	27/200	2.69	9.46e-07	-	no
B	5	GO:0031326	regulation of cellular biosynthetic process	27/200	2.69	9.46e-07	-	no
B	4	GO:0051171	regulation of nitrogen compound metabolic process	27/200	2.67	1.11e-06	-	no
B	5	GO:0006350	transcription	27/200	2.65	1.29e-06	-	no
B	5	GO:0051252	regulation of RNA metabolic process	18/200	3.44	1.47e-06	-	no
B	4	GO:0080090	regulation of primary metabolic process	27/200	2.56	2.36e-06	-	no
B	5	GO:0032774	RNA biosynthetic process	18/200	3.29	2.92e-06	-	no
B	5	GO:0010468	regulation of gene expression	27/200	2.53	2.97e-06	-	no
B	4	GO:0031323	regulation of cellular metabolic process	27/200	2.50	3.91e-06	-	no
B	4	GO:0010033	response to organic substance	20/200	2.99	4.04e-06	-	no
B	4	GO:0060255	regulation of macromolecule metabolic process	27/200	2.47	4.92e-06	-	no
B	4	GO:0006970	response to osmotic stress	11/200	4.39	9.49e-06	-	no
B	3	GO:0006807	nitrogen compound metabolic process	39/200	1.97	1.32e-05	-	no
B	3	GO:0019222	regulation of metabolic process	27/200	2.29	1.88e-05	-	no
B	4	GO:0034641	cellular nitrogen compound metabolic process	38/200	1.95	1.98e-05	-	no
B	3	GO:0051707	response to other organism	12/200	3.58	3.64e-05	-	no
B	5	GO:0090304	nucleic acid metabolic process	31/200	2.06	4.00e-05	-	no
B	5	GO:0016070	RNA metabolic process	21/200	2.47	4.69e-05	-	no
B	4	GO:0006952	defense response	14/200	3.08	5.97e-05	-	no
B	3	GO:0009719	response to endogenous stimulus	15/200	2.91	6.82e-05	-	no
B	3	GO:0009607	response to biotic stimulus	12/200	3.32	7.86e-05	-	no
B	3	GO:0044237	cellular metabolic process	70/200	1.48	9.86e-05	-	no
B	5	GO:0006796	phosphate metabolic process	17/200	2.56	1.33e-04	-	no
B	4	GO:0006793	phosphorus metabolic process	17/200	2.56	1.35e-04	-	no
B	4	GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	32/200	1.90	1.53e-04	-	no
B	4	GO:0009725	response to hormone stimulus	13/200	2.75	3.14e-04	-	no
B	4	GO:0044260	cellular macromolecule metabolic process	54/200	1.53	3.40e-04	-	no
B	3	GO:0009058	biosynthetic process	46/200	1.58	5.06e-04	-	no
B	3	GO:0051716	cellular response to stimulus	12/200	2.71	5.48e-04	-	no
B	3	GO:0023033	signaling pathway	10/200	2.96	6.43e-04	-	no
B	5	GO:0006464	protein modification process	21/200	2.02	7.83e-04	-	no
B	4	GO:0044249	cellular biosynthetic process	43/200	1.53	1.53e-03	-	no
B	3	GO:0044238	primary metabolic process	67/200	1.35	2.12e-03	-	no
B	4	GO:0043412	macromolecule modification	21/200	1.85	2.31e-03	-	no
B	3	GO:0043170	macromolecule metabolic process	54/200	1.40	3.16e-03	-	no
B	5	GO:0034645	cellular macromolecule biosynthetic process	33/200	1.53	5.01e-03	-	no
B	4	GO:0009059	macromolecule biosynthetic process	33/200	1.53	5.25e-03	-	no

C	5	GO:0005634	nucleus	34/200	2.17	5.61e-06	-	no
C	4	GO:0043231	intracellular membrane-bounded organelle	69/200	1.57	1.61e-05	-	no
C	3	GO:0043227	membrane-bounded organelle	69/200	1.57	1.62e-05	-	no
C	3	GO:0043229	intracellular organelle	69/200	1.49	8.69e-05	-	no
C	3	GO:0005622	intracellular	76/200	1.43	1.54e-04	-	no
C	3	GO:0044424	intracellular part	71/200	1.39	6.12e-04	-	no
C	3	GO:0044464	cell part	111/200	1.21	2.24e-03	-	no

M	3	GO:0003700	transcription factor activity	32/200	3.17	1.94e-09	-	no
M	4	GO:0003677	DNA binding	36/200	2.60	3.82e-08	-	no
M	3	GO:0016740	transferase activity	39/200	2.38	1.05e-07	-	no
M	5	GO:0016301	kinase activity	25/200	3.11	1.52e-07	-	no
M	4	GO:0016772	transferase activity, transferring phosphorus-containing groups	27/200	2.94	1.54e-07	-	no
M	3	GO:0004871	signal transducer activity	10/200	4.45	1.84e-05	-	no
M	3	GO:0003676	nucleic acid binding	41/200	1.73	1.57e-04	-	no
M	5	GO:0016773	phosphotransferase activity, alcohol group as acceptor	16/200	2.58	1.82e-04	-	no
M	3	GO:0005515	protein binding	27/200	1.73	1.95e-03	-	no
M	5	GO:0046872	metal ion binding	24/200	1.77	2.35e-03	-	no
M	4	GO:0043169	cation binding	24/200	1.67	4.89e-03	-	no
M	3	GO:0043167	ion binding	24/200	1.67	4.89e-03	-	no

PS	4	PO:0020030	cotyledon	142/200	1.93	1.32e-23	-	yes
PS	4	PO:0009047	stem	152/200	1.80	4.23e-23	-	yes
PS	5	PO:0009028	microsporophyll	149/200	1.78	1.71e-21	-	yes
PS	3	PO:0006001	phyllome	165/200	1.61	5.05e-21	-	yes
PS	4	PO:0009025	leaf	155/200	1.69	1.59e-20	-	yes
PS	4	PO:0009026	sporophyll	152/200	1.69	8.84e-20	-	yes
PS	5	PO:0008037	seedling	150/200	1.70	1.49e-19	-	yes
PS	3	PO:0009006	shoot	167/200	1.54	4.40e-19	-	yes
PS	5	PO:0020039	leaf lamina	142/200	1.72	3.50e-18	-	yes
PS	5	PO:0009046	flower	161/200	1.55	1.07e-17	-	yes
PS	4	PO:0009049	inflorescence	161/200	1.54	2.21e-17	-	yes
PS	4	PO:0009009	embryo	153/200	1.58	7.63e-17	-	yes
PS	5	PO:0008034	leaf whorl	150/200	1.59	2.33e-16	-	yes
PS	4	PO:0008033	phyllome whorl	150/200	1.59	2.33e-16	-	yes
PS	3	PO:0009010	seed	153/200	1.56	3.07e-16	-	yes
PS	4	PO:0009001	fruit	153/200	1.56	5.47e-16	-	yes
PS	3	PO:0006342	infructescence	153/200	1.56	5.47e-16	-	yes
PS	5	PO:0020038	petiole	131/200	1.72	1.01e-15	-	yes
PS	5	PO:0000013	cauline leaf	132/200	1.71	1.22e-15	-	yes
PS	3	PO:0009031	sepal	146/200	1.58	3.39e-15	-	yes
PS	4	PO:0000230	inflorescence meristem	131/200	1.69	6.47e-15	-	yes
PS	3	PO:0009013	meristem	133/200	1.66	1.44e-14	-	yes
PS	3	PO:0009005	root	140/200	1.56	2.33e-13	-	yes
PS	3	PO:0009032	petal	136/200	1.55	1.45e-12	-	yes
PS	5	PO:0009027	megasporophyll	132/200	1.57	2.07e-12	-	yes
PS	4	PO:0000037	shoot apex	130/200	1.51	1.14e-10	-	yes
PS	3	PO:0020091	male gametophyte	126/200	1.52	2.54e-10	-	yes
PS	5	PO:0009052	pedicel	118/200	1.45	5.51e-08	-	yes
PS	4	PO:0006345	pollen tube	45/200	1.54	9.45e-04	-	no

PG	3	PO:0007134	A vegetative growth	146/200	1.72	3.45e-19	-	yes
PG	5	PO:0007133	leaf production	145/200	1.72	6.07e-19	-	yes
PG	4	PO:0007112	1 main shoot growth	145/200	1.72	6.21e-19	-	yes
PG	3	PO:0007615	flower development stages	160/200	1.53	9.32e-17	-	yes
PG	4	PO:0007600	3 floral organ development stages	157/200	1.54	1.85e-16	-	yes
PG	4	PO:0007616	4 anthesis	152/200	1.57	4.05e-16	-	yes
PG	4	PO:0001054	4 leaf senescence stage	132/200	1.72	8.13e-16	-	yes
PG	5	PO:0007604	corolla developmental stages	153/200	1.55	8.38e-16	-	yes
PG	3	PO:0001050	leaf development stages	132/200	1.72	8.55e-16	-	yes
PG	5	PO:0001185	C globular stage	126/200	1.54	1.11e-10	-	yes
PG	4	PO:0007631	embryo development stages	133/200	1.48	2.80e-10	-	yes
PG	3	PO:0001170	seed development stages	133/200	1.47	3.98e-10	-	yes
PG	5	PO:0004507	D bilateral stage	122/200	1.48	5.18e-09	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	119/200	1.43	9.74e-08	-	no
PG	5	PO:0001081	F mature embryo stage	108/200	1.36	1.70e-05	-	no
PG	5	PO:0007605	androecium developmental stages	41/200	1.40	9.30e-03	-	no

KW	0	response	-	50/200	2.79	4.86e-12	-	no
KW	0	transcription	-	41/200	2.82	3.51e-10	-	no
KW	0	nucleus	-	34/200	2.64	6.54e-08	-	no
KW	0	factor	-	40/200	2.28	2.26e-07	-	no
KW	0	stress	-	18/200	3.84	2.94e-07	-	no
KW	0	ipr000719	-	21/200	3.37	3.40e-07	-	no
KW	0	ipr008271	-	18/200	3.69	5.39e-07	-	no
KW	0	ipr011009	-	21/200	3.25	6.31e-07	-	no
KW	0	ipr017442	-	18/200	3.42	1.65e-06	-	no
KW	0	threonine	-	21/200	2.80	6.93e-06	-	no
KW	0	kinase	-	26/200	2.46	7.39e-06	-	no
KW	0	ipr017441	-	15/200	3.49	7.56e-06	-	no
KW	0	active	-	21/200	2.57	2.65e-05	-	no
KW	0	transduction	-	12/200	3.63	3.20e-05	-	no
KW	0	serine	-	22/200	2.47	3.24e-05	-	no
KW	0	stimulus	-	13/200	3.02	1.21e-04	-	no
KW	0	regulation	-	27/200	2.04	1.40e-04	-	no
KW	0	signal	-	13/200	2.96	1.48e-04	-	no
KW	0	major	-	10/200	3.50	1.56e-04	-	no
KW	0	phosphorylation	-	16/200	2.60	1.62e-04	-	no
KW	0	regulator	-	10/200	3.42	1.90e-04	-	no
KW	0	defense	-	11/200	3.15	2.23e-04	-	no
KW	0	related	-	44/200	1.57	8.06e-04	-	no
KW	0	amino	-	18/200	2.09	1.10e-03	-	no
KW	0	leucine	-	12/200	2.29	2.55e-03	-	no
KW	0	finger	-	17/200	1.84	5.55e-03	-	no
KW	0	class	-	12/200	2.00	7.55e-03	-	no
KW	0	dependent	-	22/200	1.64	8.03e-03	-	no

(*1)	[B]:Biological process(Gene ontology), [C]:Cellular component(Gene ontology), [M]:Molecular function(Gene ontology), [PS]:Plant Structure(Plant ontology), [PG]:Growth and developmental stages(Plant ontology), [KW]:words found in gene description.
(*2)	([# of genes with the term] / [# of sampling (200)]) / ([# of genes with the term among whole genes] / [# of whole genes])
(*3)	P-values were calculated on hypergeometric distribution in which we found n genes with a annotation term during 200 highly correlated genes, while we had N genes with the term in the whole genes.
(*4)	PosMed is a system which serve a p-values showing a relationship between the gene and the annotation term based on literature information and Gene-Gene interaction suchas co-expression or protein-protein interactions.

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