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
OMAT5P114150	0.909775	-	AT5G54380	THE1 (THESEUS1)	-	-
OMAT2P012380	0.895365	-	AT2G44500	unknown protein	-	-
OMAT3P002950	0.89308	-	AT3G08600	unknown protein	-	-
OMAT5P108700	0.88421	-	AT5G35750	AHK2 (ARABIDOPSIS HISTIDINE KINASE 2)	-	-
OMAT3P015040	0.879491	-	AT3G54810	zinc finger (GATA type) family protein	-	-
OMAT4P100805	0.873343	-	AT4G02130	GATL6	-	-
OMAT2P109480	0.87172	-	AT2G39180	CCR2 (ARABIDOPSIS THALIANA CRINKLY4 RELATED 2)	-	-
OMAT1P103180	0.865656	-	AT1G10020	unknown protein	-	-
OMAT4P102560	0.86242	-	AT4G12420	SKU5	-	-
OMAT1P022900	0.86197	-	AT1G77640	AP2 domain-containing transcription factor, putative	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
OMAT3P001090	-0.771034	-	AT3G03340	UNE6 (unfertilized embryo sac 6)	AT3G03341	unknown protein
OMAT4P008190	-0.748693	-	AT4G26000	PEP (PEPPER)	-	-
OMAT1P022050	-0.731502	-	AT1G75400	protein binding / zinc ion binding	-	-
OMAT5P020960	-0.729373	-	AT5G67330	ATNRAMP4	-	-
OMAT3P008700	-0.724468	-	AT3G22990	LFR (LEAF AND FLOWER RELATED)	-	-
OMAT2P107920	-0.724282	-	AT2G35345	unknown protein	-	-
OMAT3P015340	-0.71667	-	AT3G55520	immunophilin, putative / FKBP-type peptidyl-prolyl cis-trans isomerase, putative	-	-
OMAT3P101010	-0.711337	-	AT3G03341	unknown protein	-	-
OMAT4P004290	-0.708942	-	AT4G15410	PUX5 (Arabidopsis thaliana serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B prime gamma)	-	-
OMAT4P009710	-0.708746	-	AT4G29490	aminopeptidase/ manganese ion binding	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 2.57e-36	:20 terms with high significance
2.57e-36 <	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:0065008	regulation of biological quality	18/200	4.82	8.40e-09	-	no
B	3	GO:0016049	cell growth	11/200	6.88	8.64e-08	-	no
B	5	GO:0032535	regulation of cellular component size	11/200	6.63	1.29e-07	-	no
B	4	GO:0090066	regulation of anatomical structure size	11/200	6.63	1.29e-07	-	no
B	5	GO:0006796	phosphate metabolic process	22/200	3.31	2.52e-07	-	yes
B	4	GO:0006793	phosphorus metabolic process	22/200	3.31	2.56e-07	-	yes
B	3	GO:0009719	response to endogenous stimulus	17/200	3.30	4.89e-06	-	no
B	5	GO:0006464	protein modification process	26/200	2.50	5.76e-06	-	yes
B	3	GO:0023033	signaling pathway	13/200	3.85	8.83e-06	-	no
B	4	GO:0010033	response to organic substance	19/200	2.84	1.41e-05	-	no
B	4	GO:0009725	response to hormone stimulus	15/200	3.17	2.45e-05	-	no
B	4	GO:0043412	macromolecule modification	26/200	2.29	2.64e-05	-	yes
B	3	GO:0048869	cellular developmental process	10/200	3.60	1.22e-04	-	no
B	3	GO:0009653	anatomical structure morphogenesis	11/200	3.27	1.59e-04	-	no
B	3	GO:0042221	response to chemical stimulus	24/200	2.10	1.95e-04	-	no
B	3	GO:0009628	response to abiotic stimulus	17/200	2.29	4.97e-04	-	no
B	4	GO:0005975	carbohydrate metabolic process	13/200	2.50	8.12e-04	-	no
B	3	GO:0050794	regulation of cellular process	25/200	1.64	5.39e-03	-	no

C	4	GO:0005886	plasma membrane	43/200	3.47	1.31e-13	3.64E-21	yes
C	3	GO:0016020	membrane	59/200	2.15	1.66e-09	3.64E-21	yes
C	3	GO:0044464	cell part	132/200	1.44	2.43e-09	-	yes
C	4	GO:0005618	cell wall	17/200	5.12	7.97e-09	-	no
C	3	GO:0030312	external encapsulating structure	17/200	5.08	8.90e-09	-	no
C	5	GO:0009505	plant-type cell wall	11/200	6.98	7.33e-08	-	no
C	5	GO:0005773	vacuole	16/200	4.63	8.43e-08	-	no
C	4	GO:0005737	cytoplasm	55/200	1.47	8.61e-04	-	no
C	4	GO:0044444	cytoplasmic part	50/200	1.44	2.36e-03	-	no
C	4	GO:0031224	intrinsic to membrane	11/200	2.05	8.07e-03	-	no

M	3	GO:0016740	transferase activity	43/200	2.63	1.16e-09	-	yes
M	5	GO:0016301	kinase activity	27/200	3.36	1.00e-08	-	yes
M	4	GO:0016772	transferase activity, transferring phosphorus-containing groups	28/200	3.05	4.27e-08	-	yes
M	5	GO:0016773	phosphotransferase activity, alcohol group as acceptor	22/200	3.54	7.66e-08	-	yes
M	5	GO:0016758	transferase activity, transferring hexosyl groups	10/200	5.64	1.96e-06	-	no
M	4	GO:0016757	transferase activity, transferring glycosyl groups	11/200	3.77	4.17e-05	-	no
M	4	GO:0017076	purine nucleotide binding	20/200	1.93	1.76e-03	-	yes
M	5	GO:0032555	purine ribonucleotide binding	19/200	1.94	2.09e-03	-	yes
M	4	GO:0032553	ribonucleotide binding	19/200	1.94	2.09e-03	-	yes
M	3	GO:0000166	nucleotide binding	23/200	1.74	3.40e-03	-	yes
M	5	GO:0030554	adenyl nucleotide binding	17/200	1.88	4.43e-03	-	yes
M	4	GO:0001883	purine nucleoside binding	17/200	1.88	4.43e-03	-	yes
M	3	GO:0001882	nucleoside binding	17/200	1.87	4.55e-03	-	yes

PS	5	PO:0020038	petiole	175/200	2.30	5.49e-49	-	yes
PS	5	PO:0020039	leaf lamina	178/200	2.16	1.50e-46	-	yes
PS	4	PO:0020030	cotyledon	168/200	2.29	2.71e-44	-	yes
PS	5	PO:0000013	cauline leaf	169/200	2.19	6.75e-42	-	yes
PS	4	PO:0009025	leaf	180/200	1.96	8.47e-41	-	yes
PS	4	PO:0009026	sporophyll	178/200	1.98	2.87e-40	-	yes
PS	5	PO:0009028	microsporophyll	172/200	2.05	2.85e-39	-	yes
PS	5	PO:0009027	megasporophyll	172/200	2.05	3.44e-39	-	yes
PS	5	PO:0008037	seedling	175/200	1.98	1.17e-38	-	yes
PS	4	PO:0000037	shoot apex	173/200	2.01	1.75e-38	-	yes
PS	3	PO:0009013	meristem	168/200	2.09	2.21e-38	-	yes
PS	4	PO:0000230	inflorescence meristem	165/200	2.12	7.69e-38	-	yes
PS	5	PO:0008034	leaf whorl	178/200	1.89	5.53e-37	-	yes
PS	4	PO:0008033	phyllome whorl	178/200	1.89	5.53e-37	-	yes
PS	3	PO:0009032	petal	172/200	1.96	2.57e-36	-	yes
PS	3	PO:0006001	phyllome	183/200	1.78	5.36e-36	-	yes
PS	3	PO:0009005	root	173/200	1.92	1.81e-35	-	yes
PS	4	PO:0009047	stem	168/200	1.99	3.11e-35	-	yes
PS	3	PO:0009031	sepal	174/200	1.88	1.25e-34	-	yes
PS	5	PO:0009052	pedicel	164/200	2.02	3.97e-34	-	yes
PS	4	PO:0009009	embryo	176/200	1.82	2.07e-33	-	yes
PS	4	PO:0009001	fruit	177/200	1.80	4.01e-33	-	yes
PS	3	PO:0006342	infructescence	177/200	1.80	4.01e-33	-	yes
PS	3	PO:0009010	seed	176/200	1.80	1.45e-32	-	yes
PS	5	PO:0009046	flower	180/200	1.73	5.22e-32	-	yes
PS	3	PO:0009006	shoot	183/200	1.69	7.47e-32	-	yes
PS	4	PO:0009049	inflorescence	180/200	1.72	1.37e-31	-	yes
PS	3	PO:0020091	male gametophyte	159/200	1.92	5.81e-29	-	no
PS	5	PO:0006016	leaf epidermis	19/200	1.71	8.22e-03	-	no
PS	4	PO:0006345	pollen tube	41/200	1.41	8.53e-03	-	no
PS	3	PO:0004013	epidermal cell	20/200	1.68	8.57e-03	-	no
PS	5	PO:0006035	shoot epidermis	19/200	1.70	8.84e-03	-	no

PG	3	PO:0007134	A vegetative growth	176/200	2.08	1.67e-42	-	yes
PG	5	PO:0007133	leaf production	175/200	2.08	5.54e-42	-	yes
PG	4	PO:0007112	1 main shoot growth	175/200	2.08	5.73e-42	-	yes
PG	4	PO:0001054	4 leaf senescence stage	168/200	2.18	3.09e-41	-	yes
PG	3	PO:0001050	leaf development stages	168/200	2.18	3.36e-41	-	yes
PG	5	PO:0001185	C globular stage	166/200	2.02	2.92e-35	-	yes
PG	3	PO:0001170	seed development stages	173/200	1.91	3.95e-35	-	yes
PG	4	PO:0007631	embryo development stages	172/200	1.91	1.62e-34	-	yes
PG	5	PO:0004507	D bilateral stage	165/200	2.00	3.66e-34	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	165/200	1.99	1.09e-33	-	yes
PG	5	PO:0007604	corolla developmental stages	177/200	1.79	7.36e-33	-	yes
PG	4	PO:0007616	4 anthesis	175/200	1.80	2.90e-32	-	yes
PG	5	PO:0001081	F mature embryo stage	160/200	2.01	3.53e-32	-	yes
PG	4	PO:0007600	3 floral organ development stages	178/200	1.75	1.31e-31	-	yes
PG	3	PO:0007615	flower development stages	179/200	1.71	1.30e-30	-	yes

KW	0	plasma	-	41/200	3.58	1.89e-13	3.64E-21	yes
KW	0	ipr001245	-	15/200	5.88	7.35e-09	-	no
KW	0	membrane	-	56/200	2.10	1.15e-08	3.64E-21	yes
KW	0	ipr000719	-	23/200	3.69	1.89e-08	-	yes
KW	0	tyrosine	-	17/200	4.79	2.20e-08	2.00E-17	no
KW	0	ipr011009	-	23/200	3.56	3.78e-08	-	yes
KW	0	phosphorylation	-	22/200	3.58	6.44e-08	-	yes
KW	0	ipr017441	-	18/200	4.19	7.59e-08	-	yes
KW	0	vacuole	-	15/200	4.76	1.36e-07	-	no
KW	0	threonine	-	24/200	3.20	1.50e-07	2.00E-71	yes
KW	0	kinase	-	29/200	2.75	2.45e-07	0	yes
KW	0	ipr008271	-	17/200	3.48	2.32e-06	-	yes
KW	0	active	-	23/200	2.81	2.59e-06	-	yes
KW	0	terminal	-	40/200	2.08	2.70e-06	-	no
KW	0	serine	-	24/200	2.69	3.44e-06	2.00E-71	yes
KW	0	amino	-	23/200	2.67	6.12e-06	6.00E-30	yes
KW	0	ipr002290	-	12/200	4.07	9.58e-06	-	no
KW	0	ipr017442	-	15/200	2.85	8.79e-05	-	yes
KW	0	signaling	-	12/200	3.22	1.05e-04	-	no
KW	0	glycosyl	-	12/200	2.81	3.91e-04	-	no
KW	0	function	-	28/200	1.80	8.94e-04	7.00E-59	no
KW	0	carbohydrate	-	10/200	2.55	2.10e-03	-	no
KW	0	subgroup	-	10/200	2.46	2.74e-03	1.00E-56	no
KW	0	encodes	-	38/200	1.49	4.43e-03	-	no
KW	0	response	-	28/200	1.56	6.81e-03	-	no
KW	0	receptor	-	10/200	2.10	8.73e-03	7.00E-74	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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