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
OMAT2P013920	0.943437	-	AT2G48010	RKF3 (RECEPTOR-LIKE KINASE IN IN FLOWERS 3)	-	-
OMAT5P000430	0.887443	-	AT5G02100	UNE18 (UNFERTILIZED EMBRYO SAC 18)	-	-
OMAT1P007120	0.886589	-	AT1G19394,AT1G19397	[AT1G19394]unknown protein, [AT1G19397]unknown protein	-	-
OMAT5P020565	0.882901	-	AT5G66250	kinectin-related	-	-
OMAT1P109270	0.878553	-	AT1G29350,AT1G29357	[AT1G29350]FUNCTIONS IN: molecular_function unknown, [AT1G29357]other RNA	AT1G29355	unknown protein
OMAT2P010160	0.877724	-	AT2G38800	calmodulin-binding protein-related	-	-
OMAT5P006500	0.871496	-	AT5G18780	F-box family protein	-	-
OMAT4P003290	0.867409	-	AT4G12760	unknown protein	-	-
OMAT2P103840	0.856309	-	AT2G22570	NIC1 (NICOTINAMIDASE 1)	-	-
OMAT4P002360	0.849073	-	AT4G09830	FUNCTIONS IN: molecular_function unknown	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
OMAT3P017690	-0.787302	-	AT3G62030	peptidyl-prolyl cis-trans isomerase, chloroplast / cyclophilin / rotamase / cyclosporin A-binding protein (ROC4)	-	-
OMAT3P109280	-0.777349	-	AT3G28460	unknown protein	-	-
OMAT5P016080	-0.776937	-	AT5G54600	50S ribosomal protein L24, chloroplast (CL24)	-	-
OMAT3P005490	-0.761752	-	AT3G15190	chloroplast 30S ribosomal protein S20, putative	-	-
OMAT1P023410	-0.759073	-	AT1G78630	emb1473 (embryo defective 1473)	-	-
OMAT2P100520	-0.757316	-	AT2G02500	ISPD	-	-
OMAT3P108430	-0.755476	-	AT3G25920	RPL15	-	-
OMAT3P102800	-0.752132	-	AT3G08740	elongation factor P (EF-P) family protein	-	-
OMAT3P004090	-0.741442	-	AT3G11630	2-cys peroxiredoxin, chloroplast (BAS1)	-	-
OMAT3P108340	-0.740974	-	AT3G25660	glutamyl-tRNA(Gln) amidotransferase, putative	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 1.34e-19	:20 terms with high significance
1.34e-19 <	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	5	GO:0006796	phosphate metabolic process	18/200	2.71	4.23e-05	-	no
B	4	GO:0006793	phosphorus metabolic process	18/200	2.71	4.28e-05	-	no
B	3	GO:0050794	regulation of cellular process	30/200	1.97	1.26e-04	-	no
B	3	GO:0050789	regulation of biological process	31/200	1.79	5.19e-04	-	no
B	4	GO:0031323	regulation of cellular metabolic process	22/200	2.03	5.43e-04	-	no
B	5	GO:0006464	protein modification process	21/200	2.02	7.83e-04	-	no
B	4	GO:0080090	regulation of primary metabolic process	21/200	1.99	9.09e-04	-	no
B	5	GO:0010556	regulation of macromolecule biosynthetic process	20/200	2.03	9.27e-04	-	no
B	5	GO:0090304	nucleic acid metabolic process	27/200	1.80	1.07e-03	-	no
B	5	GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	20/200	1.99	1.15e-03	-	no
B	4	GO:0009889	regulation of biosynthetic process	20/200	1.99	1.18e-03	-	no
B	5	GO:0031326	regulation of cellular biosynthetic process	20/200	1.99	1.18e-03	-	no
B	4	GO:0051171	regulation of nitrogen compound metabolic process	20/200	1.97	1.31e-03	-	no
B	5	GO:0006350	transcription	20/200	1.96	1.44e-03	-	no
B	4	GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	29/200	1.72	1.47e-03	-	no
B	4	GO:0060255	regulation of macromolecule metabolic process	21/200	1.92	1.49e-03	-	no
B	3	GO:0019222	regulation of metabolic process	22/200	1.87	1.68e-03	-	no
B	4	GO:0034641	cellular nitrogen compound metabolic process	32/200	1.64	1.82e-03	-	no
B	4	GO:0043412	macromolecule modification	21/200	1.85	2.31e-03	-	no
B	5	GO:0010468	regulation of gene expression	20/200	1.88	2.41e-03	-	no
B	3	GO:0006807	nitrogen compound metabolic process	32/200	1.61	2.50e-03	-	no
B	4	GO:0044260	cellular macromolecule metabolic process	50/200	1.42	3.22e-03	-	no
B	3	GO:0044237	cellular metabolic process	63/200	1.33	4.17e-03	-	no
B	3	GO:0051234	establishment of localization	18/200	1.75	7.53e-03	-	no
B	3	GO:0043170	macromolecule metabolic process	52/200	1.34	8.23e-03	-	no

C	4	GO:0005886	plasma membrane	35/200	2.83	7.14e-09	-	no
C	3	GO:0016020	membrane	49/200	1.79	1.34e-05	-	no
C	5	GO:0005634	nucleus	29/200	1.85	4.35e-04	-	no
C	3	GO:0044464	cell part	109/200	1.19	5.27e-03	-	no

M	5	GO:0016773	phosphotransferase activity, alcohol group as acceptor	18/200	2.90	1.69e-05	-	no
M	4	GO:0016772	transferase activity, transferring phosphorus-containing groups	21/200	2.29	1.40e-04	-	no
M	5	GO:0016301	kinase activity	19/200	2.36	1.79e-04	-	no
M	3	GO:0000166	nucleotide binding	25/200	1.89	7.44e-04	-	no
M	3	GO:0003700	transcription factor activity	20/200	1.98	1.26e-03	-	no
M	4	GO:0003677	DNA binding	25/200	1.80	1.47e-03	-	no
M	4	GO:0017076	purine nucleotide binding	20/200	1.93	1.76e-03	-	no
M	5	GO:0030554	adenyl nucleotide binding	18/200	1.99	1.92e-03	-	no
M	4	GO:0001883	purine nucleoside binding	18/200	1.99	1.92e-03	-	no
M	3	GO:0001882	nucleoside binding	18/200	1.98	1.98e-03	-	no
M	5	GO:0032555	purine ribonucleotide binding	19/200	1.94	2.09e-03	-	no
M	4	GO:0032553	ribonucleotide binding	19/200	1.94	2.09e-03	-	no
M	3	GO:0005515	protein binding	26/200	1.66	3.88e-03	-	yes
M	3	GO:0003676	nucleic acid binding	36/200	1.52	4.00e-03	-	no
M	3	GO:0016740	transferase activity	26/200	1.59	6.91e-03	-	no

PS	4	PO:0000230	inflorescence meristem	158/200	2.03	5.57e-32	-	yes
PS	3	PO:0009013	meristem	160/200	1.99	1.38e-31	-	yes
PS	4	PO:0009047	stem	158/200	1.87	3.05e-27	-	yes
PS	3	PO:0009005	root	163/200	1.81	3.36e-27	-	yes
PS	5	PO:0000013	cauline leaf	146/200	1.89	1.08e-23	-	yes
PS	4	PO:0009025	leaf	159/200	1.73	4.04e-23	-	yes
PS	5	PO:0009028	microsporophyll	151/200	1.80	9.23e-23	-	yes
PS	5	PO:0008037	seedling	155/200	1.76	1.12e-22	-	yes
PS	4	PO:0009026	sporophyll	156/200	1.73	2.72e-22	-	yes
PS	4	PO:0020030	cotyledon	139/200	1.89	9.89e-22	-	yes
PS	5	PO:0020039	leaf lamina	148/200	1.80	9.97e-22	-	yes
PS	5	PO:0009027	megasporophyll	147/200	1.75	3.28e-20	-	yes
PS	3	PO:0009031	sepal	154/200	1.67	1.12e-19	-	yes
PS	5	PO:0008034	leaf whorl	155/200	1.64	3.19e-19	-	yes
PS	4	PO:0008033	phyllome whorl	155/200	1.64	3.19e-19	-	yes
PS	4	PO:0009009	embryo	157/200	1.62	3.55e-19	-	yes
PS	3	PO:0006001	phyllome	162/200	1.58	4.40e-19	-	yes
PS	5	PO:0009046	flower	163/200	1.57	6.36e-19	-	yes
PS	4	PO:0009001	fruit	158/200	1.61	7.33e-19	-	yes
PS	3	PO:0006342	infructescence	158/200	1.61	7.33e-19	-	yes
PS	3	PO:0009032	petal	148/200	1.69	1.00e-18	-	yes
PS	4	PO:0009049	inflorescence	163/200	1.56	1.35e-18	-	yes
PS	3	PO:0009010	seed	157/200	1.60	1.57e-18	-	yes
PS	3	PO:0020091	male gametophyte	143/200	1.72	1.83e-18	-	yes
PS	3	PO:0009006	shoot	166/200	1.53	1.92e-18	-	yes
PS	5	PO:0009052	pedicel	139/200	1.71	3.82e-17	-	yes
PS	4	PO:0000037	shoot apex	142/200	1.65	2.92e-16	-	yes
PS	5	PO:0020038	petiole	130/200	1.71	3.21e-15	-	yes
PS	4	PO:0006345	pollen tube	53/200	1.82	3.35e-06	-	no
PS	3	PO:0000084	sperm cell	52/200	1.60	1.45e-04	-	yes
PS	3	PO:0020097	generative cell	52/200	1.60	1.45e-04	-	yes

PG	5	PO:0007133	leaf production	155/200	1.84	2.86e-25	-	yes
PG	4	PO:0007112	1 main shoot growth	155/200	1.84	2.94e-25	-	yes
PG	3	PO:0007134	A vegetative growth	155/200	1.83	6.91e-25	-	yes
PG	4	PO:0001054	4 leaf senescence stage	141/200	1.83	8.70e-21	-	yes
PG	3	PO:0001050	leaf development stages	141/200	1.83	9.22e-21	-	yes
PG	5	PO:0007604	corolla developmental stages	160/200	1.62	6.81e-20	-	yes
PG	4	PO:0007616	4 anthesis	158/200	1.63	1.34e-19	-	yes
PG	4	PO:0007600	3 floral organ development stages	162/200	1.59	1.93e-19	-	yes
PG	3	PO:0007615	flower development stages	164/200	1.57	3.51e-19	-	yes
PG	4	PO:0007631	embryo development stages	149/200	1.65	5.37e-18	-	yes
PG	3	PO:0001170	seed development stages	149/200	1.65	8.66e-18	-	yes
PG	5	PO:0001185	C globular stage	139/200	1.69	9.50e-17	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	139/200	1.67	2.98e-16	-	yes
PG	5	PO:0001081	F mature embryo stage	135/200	1.70	5.67e-16	-	yes
PG	5	PO:0004507	D bilateral stage	137/200	1.66	1.52e-15	-	yes
PG	5	PO:0007605	androecium developmental stages	52/200	1.78	8.59e-06	-	no

KW	0	plasma	-	34/200	2.97	3.40e-09	-	no
KW	0	threonine	-	22/200	2.93	2.02e-06	-	no
KW	0	membrane	-	50/200	1.88	2.67e-06	-	no
KW	0	regulation	-	30/200	2.27	8.38e-06	-	no
KW	0	serine	-	23/200	2.58	1.08e-05	-	no
KW	0	ipr000719	-	18/200	2.89	1.79e-05	-	no
KW	0	finger	-	23/200	2.49	1.98e-05	-	yes
KW	0	ipr011009	-	18/200	2.78	2.95e-05	-	no
KW	0	kinase	-	24/200	2.27	5.84e-05	-	no
KW	0	ipr013083	-	11/200	3.51	8.25e-05	-	no
KW	0	ipr017441	-	13/200	3.03	1.18e-04	-	no
KW	0	ipr008271	-	14/200	2.87	1.29e-04	-	no
KW	0	phosphorylation	-	16/200	2.60	1.62e-04	-	no
KW	0	active	-	19/200	2.32	2.24e-04	-	no
KW	0	ipr017442	-	13/200	2.47	9.06e-04	-	no
KW	0	nucleus	-	24/200	1.86	1.18e-03	-	no
KW	0	motif	-	12/200	2.47	1.30e-03	-	no
KW	0	nucleic	-	14/200	2.14	2.52e-03	-	no
KW	0	region	-	25/200	1.73	2.63e-03	-	no
KW	0	transmembrane	-	15/200	2.07	2.72e-03	-	no
KW	0	transcription	-	25/200	1.72	2.82e-03	-	no
KW	0	transporter	-	14/200	2.01	4.46e-03	-	no
KW	0	amino	-	16/200	1.86	6.09e-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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