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
AT3G01120.1	0.868008	MTO1 (METHIONINE OVERACCUMULATION 1)	OMAT3P100040	-	-	-
AT5G56730.1	0.842033	peptidase M16 family protein / insulinase family protein	-	-	-	-
AT3G56980.1	0.835885	BHLH039	OMAT3P113980	-	-	-
AT3G56970.1	0.832135	BHLH038	OMAT3P113970	-	-	-
AT1G78320.1	0.830137	ATGSTU23 (GLUTATHIONE S-TRANSFERASE TAU 23)	OMAT1P120530	-	-	-
AT3G43600.1	0.828975	AAO2 (ALDEHYDE OXIDASE 2)	OMAT3P109830	-	-	-
AT5G04950.1	0.821419	NAS1 (NICOTIANAMINE SYNTHASE 1)	OMAT5P101220	-	-	-
AT1G64780.1	0.815069	ATAMT1	OMAT1P115970	-	-	-
AT2G20610.1	0.809358	SUR1 (SUPERROOT 1)	OMAT2P103170	-	-	-
AT3G62270.1	0.801722	anion exchange family protein	OMAT3P115530	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT1G35405.1	-0.758868	transposable element gene	-	-	-	-
AT3G28958.1	-0.744417	plastocyanin-like domain-containing protein	-	-	-	-
AT1G14590.1	-0.741535	FUNCTIONS IN: molecular_function unknown	-	-	-	-
AT1G20970.1	-0.735661	FUNCTIONS IN: molecular_function unknown	OMAT1P007680	-	-	-
AT2G10620.1	-0.723611	transposable element gene	-	-	-	-
AT1G61060.1	-0.700068	F-box family protein	-	-	-	-
AT3G42356.1	-0.681894	transposable element gene	-	-	-	-
AT5G35425.1	-0.679362	transposable element gene	-	-	-	-
AT5G63168.1	-0.67833	unknown protein	-	-	-	-
AT5G08565.1	-0.669632	positive transcription elongation factor/ zinc ion binding	-	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 1.00e-06	:20 terms with high significance
1.00e-06 <	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:0006950	response to stress	33/200	2.66	8.11e-08	-	no
B	4	GO:0006519	cellular amino acid and derivative metabolic process	14/200	4.03	2.55e-06	-	no
B	5	GO:0044271	cellular nitrogen compound biosynthetic process	12/200	4.53	3.01e-06	-	no
B	5	GO:0044106	cellular amine metabolic process	11/200	4.84	3.52e-06	-	no
B	4	GO:0006811	ion transport	11/200	4.55	6.57e-06	-	no
B	4	GO:0009308	amine metabolic process	11/200	4.40	9.27e-06	-	no
B	5	GO:0006520	cellular amino acid metabolic process	10/200	4.75	9.93e-06	-	no
B	4	GO:0006952	defense response	14/200	3.08	5.97e-05	-	no
B	3	GO:0009058	biosynthetic process	49/200	1.68	6.81e-05	-	no
B	4	GO:0034641	cellular nitrogen compound metabolic process	36/200	1.85	1.01e-04	-	no
B	3	GO:0006807	nitrogen compound metabolic process	36/200	1.81	1.51e-04	-	no
B	5	GO:0043436	oxoacid metabolic process	13/200	2.95	1.52e-04	-	no
B	3	GO:0051707	response to other organism	11/200	3.28	1.54e-04	-	no
B	4	GO:0006082	organic acid metabolic process	13/200	2.94	1.57e-04	-	no
B	3	GO:0044237	cellular metabolic process	69/200	1.46	1.79e-04	-	yes
B	4	GO:0042180	cellular ketone metabolic process	13/200	2.90	1.85e-04	-	no
B	4	GO:0044283	small molecule biosynthetic process	13/200	2.86	2.09e-04	-	no
B	3	GO:0044281	small molecule metabolic process	20/200	2.23	2.82e-04	-	no
B	3	GO:0009607	response to biotic stimulus	11/200	3.04	3.07e-04	-	no
B	4	GO:0044249	cellular biosynthetic process	45/200	1.60	4.46e-04	-	no
B	3	GO:0042221	response to chemical stimulus	23/200	2.02	4.75e-04	-	no
B	3	GO:0050794	regulation of cellular process	27/200	1.77	1.35e-03	-	no
B	3	GO:0051716	cellular response to stimulus	11/200	2.49	1.75e-03	-	no
B	3	GO:0044238	primary metabolic process	67/200	1.35	2.12e-03	-	yes
B	3	GO:0050789	regulation of biological process	29/200	1.68	2.16e-03	-	no
B	3	GO:0048856	anatomical structure development	17/200	1.90	3.97e-03	-	no
B	5	GO:0010556	regulation of macromolecule biosynthetic process	18/200	1.83	4.86e-03	-	no
B	5	GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	18/200	1.80	5.83e-03	-	no
B	4	GO:0009889	regulation of biosynthetic process	18/200	1.79	5.94e-03	-	no
B	5	GO:0031326	regulation of cellular biosynthetic process	18/200	1.79	5.94e-03	-	no
B	4	GO:0051171	regulation of nitrogen compound metabolic process	18/200	1.78	6.47e-03	-	no
B	5	GO:0006350	transcription	18/200	1.76	7.01e-03	-	no
B	4	GO:0080090	regulation of primary metabolic process	18/200	1.71	9.60e-03	-	no

C	3	GO:0044464	cell part	144/200	1.57	1.33e-14	-	yes
C	3	GO:0016020	membrane	50/200	1.83	6.09e-06	3.64E-21	yes
C	3	GO:0012505	endomembrane system	42/200	1.73	1.30e-04	-	no
C	3	GO:0044424	intracellular part	72/200	1.41	3.55e-04	-	no
C	4	GO:0043231	intracellular membrane-bounded organelle	64/200	1.46	3.66e-04	-	no
C	3	GO:0043227	membrane-bounded organelle	64/200	1.46	3.67e-04	-	no
C	4	GO:0005618	cell wall	10/200	3.01	5.55e-04	-	no
C	3	GO:0030312	external encapsulating structure	10/200	2.99	5.89e-04	-	no
C	3	GO:0005622	intracellular	73/200	1.37	7.97e-04	-	no
C	3	GO:0043229	intracellular organelle	65/200	1.41	8.62e-04	-	no
C	5	GO:0005634	nucleus	28/200	1.79	9.33e-04	-	no
C	4	GO:0005886	plasma membrane	23/200	1.86	1.49e-03	3.64E-21	yes
C	5	GO:0009536	plastid	30/200	1.62	2.97e-03	-	no
C	5	GO:0005739	mitochondrion	13/200	2.03	5.27e-03	-	no
C	4	GO:0005737	cytoplasm	51/200	1.36	6.79e-03	-	no
C	4	GO:0031224	intrinsic to membrane	11/200	2.05	8.07e-03	-	no
C	3	GO:0044446	intracellular organelle part	23/200	1.60	9.19e-03	-	no
C	3	GO:0044422	organelle part	23/200	1.60	9.27e-03	-	no

M	3	GO:0016491	oxidoreductase activity	25/200	2.96	3.71e-07	-	no
M	5	GO:0046872	metal ion binding	32/200	2.36	1.90e-06	-	no
M	4	GO:0043169	cation binding	32/200	2.23	6.35e-06	-	no
M	3	GO:0043167	ion binding	32/200	2.23	6.35e-06	-	no
M	5	GO:0015075	ion transmembrane transporter activity	12/200	3.83	1.83e-05	-	no
M	4	GO:0022891	substrate-specific transmembrane transporter activity	12/200	2.72	5.34e-04	-	no
M	3	GO:0016740	transferase activity	29/200	1.77	8.99e-04	-	yes
M	3	GO:0022857	transmembrane transporter activity	13/200	2.31	1.65e-03	-	no
M	3	GO:0022892	substrate-specific transporter activity	12/200	2.32	2.22e-03	-	no
M	4	GO:0016788	hydrolase activity, acting on ester bonds	12/200	2.02	7.08e-03	-	no

PS	3	PO:0009005	root	143/200	1.59	8.07e-15	-	yes
PS	5	PO:0008037	seedling	127/200	1.44	1.14e-08	-	yes
PS	4	PO:0009001	fruit	132/200	1.34	5.24e-07	-	yes
PS	3	PO:0006342	infructescence	132/200	1.34	5.24e-07	-	yes
PS	4	PO:0009009	embryo	130/200	1.35	6.67e-07	-	yes
PS	3	PO:0009010	seed	131/200	1.34	7.58e-07	-	yes
PS	4	PO:0005679	epidermis	29/200	2.34	6.36e-06	-	no
PS	3	PO:0009014	dermal tissue	29/200	2.34	6.42e-06	-	no
PS	5	PO:0000349	epidermal initial	27/200	2.39	8.55e-06	-	no
PS	3	PO:0004013	epidermal cell	28/200	2.35	8.63e-06	-	no
PS	4	PO:0004011	initial cell	27/200	2.38	9.62e-06	-	no
PS	3	PO:0004010	meristematic cell	27/200	2.38	9.90e-06	-	no
PS	4	PO:0009025	leaf	121/200	1.32	1.33e-05	-	yes
PS	5	PO:0020039	leaf lamina	110/200	1.33	3.07e-05	-	yes
PS	4	PO:0000293	guard cell	24/200	2.23	7.93e-05	-	no
PS	4	PO:0020030	cotyledon	99/200	1.35	8.05e-05	-	yes
PS	4	PO:0000351	guard mother cell	24/200	2.22	8.51e-05	-	no
PS	3	PO:0000070	meristemoid	24/200	2.22	8.73e-05	-	no
PS	5	PO:0006016	leaf epidermis	24/200	2.16	1.33e-04	-	no
PS	5	PO:0006035	shoot epidermis	24/200	2.14	1.48e-04	-	no
PS	3	PO:0009006	shoot	133/200	1.22	1.65e-04	-	yes
PS	3	PO:0006001	phyllome	124/200	1.21	8.74e-04	-	yes
PS	5	PO:0020038	petiole	97/200	1.27	1.02e-03	-	yes
PS	4	PO:0000037	shoot apex	103/200	1.20	6.42e-03	-	yes

PG	3	PO:0007134	A vegetative growth	110/200	1.30	1.19e-04	-	yes
PG	5	PO:0007133	leaf production	109/200	1.30	1.48e-04	-	yes
PG	4	PO:0007112	1 main shoot growth	109/200	1.30	1.50e-04	-	yes
PG	4	PO:0001054	4 leaf senescence stage	98/200	1.27	9.32e-04	-	yes
PG	3	PO:0001050	leaf development stages	98/200	1.27	9.52e-04	-	yes
PG	3	PO:0007615	flower development stages	121/200	1.16	8.45e-03	-	yes

KW	0	hypocotyl	-	15/200	6.43	2.09e-09	-	no
KW	0	response	-	42/200	2.34	5.49e-08	-	no
KW	0	electron	-	15/200	4.21	6.90e-07	-	no
KW	0	class	-	19/200	3.17	2.80e-06	-	no
KW	0	process	-	41/200	2.00	5.02e-06	-	yes
KW	0	stress	-	16/200	3.41	5.60e-06	-	no
KW	0	defense	-	13/200	3.73	1.26e-05	-	no
KW	0	membrane	-	48/200	1.80	1.35e-05	3.64E-21	yes
KW	0	carrier	-	14/200	3.49	1.41e-05	-	no
KW	0	dimerisation	-	10/200	4.16	3.39e-05	-	no
KW	0	biosynthetic	-	19/200	2.66	3.59e-05	-	no
KW	0	phosphate	-	11/200	3.63	6.03e-05	0	yes
KW	0	endomembrane	-	42/200	1.78	6.96e-05	-	no
KW	0	active	-	20/200	2.44	7.90e-05	-	no
KW	0	system	-	42/200	1.73	1.22e-04	-	no
KW	0	terminal	-	35/200	1.82	1.83e-04	-	no
KW	0	region	-	27/200	1.87	5.86e-04	-	no
KW	0	encodes	-	41/200	1.61	7.38e-04	-	no
KW	0	plasma	-	22/200	1.92	1.19e-03	3.64E-21	yes
KW	0	catalytic	-	20/200	1.97	1.36e-03	-	no
KW	0	member	-	21/200	1.92	1.51e-03	-	no
KW	0	synthase	-	11/200	2.51	1.65e-03	-	no
KW	0	ipr017442	-	12/200	2.28	2.62e-03	-	no
KW	0	transcription	-	25/200	1.72	2.82e-03	-	no
KW	0	regulation	-	23/200	1.74	3.44e-03	-	no
KW	0	threonine	-	15/200	2.00	3.73e-03	-	no
KW	0	ipr008271	-	11/200	2.25	3.92e-03	-	no
KW	0	ipr017441	-	10/200	2.33	4.17e-03	-	no
KW	0	putative	-	35/200	1.52	4.58e-03	-	no
KW	0	nucleus	-	22/200	1.71	5.19e-03	-	no
KW	0	chloroplast	-	28/200	1.59	5.54e-03	-	no
KW	0	receptor	-	10/200	2.10	8.73e-03	-	no
KW	0	conserved	-	22/200	1.63	9.07e-03	3.00E-09	no
KW	0	mitochondrion	-	11/200	2.01	9.51e-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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