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
AT2G30170.1	0.918897	catalytic	OMAT2P106210	-	-	-
AT5G43470.1	0.91479	RPP8 (RECOGNITION OF PERONOSPORA PARASITICA 8)	OMAT5P110530	-	-	-
AT2G44920.2	0.912975	thylakoid lumenal 15 kDa protein, chloroplast	OMAT2P012530	-	-	-
AT4G31030.1	0.907342	unknown protein	OMAT4P108790	-	-	-
AT3G06483.1	0.907211	PDK (PYRUVATE DEHYDROGENASE KINASE)	OMAT3P102250	-	-	-
AT4G33470.1	0.903008	hda14 (histone deacetylase 14)	OMAT4P109675	-	OMAT4P011290	-
AT1G64150.1	0.900515	unknown protein	-	-	-	-
AT4G37270.1	0.899531	HMA1	OMAT4P111220	-	-	-
AT5G58330.1	0.898025	malate dehydrogenase (NADP), chloroplast, putative	OMAT5P115400	-	OMAT5P017620,OMAT5P017630	[OMAT5P017620]-, [OMAT5P017630]-
AT5G59250.1	0.896681	sugar transporter family protein	OMAT5P018000	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT4G28480.1	-0.896399	DNAJ heat shock family protein	OMAT4P009250	-	-	-
AT4G29040.1	-0.880951	RPT2a (regulatory particle AAA-ATPase 2a)	OMAT4P009520	-	-	-
AT3G22290.1	-0.87438	unknown protein	OMAT3P008390	-	-	-
AT1G80970.1	-0.867255	XH domain-containing protein	-	-	-	-
AT3G08910.1	-0.843825	DNAJ heat shock protein, putative	-	-	-	-
AT5G18900.1	-0.837954	oxidoreductase, 2OG-Fe(II) oxygenase family protein	OMAT5P105520	-	-	-
AT5G17430.1	-0.830467	BBM (BABY BOOM)	-	-	-	-
AT5G23540.1	-0.829794	26S proteasome regulatory subunit, putative	OMAT5P008000	-	-	-
AT3G11440.1	-0.827402	MYB65 (MYB DOMAIN PROTEIN 65)	-	-	-	-
AT5G59910.1	-0.827295	HTB4	OMAT5P018270	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 5.69e-48	:20 terms with high significance
5.69e-48 <	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	4	GO:0015979	photosynthesis	35/200	43.76	1.04e-49	-	no
B	4	GO:0006091	generation of precursor metabolites and energy	29/200	18.13	2.89e-29	-	no
B	3	GO:0044237	cellular metabolic process	91/200	1.93	3.15e-12	-	no
B	4	GO:0006461	protein complex assembly	11/200	11.09	4.06e-10	-	no
B	3	GO:0070271	protein complex biogenesis	11/200	11.09	4.06e-10	-	no
B	5	GO:0009416	response to light stimulus	17/200	5.91	8.42e-10	-	no
B	4	GO:0009314	response to radiation	17/200	5.72	1.42e-09	-	no
B	3	GO:0009628	response to abiotic stimulus	26/200	3.51	7.25e-09	-	no
B	4	GO:0006952	defense response	20/200	4.39	7.35e-09	-	no
B	4	GO:0065003	macromolecular complex assembly	11/200	7.72	2.44e-08	-	no
B	3	GO:0006950	response to stress	34/200	2.74	2.48e-08	-	no
B	3	GO:0022607	cellular component assembly	12/200	6.86	2.77e-08	-	no
B	3	GO:0043933	macromolecular complex subunit organization	11/200	7.12	5.94e-08	-	no
B	3	GO:0051707	response to other organism	14/200	4.18	1.63e-06	-	no
B	5	GO:0043436	oxoacid metabolic process	16/200	3.63	2.42e-06	-	no
B	4	GO:0006082	organic acid metabolic process	16/200	3.62	2.51e-06	-	no
B	4	GO:0042180	cellular ketone metabolic process	16/200	3.57	3.11e-06	-	no
B	3	GO:0009607	response to biotic stimulus	14/200	3.87	4.09e-06	-	no
B	3	GO:0044281	small molecule metabolic process	23/200	2.56	1.23e-05	-	no
B	4	GO:0044262	cellular carbohydrate metabolic process	11/200	3.56	7.26e-05	-	no
B	4	GO:0005975	carbohydrate metabolic process	14/200	2.69	2.58e-04	-	no
B	3	GO:0009056	catabolic process	13/200	2.73	3.43e-04	-	no
B	3	GO:0050789	regulation of biological process	31/200	1.79	5.19e-04	-	no
B	3	GO:0050794	regulation of cellular process	28/200	1.84	6.35e-04	-	no
B	3	GO:0009791	post-embryonic development	13/200	2.20	2.66e-03	-	no
B	4	GO:0048608	reproductive structure development	11/200	2.26	3.88e-03	-	no
B	4	GO:0006629	lipid metabolic process	10/200	2.30	4.58e-03	-	no
B	3	GO:0042221	response to chemical stimulus	20/200	1.75	5.25e-03	-	no
B	3	GO:0022414	reproductive process	12/200	1.99	7.92e-03	-	no
B	3	GO:0044238	primary metabolic process	64/200	1.29	8.30e-03	-	no
B	3	GO:0003006	reproductive developmental process	11/200	2.00	9.82e-03	-	no

C	5	GO:0009536	plastid	127/200	6.88	1.41e-81	3.64E-21	yes
C	4	GO:0044435	plastid part	83/200	14.59	1.17e-75	-	yes
C	5	GO:0044434	chloroplast part	82/200	14.80	3.35e-75	-	yes
C	4	GO:0044444	cytoplasmic part	141/200	4.06	6.76e-63	-	yes
C	4	GO:0005737	cytoplasm	142/200	3.79	1.20e-59	-	yes
C	4	GO:0009579	thylakoid	54/200	21.69	6.84e-58	-	no
C	4	GO:0044436	thylakoid part	49/200	23.75	1.40e-54	-	no
C	4	GO:0043231	intracellular membrane-bounded organelle	145/200	3.30	1.56e-53	-	yes
C	3	GO:0043227	membrane-bounded organelle	145/200	3.30	1.59e-53	-	yes
C	5	GO:0031976	plastid thylakoid	47/200	23.61	3.10e-52	-	no
C	4	GO:0031984	organelle subcompartment	47/200	23.47	4.20e-52	-	no
C	3	GO:0043229	intracellular organelle	145/200	3.14	1.13e-50	-	yes
C	3	GO:0005622	intracellular	153/200	2.87	4.54e-50	-	yes
C	3	GO:0044424	intracellular part	150/200	2.94	9.21e-50	-	yes
C	4	GO:0034357	photosynthetic membrane	44/200	23.99	2.88e-49	-	no
C	5	GO:0042651	thylakoid membrane	43/200	23.75	5.69e-48	-	no
C	5	GO:0055035	plastid thylakoid membrane	42/200	24.25	2.78e-47	-	no
C	3	GO:0044446	intracellular organelle part	83/200	5.79	3.36e-43	-	yes
C	3	GO:0044422	organelle part	83/200	5.78	3.59e-43	-	yes
C	5	GO:0009532	plastid stroma	38/200	15.37	5.33e-35	-	no
C	3	GO:0044464	cell part	171/200	1.87	1.34e-32	-	yes
C	5	GO:0009526	plastid envelope	37/200	13.46	6.10e-32	-	yes
C	4	GO:0031967	organelle envelope	37/200	8.88	2.51e-25	-	yes
C	3	GO:0031975	envelope	37/200	8.88	2.51e-25	-	yes
C	3	GO:0016020	membrane	69/200	2.52	1.99e-14	-	no
C	3	GO:0048046	apoplast	16/200	8.11	1.88e-11	-	no
C	3	GO:0043234	protein complex	22/200	3.36	1.95e-07	-	no
C	3	GO:0044425	membrane part	23/200	2.91	1.43e-06	-	no

M	3	GO:0016853	isomerase activity	10/200	7.59	1.03e-07	-	no
M	3	GO:0046906	tetrapyrrole binding	11/200	5.77	5.66e-07	-	no
M	3	GO:0016491	oxidoreductase activity	23/200	2.73	4.29e-06	-	no
M	5	GO:0032555	purine ribonucleotide binding	21/200	2.14	3.58e-04	-	no
M	4	GO:0032553	ribonucleotide binding	21/200	2.14	3.58e-04	-	no
M	3	GO:0016740	transferase activity	30/200	1.83	4.23e-04	-	no
M	4	GO:0017076	purine nucleotide binding	21/200	2.02	7.54e-04	-	no
M	5	GO:0030554	adenyl nucleotide binding	19/200	2.10	7.90e-04	-	no
M	4	GO:0001883	purine nucleoside binding	19/200	2.10	7.90e-04	-	no
M	3	GO:0001882	nucleoside binding	19/200	2.09	8.16e-04	-	no
M	3	GO:0000166	nucleotide binding	24/200	1.82	1.62e-03	-	no
M	4	GO:0016772	transferase activity, transferring phosphorus-containing groups	17/200	1.85	5.10e-03	-	no

PS	4	PO:0020030	cotyledon	174/200	2.37	1.88e-50	-	yes
PS	5	PO:0020038	petiole	176/200	2.31	4.49e-50	-	yes
PS	3	PO:0009013	meristem	177/200	2.20	2.65e-47	-	yes
PS	5	PO:0000013	cauline leaf	174/200	2.25	6.76e-47	-	yes
PS	5	PO:0020039	leaf lamina	178/200	2.16	1.50e-46	-	yes
PS	4	PO:0000230	inflorescence meristem	172/200	2.21	1.89e-44	-	yes
PS	4	PO:0009047	stem	176/200	2.09	8.50e-43	-	yes
PS	5	PO:0009028	microsporophyll	175/200	2.09	3.34e-42	-	yes
PS	4	PO:0009025	leaf	181/200	1.97	7.40e-42	-	yes
PS	5	PO:0008037	seedling	175/200	1.98	1.17e-38	-	yes
PS	4	PO:0009026	sporophyll	175/200	1.94	2.56e-37	-	yes
PS	5	PO:0008034	leaf whorl	177/200	1.88	5.13e-36	-	yes
PS	4	PO:0008033	phyllome whorl	177/200	1.88	5.13e-36	-	yes
PS	4	PO:0000037	shoot apex	169/200	1.96	7.74e-35	-	yes
PS	3	PO:0006001	phyllome	181/200	1.76	5.50e-34	-	yes
PS	4	PO:0009009	embryo	176/200	1.82	2.07e-33	-	yes
PS	3	PO:0009032	petal	168/200	1.92	8.49e-33	-	yes
PS	3	PO:0009010	seed	176/200	1.80	1.45e-32	-	yes
PS	4	PO:0009001	fruit	176/200	1.79	3.26e-32	-	yes
PS	3	PO:0006342	infructescence	176/200	1.79	3.26e-32	-	yes
PS	3	PO:0009031	sepal	170/200	1.84	3.91e-31	-	yes
PS	5	PO:0009052	pedicel	160/200	1.97	6.96e-31	-	yes
PS	5	PO:0009027	megasporophyll	162/200	1.93	1.50e-30	-	yes
PS	3	PO:0009006	shoot	181/200	1.67	6.03e-30	-	yes
PS	5	PO:0009046	flower	177/200	1.70	2.72e-29	-	yes
PS	4	PO:0009049	inflorescence	177/200	1.69	6.89e-29	-	yes
PS	3	PO:0020091	male gametophyte	152/200	1.83	5.39e-24	-	yes
PS	4	PO:0000293	guard cell	46/200	4.28	5.92e-18	-	no
PS	4	PO:0000351	guard mother cell	46/200	4.26	7.04e-18	-	no
PS	3	PO:0000070	meristemoid	46/200	4.25	7.52e-18	-	no
PS	5	PO:0006016	leaf epidermis	46/200	4.14	2.14e-17	-	no
PS	5	PO:0006035	shoot epidermis	46/200	4.11	2.81e-17	-	no
PS	5	PO:0000349	epidermal initial	46/200	4.08	3.67e-17	-	no
PS	4	PO:0004011	initial cell	46/200	4.05	4.70e-17	-	no
PS	3	PO:0004010	meristematic cell	46/200	4.05	5.00e-17	-	no
PS	3	PO:0004013	epidermal cell	46/200	3.86	3.15e-16	-	no
PS	4	PO:0005679	epidermis	46/200	3.71	1.31e-15	-	no
PS	3	PO:0009014	dermal tissue	46/200	3.71	1.34e-15	-	no
PS	3	PO:0009005	root	128/200	1.42	2.04e-08	-	yes

PG	4	PO:0001054	4 leaf senescence stage	174/200	2.26	3.35e-47	-	yes
PG	3	PO:0001050	leaf development stages	174/200	2.26	3.66e-47	-	yes
PG	5	PO:0007133	leaf production	177/200	2.10	4.95e-44	-	yes
PG	4	PO:0007112	1 main shoot growth	177/200	2.10	5.12e-44	-	yes
PG	3	PO:0007134	A vegetative growth	177/200	2.09	1.56e-43	-	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:0001185	C globular stage	164/200	2.00	1.45e-33	-	yes
PG	5	PO:0001081	F mature embryo stage	161/200	2.02	5.53e-33	-	yes
PG	5	PO:0007604	corolla developmental stages	176/200	1.78	5.94e-32	-	yes
PG	4	PO:0007600	3 floral organ development stages	178/200	1.75	1.31e-31	-	yes
PG	4	PO:0007616	4 anthesis	174/200	1.79	2.20e-31	-	yes
PG	3	PO:0007615	flower development stages	178/200	1.70	1.03e-29	-	yes
PG	4	PO:0007631	embryo development stages	166/200	1.84	1.82e-29	-	yes
PG	3	PO:0001170	seed development stages	166/200	1.84	3.36e-29	-	yes

KW	0	chloroplast	-	111/200	6.28	1.16e-64	-	yes
KW	0	thylakoid	-	38/200	17.85	1.52e-37	-	no
KW	0	components	-	30/200	18.48	1.82e-30	-	no
KW	0	photosystem	-	21/200	34.92	2.07e-28	-	no
KW	0	light	-	28/200	10.49	1.56e-21	-	no
KW	0	stroma	-	20/200	10.73	3.58e-16	-	no
KW	0	envelope	-	18/200	7.88	2.19e-12	-	yes
KW	0	response	-	45/200	2.51	2.04e-09	-	no
KW	0	encodes	-	56/200	2.19	2.50e-09	-	no
KW	0	defense	-	18/200	5.16	2.79e-09	-	no
KW	0	subunit	-	26/200	3.55	5.80e-09	-	no
KW	0	isomerase	-	10/200	9.72	8.06e-09	-	no
KW	0	phosphate	-	16/200	5.28	1.29e-08	-	no
KW	0	catalytic	-	30/200	2.95	3.12e-08	-	no
KW	0	class	-	22/200	3.67	4.05e-08	-	no
KW	0	localized	-	12/200	5.82	1.87e-07	-	no
KW	0	disease	-	11/200	6.29	2.28e-07	-	no
KW	0	membrane	-	52/200	1.95	4.80e-07	-	yes
KW	0	resistance	-	13/200	4.57	1.22e-06	1.00E-45	no
KW	0	dependent	-	30/200	2.24	1.09e-05	-	no
KW	0	process	-	40/200	1.95	1.19e-05	-	no
KW	0	ipr016040	-	10/200	4.64	1.23e-05	-	no
KW	0	electron	-	13/200	3.65	1.58e-05	-	no
KW	0	biosynthesis	-	10/200	4.12	3.71e-05	-	no
KW	0	dehydrogenase	-	11/200	3.79	3.93e-05	-	no
KW	0	complex	-	21/200	2.48	4.40e-05	-	no
KW	0	reductase	-	10/200	3.67	1.03e-04	-	no
KW	0	enzyme	-	11/200	3.26	1.64e-04	-	no
KW	0	atpase	-	11/200	3.12	2.45e-04	0	yes
KW	0	biosynthetic	-	17/200	2.38	3.24e-04	-	no
KW	0	metabolic	-	23/200	2.00	5.28e-04	-	no
KW	0	stimulus	-	11/200	2.55	1.41e-03	-	no
KW	0	kinase	-	20/200	1.89	2.15e-03	-	no
KW	0	region	-	25/200	1.73	2.63e-03	4.00E-122	yes
KW	0	putative	-	34/200	1.47	8.00e-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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