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
AT1G74730.1	0.957263	unknown protein	OMAT1P021800	-	-	-
AT1G54780.1	0.956525	thylakoid lumen 18.3 kDa protein	OMAT1P015210	-	OMAT1P113600	-
AT4G09650.1	0.946015	ATPD (ATP SYNTHASE DELTA-SUBUNIT GENE)	OMAT4P002310	-	OMAT4P101870	-
AT3G18890.1	0.940551	binding / catalytic/ coenzyme binding	OMAT3P007140	-	-	-
AT2G05100.1	0.93912	LHCB2.1	OMAT2P101060	-	-	-
AT1G26761.1	0.938381	unknown protein	OMAT1P108360	-	-	-
AT5G36120.1	0.935161	CCB3 (COFACTOR ASSEMBLY, COMPLEX C (B6F),)	OMAT5P108790	-	-	-
AT1G44000.1	0.933858	unknown protein	OMAT1P111160	-	-	-
AT3G01550.1	0.932494	PPT2 (PHOSPHOENOLPYRUVATE (PEP)/PHOSPHATE TRANSLOCATOR 2)	OMAT3P100350	-	-	-
AT5G14060.1	0.930427	CARAB-AK-LYS	OMAT5P004790	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT2G37110.1	-0.847258	unknown protein	OMAT2P009530	-	OMAT2P108630	-
AT2G45140.1	-0.834692	PVA12 (PLANT VAP HOMOLOG 12)	OMAT2P012610	-	-	-
AT5G26600.2	-0.813754	catalytic/ pyridoxal phosphate binding	OMAT5P009080	-	-	-
AT3G62920.1	-0.80037	unknown protein	-	-	-	-
AT5G60580.2	-0.799213	zinc finger (C3HC4-type RING finger) family protein	OMAT5P018440	-	-	-
AT3G63000.1	-0.796283	NPL41 (NPL4-LIKE PROTEIN 1)	OMAT3P018000	-	-	-
AT2G10510.1	-0.791229	transposable element gene	-	-	-	-
AT5G63640.1	-0.782231	VHS domain-containing protein / GAT domain-containing protein	OMAT5P019500	-	-	-
AT3G13224.2	-0.776338	RNA recognition motif (RRM)-containing protein	OMAT3P004620	-	-	-
AT1G53910.1	-0.761978	RAP2.12	OMAT1P014940	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 7.27e-48	:20 terms with high significance
7.27e-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	23/200	28.75	1.14e-28	2.56E-17	no
B	3	GO:0042440	pigment metabolic process	12/200	16.91	3.64e-13	-	yes
B	4	GO:0006091	generation of precursor metabolites and energy	16/200	10.00	6.68e-13	-	no
B	5	GO:0051188	cofactor biosynthetic process	13/200	13.86	7.70e-13	-	yes
B	4	GO:0051186	cofactor metabolic process	15/200	10.10	2.65e-12	-	yes
B	5	GO:0018130	heterocycle biosynthetic process	11/200	12.88	7.06e-11	-	yes
B	5	GO:0005996	monosaccharide metabolic process	11/200	11.95	1.69e-10	-	no
B	4	GO:0006066	alcohol metabolic process	13/200	8.35	6.93e-10	-	no
B	4	GO:0044262	cellular carbohydrate metabolic process	16/200	5.18	1.72e-08	-	no
B	3	GO:0009628	response to abiotic stimulus	24/200	3.24	1.20e-07	-	no
B	4	GO:0005975	carbohydrate metabolic process	19/200	3.65	3.28e-07	-	no
B	5	GO:0044271	cellular nitrogen compound biosynthetic process	13/200	4.91	5.19e-07	-	yes
B	4	GO:0009409	response to cold	10/200	6.42	5.49e-07	-	no
B	4	GO:0009266	response to temperature stimulus	12/200	5.26	5.79e-07	-	no
B	4	GO:0046483	heterocycle metabolic process	13/200	4.80	6.78e-07	-	yes
B	3	GO:0044237	cellular metabolic process	76/200	1.61	1.77e-06	-	yes
B	5	GO:0009416	response to light stimulus	12/200	4.17	7.36e-06	-	no
B	4	GO:0009314	response to radiation	12/200	4.04	1.04e-05	1.18E-16	no
B	3	GO:0044281	small molecule metabolic process	23/200	2.56	1.23e-05	-	no
B	3	GO:0051707	response to other organism	11/200	3.28	1.54e-04	-	no
B	3	GO:0009607	response to biotic stimulus	11/200	3.04	3.07e-04	-	no
B	4	GO:0042180	cellular ketone metabolic process	11/200	2.45	1.98e-03	-	no
B	5	GO:0043436	oxoacid metabolic process	10/200	2.27	5.01e-03	-	no
B	4	GO:0006082	organic acid metabolic process	10/200	2.27	5.11e-03	-	no
B	3	GO:0042221	response to chemical stimulus	20/200	1.75	5.25e-03	-	no
B	4	GO:0006952	defense response	10/200	2.20	6.39e-03	-	no
B	4	GO:0009725	response to hormone stimulus	10/200	2.12	8.35e-03	-	no

C	5	GO:0044434	chloroplast part	100/200	18.05	1.45e-102	-	yes
C	5	GO:0009536	plastid	142/200	7.69	1.43e-101	2.54E-26	yes
C	4	GO:0044435	plastid part	100/200	17.58	2.35e-101	3.85E-19	yes
C	4	GO:0009579	thylakoid	69/200	27.71	2.69e-82	6.75E-18	yes
C	4	GO:0044436	thylakoid part	60/200	29.09	1.20e-72	4.04E-19	yes
C	5	GO:0031976	plastid thylakoid	59/200	29.64	6.06e-72	5.82E-19	yes
C	4	GO:0031984	organelle subcompartment	59/200	29.46	8.94e-72	-	yes
C	5	GO:0055035	plastid thylakoid membrane	56/200	32.33	1.43e-70	3.53E-19	yes
C	5	GO:0042651	thylakoid membrane	56/200	30.93	2.20e-69	4.14E-18	yes
C	4	GO:0034357	photosynthetic membrane	56/200	30.53	4.98e-69	5.46E-18	yes
C	4	GO:0044444	cytoplasmic part	144/200	4.15	3.61e-66	-	yes
C	3	GO:0044446	intracellular organelle part	101/200	7.04	2.01e-62	-	yes
C	3	GO:0044422	organelle part	101/200	7.04	2.18e-62	1.23E-18	yes
C	4	GO:0005737	cytoplasm	144/200	3.85	9.29e-62	2.55E-16	yes
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	3	GO:0043229	intracellular organelle	146/200	3.16	1.22e-51	-	yes
C	3	GO:0044424	intracellular part	148/200	2.90	7.27e-48	-	yes
C	3	GO:0005622	intracellular	150/200	2.82	3.26e-47	8.12E-16	yes
C	5	GO:0009526	plastid envelope	48/200	17.46	1.00e-46	3.07E-22	yes
C	4	GO:0031967	organelle envelope	48/200	11.52	6.34e-38	5.89E-19	yes
C	3	GO:0031975	envelope	48/200	11.52	6.34e-38	1.04E-16	yes
C	5	GO:0009532	plastid stroma	40/200	16.18	1.08e-37	-	no
C	3	GO:0044464	cell part	172/200	1.88	1.79e-33	-	yes
C	3	GO:0016020	membrane	80/200	2.92	6.17e-21	1.96E-15	yes
C	3	GO:0048046	apoplast	19/200	9.63	1.38e-14	-	no
C	3	GO:0043234	protein complex	27/200	4.13	1.04e-10	5.61E-16	no
C	3	GO:0044425	membrane part	18/200	2.28	3.97e-04	-	no

M	3	GO:0046906	tetrapyrrole binding	10/200	5.25	3.90e-06	-	no
M	3	GO:0016491	oxidoreductase activity	20/200	2.37	1.19e-04	1.56E-17	yes

PS	5	PO:0020038	petiole	173/200	2.27	7.12e-47	8.07E-19	yes
PS	5	PO:0020039	leaf lamina	178/200	2.16	1.50e-46	-	yes
PS	4	PO:0020030	cotyledon	170/200	2.32	2.82e-46	2.43E-20	yes
PS	5	PO:0000013	cauline leaf	172/200	2.23	7.66e-45	-	yes
PS	3	PO:0009013	meristem	170/200	2.12	3.09e-40	-	yes
PS	4	PO:0009025	leaf	178/200	1.94	9.37e-39	4.19E-17	yes
PS	4	PO:0009047	stem	171/200	2.03	6.21e-38	-	yes
PS	4	PO:0000230	inflorescence meristem	165/200	2.12	7.69e-38	-	yes
PS	3	PO:0009032	petal	173/200	1.97	3.06e-37	-	yes
PS	5	PO:0009028	microsporophyll	169/200	2.02	1.66e-36	-	yes
PS	5	PO:0008037	seedling	172/200	1.95	7.64e-36	8.66E-24	yes
PS	4	PO:0009026	sporophyll	173/200	1.92	1.87e-35	-	yes
PS	4	PO:0000037	shoot apex	168/200	1.95	5.72e-34	-	yes
PS	3	PO:0006001	phyllome	180/200	1.76	5.09e-33	-	yes
PS	5	PO:0009052	pedicel	162/200	1.99	1.78e-32	-	yes
PS	5	PO:0009027	megasporophyll	164/200	1.95	3.74e-32	-	yes
PS	3	PO:0009031	sepal	171/200	1.85	5.57e-32	-	yes
PS	4	PO:0009009	embryo	174/200	1.80	1.27e-31	2.90E-16	yes
PS	3	PO:0009010	seed	174/200	1.78	8.46e-31	3.72E-17	yes
PS	5	PO:0008034	leaf whorl	171/200	1.81	1.21e-30	-	yes
PS	4	PO:0008033	phyllome whorl	171/200	1.81	1.21e-30	-	yes
PS	4	PO:0009001	fruit	174/200	1.77	1.87e-30	-	yes
PS	3	PO:0006342	infructescence	174/200	1.77	1.87e-30	-	yes
PS	5	PO:0009046	flower	177/200	1.70	2.72e-29	-	yes
PS	3	PO:0009006	shoot	180/200	1.66	4.94e-29	-	yes
PS	4	PO:0009049	inflorescence	177/200	1.69	6.89e-29	-	yes
PS	4	PO:0000293	guard cell	49/200	4.55	2.99e-20	-	yes
PS	4	PO:0000351	guard mother cell	49/200	4.53	3.61e-20	-	yes
PS	3	PO:0000070	meristemoid	49/200	4.53	3.87e-20	-	yes
PS	5	PO:0006016	leaf epidermis	49/200	4.41	1.20e-19	-	yes
PS	5	PO:0006035	shoot epidermis	49/200	4.38	1.61e-19	-	yes
PS	5	PO:0000349	epidermal initial	49/200	4.35	2.16e-19	-	yes
PS	4	PO:0004011	initial cell	49/200	4.32	2.82e-19	-	yes
PS	3	PO:0004010	meristematic cell	49/200	4.31	3.01e-19	-	yes
PS	3	PO:0004013	epidermal cell	50/200	4.19	4.03e-19	-	yes
PS	3	PO:0020091	male gametophyte	144/200	1.74	4.91e-19	-	yes
PS	4	PO:0005679	epidermis	50/200	4.04	1.97e-18	-	yes
PS	3	PO:0009014	dermal tissue	50/200	4.04	2.01e-18	-	yes

PG	4	PO:0001054	4 leaf senescence stage	171/200	2.22	3.87e-44	-	yes
PG	3	PO:0001050	leaf development stages	171/200	2.22	4.22e-44	-	yes
PG	5	PO:0007133	leaf production	173/200	2.06	5.14e-40	-	yes
PG	4	PO:0007112	1 main shoot growth	173/200	2.06	5.32e-40	-	yes
PG	3	PO:0007134	A vegetative growth	173/200	2.04	1.55e-39	-	yes
PG	5	PO:0001081	F mature embryo stage	160/200	2.01	3.53e-32	-	yes
PG	5	PO:0004507	D bilateral stage	161/200	1.95	6.71e-31	-	yes
PG	4	PO:0007616	4 anthesis	173/200	1.78	1.60e-30	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	161/200	1.94	1.90e-30	-	yes
PG	5	PO:0001185	C globular stage	160/200	1.95	2.40e-30	-	yes
PG	5	PO:0007604	corolla developmental stages	174/200	1.76	3.35e-30	-	yes
PG	4	PO:0007600	3 floral organ development stages	175/200	1.72	5.71e-29	-	yes
PG	4	PO:0007631	embryo development stages	165/200	1.83	1.11e-28	-	yes
PG	3	PO:0001170	seed development stages	165/200	1.82	2.03e-28	-	yes
PG	3	PO:0007615	flower development stages	175/200	1.67	3.77e-27	-	yes

KW	0	chloroplast	-	126/200	7.13	1.07e-82	5.96E-22	yes
KW	0	thylakoid	-	52/200	24.42	1.36e-58	6.75E-18	yes
KW	0	photosystem	-	19/200	31.59	5.11e-25	1.30E-17	no
KW	0	envelope	-	28/200	12.25	2.01e-23	1.04E-16	yes
KW	0	stroma	-	24/200	12.87	6.84e-21	-	no
KW	0	components	-	22/200	13.55	7.81e-20	5.72E-16	no
KW	0	light	-	20/200	7.49	4.17e-13	7.26E-26	yes
KW	0	membrane	-	61/200	2.29	6.34e-11	1.96E-15	yes
KW	0	response	-	44/200	2.45	6.28e-09	3.49E-15	no
KW	0	biosynthetic	-	25/200	3.50	1.45e-08	6.61E-17	yes
KW	0	stimulus	-	18/200	4.18	7.93e-08	-	no
KW	0	subunit	-	24/200	3.27	9.79e-08	-	no
KW	0	complex	-	26/200	3.07	1.11e-07	1.40E-15	no
KW	0	dehydrogenase	-	14/200	4.83	2.67e-07	0	yes
KW	0	phosphate	-	14/200	4.62	4.69e-07	-	no
KW	0	encodes	-	50/200	1.96	7.73e-07	1.59E-16	yes
KW	0	ipr016040	-	10/200	4.64	1.23e-05	-	yes
KW	0	electron	-	13/200	3.65	1.58e-05	7.99E-16	no
KW	0	process	-	39/200	1.90	2.76e-05	9.34E-16	yes
KW	0	oxidoreductase	-	12/200	2.57	8.91e-04	0	yes
KW	0	putative	-	37/200	1.60	1.37e-03	2.87E-16	no
KW	0	transport	-	18/200	1.85	4.26e-03	8.46E-16	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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