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
AT1G34000.1	0.946832	OHP2 (ONE-HELIX PROTEIN 2)	OMAT1P110590	-	-	-
AT3G28220.1	0.92564	meprin and TRAF homology domain-containing protein / MATH domain-containing protein	OMAT3P010610	-	-	-
AT1G50320.1	0.92145	ATHX	OMAT1P112280	-	-	-
AT1G09340.1	0.916956	CRB (CHLOROPLAST RNA BINDING)	OMAT1P003170	-	-	-
AT1G64510.1	0.914932	ribosomal protein S6 family protein	OMAT1P115870	-	-	-
AT3G01500.2	0.913559	CA1 (CARBONIC ANHYDRASE 1)	OMAT3P100290,OMAT3P100300	[OMAT3P100290]-, [OMAT3P100300]-	OMAT3P000260,OMAT3P000270	[OMAT3P000260]-, [OMAT3P000270]-
AT3G12345.1	0.910797	unknown protein	OMAT3P104050	-	-	-
AT4G09010.1	0.909052	APX4 (ASCORBATE PEROXIDASE 4)	OMAT4P101770	-	-	-
AT4G13500.1	0.908778	unknown protein	-	-	-	-
AT4G04640.1	0.90556	ATPC1	OMAT4P101280	-	OMAT4P001490	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT3G13670.1	-0.85485	protein kinase family protein	OMAT3P004850	-	-	-
AT1G29220.1	-0.850168	transcriptional regulator family protein	-	-	-	-
AT5G43560.1	-0.829845	meprin and TRAF homology domain-containing protein / MATH domain-containing protein	OMAT5P012040	-	-	-
AT4G29490.1	-0.829083	aminopeptidase/ manganese ion binding	OMAT4P009710	-	-	-
AT3G46220.1	-0.824801	unknown protein	OMAT3P011900,OMAT3P011905	[OMAT3P011900]-, [OMAT3P011905]-	OMAT3P110370	-
AT4G38790.1	-0.818567	ER lumen protein retaining receptor family protein	-	-	-	-
AT4G25680.1	-0.818225	unknown protein	OMAT4P008040	-	-	-
AT2G04880.1	-0.816294	ZAP1 (ZINC-DEPENDENT ACTIVATOR PROTEIN-1)	OMAT2P001130	-	-	-
AT3G13224.2	-0.81342	RNA recognition motif (RRM)-containing protein	OMAT3P004620	-	-	-
AT2G01220.2	-0.809083	nucleotidyltransferase	OMAT2P000070	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 1.03e-54	:20 terms with high significance
1.03e-54 <	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	27/200	33.76	2.43e-35	-	no
B	4	GO:0006091	generation of precursor metabolites and energy	17/200	10.63	5.12e-14	-	no
B	5	GO:0009416	response to light stimulus	21/200	7.30	1.93e-13	-	no
B	4	GO:0009314	response to radiation	21/200	7.07	3.73e-13	-	no
B	3	GO:0044237	cellular metabolic process	89/200	1.88	2.39e-11	-	no
B	3	GO:0009628	response to abiotic stimulus	29/200	3.91	7.91e-11	-	no
B	4	GO:0006869	lipid transport	10/200	11.63	1.22e-09	-	no
B	4	GO:0051186	cofactor metabolic process	12/200	8.08	3.95e-09	-	no
B	4	GO:0010876	lipid localization	10/200	10.33	4.29e-09	-	no
B	3	GO:0055114	oxidation reduction	10/200	10.02	5.91e-09	-	no
B	3	GO:0051707	response to other organism	12/200	3.58	3.64e-05	-	no
B	4	GO:0006952	defense response	14/200	3.08	5.97e-05	-	no
B	3	GO:0009607	response to biotic stimulus	12/200	3.32	7.86e-05	-	no
B	4	GO:0046483	heterocycle metabolic process	10/200	3.70	9.72e-05	-	no
B	3	GO:0006950	response to stress	26/200	2.10	1.19e-04	-	no
B	3	GO:0033036	macromolecule localization	11/200	3.18	2.06e-04	-	no
B	3	GO:0044281	small molecule metabolic process	19/200	2.11	7.28e-04	-	no
B	5	GO:0043436	oxoacid metabolic process	11/200	2.50	1.69e-03	-	no
B	4	GO:0006082	organic acid metabolic process	11/200	2.49	1.73e-03	-	no
B	4	GO:0042180	cellular ketone metabolic process	11/200	2.45	1.98e-03	-	no
B	4	GO:0044249	cellular biosynthetic process	42/200	1.49	2.71e-03	-	no
B	4	GO:0006629	lipid metabolic process	10/200	2.30	4.58e-03	-	no
B	3	GO:0009058	biosynthetic process	42/200	1.44	5.08e-03	-	no

C	4	GO:0044435	plastid part	115/200	20.21	3.07e-126	-	no
C	5	GO:0044434	chloroplast part	113/200	20.40	3.48e-124	-	no
C	5	GO:0009536	plastid	144/200	7.80	2.06e-104	-	no
C	4	GO:0009579	thylakoid	79/200	31.73	6.28e-100	-	no
C	4	GO:0044436	thylakoid part	73/200	35.39	7.89e-96	-	no
C	5	GO:0031976	plastid thylakoid	71/200	35.67	2.27e-93	-	no
C	4	GO:0031984	organelle subcompartment	71/200	35.45	3.67e-93	-	no
C	5	GO:0042651	thylakoid membrane	69/200	38.12	6.77e-93	-	no
C	5	GO:0055035	plastid thylakoid membrane	68/200	39.26	1.69e-92	-	no
C	4	GO:0034357	photosynthetic membrane	69/200	37.62	1.90e-92	-	no
C	3	GO:0044446	intracellular organelle part	116/200	8.09	1.22e-80	-	no
C	3	GO:0044422	organelle part	116/200	8.08	1.34e-80	-	no
C	4	GO:0044444	cytoplasmic part	151/200	4.35	3.41e-74	-	no
C	4	GO:0005737	cytoplasm	151/200	4.03	1.69e-69	-	no
C	4	GO:0043231	intracellular membrane-bounded organelle	152/200	3.46	9.84e-61	-	no
C	3	GO:0043227	membrane-bounded organelle	152/200	3.46	1.00e-60	-	no
C	3	GO:0043229	intracellular organelle	152/200	3.29	1.12e-57	-	no
C	3	GO:0044424	intracellular part	155/200	3.04	1.03e-54	-	no
C	3	GO:0005622	intracellular	155/200	2.91	4.92e-52	-	no
C	5	GO:0009532	plastid stroma	50/200	20.23	5.42e-52	-	no
C	5	GO:0009526	plastid envelope	50/200	18.19	1.39e-49	-	no
C	4	GO:0031967	organelle envelope	50/200	12.00	2.21e-40	-	no
C	3	GO:0031975	envelope	50/200	12.00	2.21e-40	-	no
C	3	GO:0044464	cell part	179/200	1.96	3.99e-40	-	yes
C	3	GO:0016020	membrane	83/200	3.03	6.67e-23	-	no
C	3	GO:0048046	apoplast	24/200	12.17	2.70e-20	-	no
C	3	GO:0043234	protein complex	33/200	5.04	3.15e-15	-	no
C	4	GO:0005840	ribosome	17/200	6.64	1.34e-10	-	no
C	3	GO:0030529	ribonucleoprotein complex	17/200	4.87	1.70e-08	-	no
C	3	GO:0043228	non-membrane-bounded organelle	19/200	3.19	2.60e-06	-	no
C	4	GO:0043232	intracellular non-membrane-bounded organelle	19/200	3.19	2.60e-06	-	no
C	3	GO:0044425	membrane part	22/200	2.78	4.86e-06	-	no

M	3	GO:0003735	structural constituent of ribosome	12/200	5.54	3.24e-07	-	no
M	3	GO:0016491	oxidoreductase activity	17/200	2.02	2.12e-03	-	no

PS	4	PO:0020030	cotyledon	172/200	2.34	2.50e-48	-	yes
PS	5	PO:0020038	petiole	170/200	2.23	7.62e-44	-	yes
PS	5	PO:0020039	leaf lamina	173/200	2.10	2.11e-41	-	yes
PS	5	PO:0000013	cauline leaf	166/200	2.15	4.20e-39	-	yes
PS	4	PO:0009047	stem	171/200	2.03	6.21e-38	-	yes
PS	4	PO:0009025	leaf	177/200	1.92	9.10e-38	-	yes
PS	3	PO:0009013	meristem	167/200	2.08	1.77e-37	-	yes
PS	5	PO:0008037	seedling	172/200	1.95	7.64e-36	-	yes
PS	4	PO:0000230	inflorescence meristem	160/200	2.06	1.39e-33	-	yes
PS	3	PO:0009032	petal	167/200	1.91	5.84e-32	-	yes
PS	4	PO:0000037	shoot apex	165/200	1.92	1.84e-31	-	yes
PS	3	PO:0009031	sepal	170/200	1.84	3.91e-31	-	yes
PS	5	PO:0009028	microsporophyll	162/200	1.93	1.27e-30	-	yes
PS	3	PO:0006001	phyllome	177/200	1.73	2.90e-30	-	yes
PS	4	PO:0009009	embryo	172/200	1.78	6.51e-30	-	yes
PS	3	PO:0009010	seed	172/200	1.76	4.14e-29	-	yes
PS	4	PO:0009001	fruit	172/200	1.75	8.96e-29	-	yes
PS	3	PO:0006342	infructescence	172/200	1.75	8.96e-29	-	yes
PS	5	PO:0008034	leaf whorl	168/200	1.78	3.31e-28	-	yes
PS	4	PO:0008033	phyllome whorl	168/200	1.78	3.31e-28	-	yes
PS	4	PO:0009026	sporophyll	164/200	1.82	6.07e-28	-	yes
PS	4	PO:0000351	guard mother cell	57/200	5.27	8.82e-27	-	no
PS	5	PO:0009046	flower	174/200	1.67	9.00e-27	-	yes
PS	3	PO:0000070	meristemoid	57/200	5.27	9.60e-27	-	no
PS	3	PO:0009006	shoot	177/200	1.63	1.96e-26	-	yes
PS	5	PO:0009052	pedicel	154/200	1.89	2.01e-26	-	no
PS	4	PO:0009049	inflorescence	174/200	1.66	2.20e-26	-	yes
PS	4	PO:0000293	guard cell	56/200	5.20	5.17e-26	-	no
PS	5	PO:0000349	epidermal initial	57/200	5.05	7.63e-26	-	no
PS	4	PO:0004011	initial cell	57/200	5.02	1.05e-25	-	no
PS	3	PO:0004010	meristematic cell	57/200	5.01	1.14e-25	-	no
PS	5	PO:0006016	leaf epidermis	56/200	5.04	2.67e-25	-	no
PS	5	PO:0006035	shoot epidermis	56/200	5.00	3.78e-25	-	no
PS	5	PO:0009027	megasporophyll	154/200	1.83	1.09e-24	-	no
PS	3	PO:0004013	epidermal cell	57/200	4.78	1.28e-24	-	no
PS	4	PO:0005679	epidermis	57/200	4.60	8.31e-24	-	no
PS	3	PO:0009014	dermal tissue	57/200	4.60	8.51e-24	-	no
PS	3	PO:0020091	male gametophyte	138/200	1.66	9.00e-16	-	yes
PS	3	PO:0000034	vascular system	11/200	3.37	1.21e-04	-	no
PS	3	PO:0009005	root	106/200	1.18	9.47e-03	-	no

PG	4	PO:0001054	4 leaf senescence stage	167/200	2.17	2.66e-40	-	yes
PG	3	PO:0001050	leaf development stages	167/200	2.17	2.88e-40	-	yes
PG	5	PO:0007133	leaf production	170/200	2.02	3.33e-37	-	yes
PG	4	PO:0007112	1 main shoot growth	170/200	2.02	3.44e-37	-	yes
PG	3	PO:0007134	A vegetative growth	170/200	2.01	9.67e-37	-	yes
PG	5	PO:0004507	D bilateral stage	161/200	1.95	6.71e-31	-	no
PG	5	PO:0001081	F mature embryo stage	158/200	1.99	1.31e-30	-	no
PG	5	PO:0001078	E expanded cotyledon stage	158/200	1.90	3.65e-28	-	no
PG	5	PO:0001185	C globular stage	157/200	1.91	4.44e-28	-	yes
PG	5	PO:0007604	corolla developmental stages	169/200	1.71	3.75e-26	-	yes
PG	4	PO:0007631	embryo development stages	161/200	1.79	1.09e-25	-	yes
PG	3	PO:0001170	seed development stages	161/200	1.78	1.93e-25	-	yes
PG	4	PO:0007616	4 anthesis	166/200	1.71	5.44e-25	-	yes
PG	4	PO:0007600	3 floral organ development stages	170/200	1.67	5.75e-25	-	yes
PG	3	PO:0007615	flower development stages	171/200	1.63	5.21e-24	-	yes

KW	0	chloroplast	-	130/200	7.36	7.36e-88	-	no
KW	0	thylakoid	-	61/200	28.65	1.89e-73	-	no
KW	0	photosystem	-	26/200	43.23	2.33e-37	-	no
KW	0	components	-	33/200	20.32	9.13e-35	-	no
KW	0	stroma	-	28/200	15.02	6.02e-26	-	no
KW	0	light	-	28/200	10.49	1.56e-21	-	no
KW	0	envelope	-	26/200	11.38	4.74e-21	-	no
KW	0	subunit	-	34/200	4.64	1.45e-14	-	no
KW	0	response	-	51/200	2.84	1.34e-12	-	yes
KW	0	membrane	-	63/200	2.37	6.72e-12	-	no
KW	0	ipr003612	-	10/200	13.74	2.03e-10	-	no
KW	0	encodes	-	58/200	2.27	3.05e-10	-	no
KW	0	ipr016140	-	10/200	12.99	3.72e-10	-	no
KW	0	amylase	-	10/200	11.63	1.22e-09	-	no
KW	0	apoplast	-	13/200	7.75	1.81e-09	-	no
KW	0	trypsin	-	10/200	10.66	3.07e-09	-	no
KW	0	bifunctional	-	10/200	10.66	3.07e-09	-	no
KW	0	plastid	-	12/200	7.95	4.79e-09	-	no
KW	0	storage	-	10/200	8.80	2.28e-08	-	no
KW	0	transfer	-	10/200	8.71	2.54e-08	-	no
KW	0	ribosomal	-	15/200	4.97	7.62e-08	-	no
KW	0	electron	-	16/200	4.49	1.31e-07	-	no
KW	0	ribosome	-	13/200	4.92	5.05e-07	-	no
KW	0	structural	-	15/200	4.28	5.64e-07	-	no
KW	0	constituent	-	13/200	4.64	1.02e-06	-	no
KW	0	complex	-	24/200	2.83	1.39e-06	-	no
KW	0	lipid	-	14/200	4.08	2.20e-06	-	no
KW	0	stimulus	-	15/200	3.48	7.82e-06	-	yes
KW	0	enzyme	-	13/200	3.85	8.65e-06	-	no
KW	0	catalytic	-	25/200	2.46	1.11e-05	-	no
KW	0	inhibitor	-	12/200	4.01	1.11e-05	-	no
KW	0	defense	-	12/200	3.44	5.50e-05	-	no
KW	0	helical	-	11/200	3.65	5.69e-05	-	no
KW	0	phosphate	-	11/200	3.63	6.03e-05	-	no
KW	0	stress	-	14/200	2.98	8.33e-05	-	no
KW	0	transport	-	22/200	2.26	1.22e-04	-	no
KW	0	translation	-	14/200	2.83	1.52e-04	-	no
KW	0	biosynthetic	-	17/200	2.38	3.24e-04	-	no
KW	0	alpha	-	17/200	2.33	4.14e-04	-	no
KW	0	protease	-	10/200	2.99	5.89e-04	-	no
KW	0	process	-	33/200	1.61	2.21e-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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