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
AT5G26000.1	0.898741	TGG1 (THIOGLUCOSIDE GLUCOHYDROLASE 1)	OMAT5P107780	-	OMAT5P008870	-
AT3G16240.1	0.89639	DELTA-TIP	OMAT3P006005,OMAT3P006000	[OMAT3P006005]-, [OMAT3P006000]-	-	-
AT1G66150.1	0.89177	TMK1 (TRANSMEMBRANE KINASE 1)	OMAT1P018400	-	OMAT1P116360	-
AT2G35450.1	0.889152	catalytic/ hydrolase	OMAT2P107950	-	-	-
AT1G77490.1	0.886737	TAPX (THYLAKOIDAL ASCORBATE PEROXIDASE)	OMAT1P022830	-	-	-
AT5G02160.1	0.8766	unknown protein	OMAT5P000460	-	OMAT5P100395	-
AT5G05590.1	0.871939	PAI2 (PHOSPHORIBOSYLANTHRANILATE ISOMERASE 2)	-	-	-	-
AT1G72610.1	0.860214	GER1 (GERMIN-LIKE PROTEIN 1)	OMAT1P118450	-	-	-
AT5G53490.1	0.859867	thylakoid lumenal 17.4 kDa protein, chloroplast	OMAT5P113840	-	OMAT5P015680	-
AT4G02130.1	0.859614	GATL6	OMAT4P100805,OMAT4P100800	[OMAT4P100805]-, [OMAT4P100800]-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT4G09180.1	-0.867141	basic helix-loop-helix (bHLH) family protein	OMAT4P002250	-	-	-
AT2G14740.1	-0.85674	ATVSR3 (ARABIDOPSIS THALIANA VACULOLAR SORTING RECEPTOR 3)	OMAT2P001830	-	-	-
AT3G24860.1	-0.853526	hydroxyproline-rich glycoprotein family protein	-	-	-	-
AT2G11450.1	-0.846671	transposable element gene	-	-	-	-
AT1G22050.1	-0.835515	MUB6 (MEMBRANE-ANCHORED UBIQUITIN-FOLD PROTEIN 6 PRECURSOR)	OMAT1P008020	-	-	-
AT4G29860.1	-0.829402	EMB2757 (EMBRYO DEFECTIVE 2757)	OMAT4P108350	-	-	-
AT5G17680.1	-0.829038	disease resistance protein (TIR-NBS-LRR class), putative	-	-	-	-
AT5G45790.1	-0.828083	ubiquitin thiolesterase	OMAT5P012840	-	-	-
AT4G01710.1	-0.821931	CRK (CROOKED)	OMAT4P000600	-	-	-
AT1G29820.1	-0.821724	unknown protein	OMAT1P010450	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 7.60e-48	:20 terms with high significance
7.60e-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	28/200	35.01	4.59e-37	-	no
B	4	GO:0006091	generation of precursor metabolites and energy	18/200	11.25	3.69e-15	-	no
B	3	GO:0009628	response to abiotic stimulus	33/200	4.45	1.12e-13	-	no
B	5	GO:0009416	response to light stimulus	20/200	6.96	1.71e-12	-	no
B	4	GO:0009314	response to radiation	20/200	6.73	3.18e-12	-	no
B	3	GO:0044237	cellular metabolic process	82/200	1.74	1.53e-08	-	no
B	4	GO:0009409	response to cold	10/200	6.42	5.49e-07	-	no
B	3	GO:0006950	response to stress	29/200	2.34	6.55e-06	-	no
B	4	GO:0009266	response to temperature stimulus	10/200	4.39	2.08e-05	-	no
B	4	GO:0044262	cellular carbohydrate metabolic process	11/200	3.56	7.26e-05	-	no
B	3	GO:0033036	macromolecule localization	11/200	3.18	2.06e-04	-	no
B	4	GO:0006952	defense response	12/200	2.64	7.19e-04	-	no
B	4	GO:0006629	lipid metabolic process	11/200	2.53	1.53e-03	-	no
B	4	GO:0005975	carbohydrate metabolic process	12/200	2.30	2.38e-03	-	no
B	4	GO:0010033	response to organic substance	14/200	2.09	3.12e-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:0042180	cellular ketone metabolic process	10/200	2.23	5.75e-03	-	no
B	4	GO:0009725	response to hormone stimulus	10/200	2.12	8.35e-03	-	no
B	3	GO:0009056	catabolic process	10/200	2.10	8.89e-03	-	no
B	3	GO:0044281	small molecule metabolic process	16/200	1.78	9.08e-03	-	no

C	5	GO:0044434	chloroplast part	85/200	15.35	1.49e-79	-	no
C	4	GO:0044435	plastid part	85/200	14.94	1.53e-78	-	no
C	5	GO:0009536	plastid	119/200	6.44	8.36e-72	-	no
C	4	GO:0009579	thylakoid	61/200	24.50	5.79e-69	-	no
C	4	GO:0044436	thylakoid part	55/200	26.66	2.98e-64	-	no
C	5	GO:0031976	plastid thylakoid	54/200	27.13	1.63e-63	-	no
C	4	GO:0031984	organelle subcompartment	54/200	26.96	2.32e-63	-	no
C	4	GO:0034357	photosynthetic membrane	52/200	28.35	3.11e-62	-	no
C	5	GO:0055035	plastid thylakoid membrane	51/200	29.44	5.89e-62	-	no
C	5	GO:0042651	thylakoid membrane	51/200	28.17	6.93e-61	-	no
C	4	GO:0044444	cytoplasmic part	129/200	3.71	9.95e-51	-	no
C	4	GO:0005737	cytoplasm	130/200	3.47	7.60e-48	-	no
C	3	GO:0044446	intracellular organelle part	86/200	6.00	3.33e-46	-	no
C	3	GO:0044422	organelle part	86/200	5.99	3.57e-46	-	no
C	4	GO:0043231	intracellular membrane-bounded organelle	134/200	3.05	2.71e-43	-	no
C	3	GO:0043227	membrane-bounded organelle	134/200	3.05	2.75e-43	-	no
C	3	GO:0043229	intracellular organelle	134/200	2.90	9.57e-41	-	no
C	3	GO:0044424	intracellular part	135/200	2.65	1.34e-36	-	no
C	5	GO:0009526	plastid envelope	40/200	14.55	8.32e-36	-	no
C	3	GO:0005622	intracellular	135/200	2.54	1.96e-34	-	no
C	4	GO:0031967	organelle envelope	40/200	9.60	1.34e-28	-	no
C	3	GO:0031975	envelope	40/200	9.60	1.34e-28	-	no
C	5	GO:0009532	plastid stroma	33/200	13.35	1.57e-28	-	no
C	3	GO:0044464	cell part	161/200	1.76	8.74e-25	-	yes
C	3	GO:0016020	membrane	83/200	3.03	6.67e-23	0	yes
C	3	GO:0048046	apoplast	20/200	10.14	1.11e-15	-	no
C	3	GO:0043234	protein complex	32/200	4.89	1.96e-14	-	no
C	4	GO:0005840	ribosome	13/200	5.07	3.53e-07	-	no
C	3	GO:0044425	membrane part	24/200	3.03	4.03e-07	-	no
C	4	GO:0005618	cell wall	13/200	3.92	7.21e-06	-	no
C	3	GO:0030312	external encapsulating structure	13/200	3.89	7.82e-06	-	no
C	3	GO:0030529	ribonucleoprotein complex	13/200	3.73	1.26e-05	-	no
C	5	GO:0005773	vacuole	10/200	2.90	7.64e-04	-	no
C	3	GO:0043228	non-membrane-bounded organelle	13/200	2.18	2.83e-03	-	no
C	4	GO:0043232	intracellular non-membrane-bounded organelle	13/200	2.18	2.83e-03	-	no

M	3	GO:0046906	tetrapyrrole binding	10/200	5.25	3.90e-06	-	no

PS	5	PO:0020038	petiole	183/200	2.40	2.56e-58	-	yes
PS	4	PO:0020030	cotyledon	177/200	2.41	8.65e-54	-	yes
PS	5	PO:0020039	leaf lamina	184/200	2.23	1.70e-53	-	yes
PS	4	PO:0009025	leaf	187/200	2.03	8.37e-49	-	yes
PS	5	PO:0000013	cauline leaf	175/200	2.27	5.94e-48	-	yes
PS	3	PO:0009013	meristem	177/200	2.20	2.65e-47	-	yes
PS	5	PO:0009028	microsporophyll	178/200	2.12	2.58e-45	-	yes
PS	4	PO:0009047	stem	178/200	2.11	6.95e-45	-	yes
PS	5	PO:0008037	seedling	180/200	2.04	9.25e-44	-	yes
PS	3	PO:0009032	petal	179/200	2.04	3.32e-43	-	yes
PS	5	PO:0009027	megasporophyll	176/200	2.10	3.92e-43	-	yes
PS	3	PO:0006001	phyllome	189/200	1.84	8.75e-43	-	yes
PS	3	PO:0009031	sepal	182/200	1.97	1.31e-42	-	yes
PS	4	PO:0009026	sporophyll	179/200	1.99	2.70e-41	-	yes
PS	4	PO:0000230	inflorescence meristem	168/200	2.16	1.42e-40	-	yes
PS	4	PO:0000037	shoot apex	175/200	2.03	2.04e-40	-	yes
PS	5	PO:0009052	pedicel	170/200	2.09	1.90e-39	-	yes
PS	3	PO:0009006	shoot	189/200	1.74	2.52e-38	-	yes
PS	4	PO:0009009	embryo	180/200	1.86	3.03e-37	-	yes
PS	5	PO:0008034	leaf whorl	178/200	1.89	5.53e-37	-	yes
PS	4	PO:0008033	phyllome whorl	178/200	1.89	5.53e-37	-	yes
PS	3	PO:0009010	seed	180/200	1.84	2.33e-36	-	yes
PS	4	PO:0009001	fruit	180/200	1.83	5.48e-36	-	yes
PS	3	PO:0006342	infructescence	180/200	1.83	5.48e-36	-	yes
PS	3	PO:0020091	male gametophyte	167/200	2.01	1.88e-35	-	yes
PS	5	PO:0009046	flower	183/200	1.76	6.01e-35	-	yes
PS	4	PO:0009049	inflorescence	183/200	1.75	1.64e-34	-	yes
PS	4	PO:0000293	guard cell	57/200	5.30	7.03e-27	-	no
PS	4	PO:0000351	guard mother cell	57/200	5.27	8.82e-27	-	no
PS	3	PO:0000070	meristemoid	57/200	5.27	9.60e-27	-	no
PS	5	PO:0000349	epidermal initial	58/200	5.14	1.06e-26	-	no
PS	4	PO:0004011	initial cell	58/200	5.11	1.48e-26	-	no
PS	3	PO:0004010	meristematic cell	58/200	5.10	1.61e-26	-	no
PS	5	PO:0006016	leaf epidermis	57/200	5.13	3.76e-26	-	no
PS	5	PO:0006035	shoot epidermis	57/200	5.09	5.37e-26	-	no
PS	3	PO:0004013	epidermal cell	58/200	4.86	1.89e-25	-	no
PS	4	PO:0005679	epidermis	58/200	4.68	1.28e-24	-	no
PS	3	PO:0009014	dermal tissue	58/200	4.68	1.31e-24	-	no
PS	3	PO:0009005	root	147/200	1.63	6.45e-17	-	yes

PG	4	PO:0001054	4 leaf senescence stage	175/200	2.28	2.92e-48	-	yes
PG	3	PO:0001050	leaf development stages	175/200	2.27	3.19e-48	-	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:0001185	C globular stage	173/200	2.11	1.04e-41	-	yes
PG	5	PO:0004507	D bilateral stage	172/200	2.09	1.78e-40	-	yes
PG	3	PO:0001170	seed development stages	178/200	1.97	6.35e-40	-	yes
PG	4	PO:0007631	embryo development stages	176/200	1.95	3.04e-38	-	yes
PG	5	PO:0001081	F mature embryo stage	167/200	2.10	4.03e-38	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	169/200	2.04	3.58e-37	-	yes
PG	4	PO:0007616	4 anthesis	178/200	1.84	4.95e-35	-	yes
PG	5	PO:0007604	corolla developmental stages	179/200	1.81	9.71e-35	-	yes
PG	4	PO:0007600	3 floral organ development stages	180/200	1.77	1.76e-33	-	yes
PG	3	PO:0007615	flower development stages	180/200	1.72	1.55e-31	-	yes

KW	0	chloroplast	-	96/200	5.43	1.21e-48	-	no
KW	0	components	-	38/200	23.40	2.87e-42	-	no
KW	0	thylakoid	-	39/200	18.32	5.86e-39	-	no
KW	0	photosystem	-	23/200	38.24	6.50e-32	-	no
KW	0	light	-	28/200	10.49	1.56e-21	-	no
KW	0	subunit	-	32/200	4.36	4.56e-13	-	no
KW	0	envelope	-	18/200	7.88	2.19e-12	-	no
KW	0	stroma	-	16/200	8.58	7.72e-12	-	no
KW	0	encodes	-	59/200	2.31	1.03e-10	-	no
KW	0	membrane	-	55/200	2.07	3.03e-08	0	yes
KW	0	plastid	-	11/200	7.29	4.59e-08	-	no
KW	0	complex	-	26/200	3.07	1.11e-07	-	no
KW	0	apoplast	-	11/200	6.56	1.45e-07	-	no
KW	0	response	-	41/200	2.29	1.55e-07	-	yes
KW	0	lipid	-	14/200	4.08	2.20e-06	-	no
KW	0	structural	-	14/200	3.99	2.84e-06	-	no
KW	0	catalytic	-	26/200	2.56	3.71e-06	-	no
KW	0	constituent	-	12/200	4.28	5.61e-06	-	no
KW	0	ribosomal	-	11/200	3.64	5.80e-05	-	no
KW	0	ribosome	-	10/200	3.79	7.81e-05	-	no
KW	0	stimulus	-	13/200	3.02	1.21e-04	-	no
KW	0	transport	-	22/200	2.26	1.22e-04	-	yes
KW	0	enzyme	-	11/200	3.26	1.64e-04	-	no
KW	0	process	-	36/200	1.76	2.84e-04	-	no
KW	0	alpha	-	17/200	2.33	4.14e-04	-	no
KW	0	defense	-	10/200	2.87	8.31e-04	-	no
KW	0	biosynthetic	-	16/200	2.24	8.94e-04	-	no
KW	0	hydrolase	-	16/200	2.19	1.12e-03	-	no
KW	0	translation	-	11/200	2.22	4.40e-03	-	no
KW	0	stress	-	10/200	2.13	7.91e-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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