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
AT3G06140.1	0.921429	zinc finger (C3HC4-type RING finger) family protein	-	-	-	-
AT5G43870.1	0.920882	phosphoinositide binding	OMAT5P110650	-	-	-
AT1G13250.1	0.911149	GATL3 (Galacturonosyltransferase-like 3)	OMAT1P104240	-	-	-
AT2G01760.1	0.899143	ARR14 (ARABIDOPSIS RESPONSE REGULATOR 14)	OMAT2P000225,OMAT2P000230	[OMAT2P000225]-, [OMAT2P000230]-	-	-
AT3G03980.1	0.889273	short-chain dehydrogenase/reductase (SDR) family protein	OMAT3P001330	-	-	-
AT5G48485.1	0.883722	DIR1 (DEFECTIVE IN INDUCED RESISTANCE 1)	OMAT5P112330	-	-	-
AT5G22580.1	0.882342	FUNCTIONS IN: molecular_function unknown	OMAT5P007610	-	-	-
AT1G29500.1	0.873143	auxin-responsive protein, putative	-	-	-	-
AT4G27440.1	0.873013	PORB (PROTOCHLOROPHYLLIDE OXIDOREDUCTASE B)	OMAT4P008750	-	OMAT4P107610	-
AT2G43550.1	0.870749	trypsin inhibitor, putative	OMAT2P011990	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT5G36935.1	-0.820603	transposable element gene	-	-	-	-
AT5G26600.2	-0.814465	catalytic/ pyridoxal phosphate binding	OMAT5P009080	-	-	-
AT1G78870.1	-0.807651	UBC35 (UBIQUITIN-CONJUGATING ENZYME 35)	OMAT1P023480	-	-	-
AT2G31585.1	-0.803378	other RNA	-	-	-	-
AT2G19140.1	-0.78827	transposable element gene	-	-	-	-
AT4G20850.1	-0.78533	TPP2 (TRIPEPTIDYL PEPTIDASE II)	OMAT4P105250	-	-	-
AT5G07470.1	-0.778012	PMSR3 (PEPTIDEMETHIONINE SULFOXIDE REDUCTASE 3)	OMAT5P102060	-	-	-
AT2G45140.1	-0.777165	PVA12 (PLANT VAP HOMOLOG 12)	OMAT2P012610	-	-	-
AT1G65820.3	-0.769864	microsomal glutathione s-transferase, putative	-	-	-	-
AT1G29970.2	-0.768759	RPL18AA (60S RIBOSOMAL PROTEIN L18A-1)	OMAT1P109460,OMAT1P109470	[OMAT1P109460]-, [OMAT1P109470]-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 7.74e-35	:20 terms with high significance
7.74e-35 <	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	14/200	17.50	3.73e-15	-	no
B	4	GO:0005975	carbohydrate metabolic process	20/200	3.84	7.27e-08	-	no
B	4	GO:0006091	generation of precursor metabolites and energy	10/200	6.25	7.14e-07	-	no
B	4	GO:0044262	cellular carbohydrate metabolic process	12/200	3.88	1.59e-05	-	no
B	3	GO:0009628	response to abiotic stimulus	19/200	2.56	5.93e-05	-	no
B	4	GO:0009314	response to radiation	10/200	3.37	2.18e-04	-	no
B	3	GO:0044237	cellular metabolic process	66/200	1.40	9.49e-04	-	yes
B	4	GO:0006629	lipid metabolic process	11/200	2.53	1.53e-03	-	no
B	3	GO:0042221	response to chemical stimulus	21/200	1.84	2.47e-03	-	no
B	3	GO:0006950	response to stress	22/200	1.77	3.23e-03	-	no
B	3	GO:0009056	catabolic process	11/200	2.31	3.25e-03	-	no
B	3	GO:0044238	primary metabolic process	64/200	1.29	8.30e-03	-	yes

C	5	GO:0044434	chloroplast part	50/200	9.03	2.54e-34	-	no
C	4	GO:0044435	plastid part	50/200	8.79	9.24e-34	-	no
C	4	GO:0009579	thylakoid	35/200	14.06	5.86e-31	-	no
C	5	GO:0009536	plastid	77/200	4.17	6.54e-30	-	no
C	5	GO:0031976	plastid thylakoid	31/200	15.57	5.04e-29	-	no
C	4	GO:0031984	organelle subcompartment	31/200	15.48	6.11e-29	-	no
C	4	GO:0044436	thylakoid part	31/200	15.03	1.57e-28	-	no
C	5	GO:0055035	plastid thylakoid membrane	28/200	16.17	7.15e-27	-	no
C	5	GO:0042651	thylakoid membrane	28/200	15.47	2.57e-26	-	no
C	4	GO:0034357	photosynthetic membrane	28/200	15.26	3.77e-26	-	no
C	3	GO:0044446	intracellular organelle part	60/200	4.18	5.88e-23	-	no
C	3	GO:0044422	organelle part	60/200	4.18	6.14e-23	-	no
C	4	GO:0044444	cytoplasmic part	88/200	2.53	3.64e-19	-	no
C	3	GO:0043229	intracellular organelle	102/200	2.21	2.07e-18	-	yes
C	3	GO:0044464	cell part	150/200	1.64	8.39e-18	-	yes
C	4	GO:0043231	intracellular membrane-bounded organelle	98/200	2.23	8.63e-18	-	yes
C	3	GO:0043227	membrane-bounded organelle	98/200	2.23	8.71e-18	-	yes
C	4	GO:0005737	cytoplasm	89/200	2.38	1.43e-17	-	no
C	5	GO:0009526	plastid envelope	24/200	8.73	7.30e-17	-	no
C	3	GO:0044424	intracellular part	104/200	2.04	2.66e-16	-	yes
C	3	GO:0005622	intracellular	105/200	1.97	2.00e-15	-	yes
C	4	GO:0031967	organelle envelope	24/200	5.76	9.07e-13	-	no
C	3	GO:0031975	envelope	24/200	5.76	9.07e-13	-	no
C	5	GO:0009532	plastid stroma	19/200	7.69	9.23e-13	-	no
C	3	GO:0016020	membrane	58/200	2.12	4.55e-09	-	no
C	3	GO:0048046	apoplast	13/200	6.59	1.42e-08	-	no
C	3	GO:0043234	protein complex	22/200	3.36	1.95e-07	-	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:0044425	membrane part	17/200	2.15	1.05e-03	-	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	4	GO:0016798	hydrolase activity, acting on glycosyl bonds	14/200	5.27	8.80e-08	-	no
M	5	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	10/200	4.04	4.43e-05	-	no
M	3	GO:0016491	oxidoreductase activity	20/200	2.37	1.19e-04	-	no
M	4	GO:0016757	transferase activity, transferring glycosyl groups	10/200	3.43	1.86e-04	-	no
M	3	GO:0016787	hydrolase activity	28/200	1.79	9.16e-04	-	no

PS	5	PO:0020038	petiole	170/200	2.23	7.62e-44	-	no
PS	5	PO:0020039	leaf lamina	174/200	2.11	2.16e-42	-	no
PS	5	PO:0009052	pedicel	172/200	2.12	2.36e-41	-	no
PS	5	PO:0000013	cauline leaf	168/200	2.17	5.98e-41	-	no
PS	4	PO:0009025	leaf	180/200	1.96	8.47e-41	-	no
PS	5	PO:0009027	megasporophyll	171/200	2.04	2.99e-38	-	no
PS	3	PO:0009031	sepal	177/200	1.92	1.87e-37	-	no
PS	3	PO:0009032	petal	173/200	1.97	3.06e-37	-	no
PS	4	PO:0000037	shoot apex	169/200	1.96	7.74e-35	-	no
PS	5	PO:0008037	seedling	170/200	1.93	4.63e-34	-	no
PS	3	PO:0006001	phyllome	181/200	1.76	5.50e-34	-	no
PS	4	PO:0009026	sporophyll	171/200	1.90	1.15e-33	-	no
PS	4	PO:0009009	embryo	176/200	1.82	2.07e-33	-	no
PS	5	PO:0008034	leaf whorl	174/200	1.85	3.05e-33	-	no
PS	4	PO:0008033	phyllome whorl	174/200	1.85	3.05e-33	-	no
PS	5	PO:0009028	microsporophyll	165/200	1.97	4.72e-33	-	no
PS	4	PO:0020030	cotyledon	155/200	2.11	7.06e-33	-	no
PS	3	PO:0009010	seed	176/200	1.80	1.45e-32	-	no
PS	4	PO:0009001	fruit	176/200	1.79	3.26e-32	-	no
PS	3	PO:0006342	infructescence	176/200	1.79	3.26e-32	-	no
PS	3	PO:0009013	meristem	159/200	1.98	8.42e-31	-	no
PS	5	PO:0009046	flower	178/200	1.71	3.56e-30	-	no
PS	3	PO:0009006	shoot	181/200	1.67	6.03e-30	-	no
PS	4	PO:0009049	inflorescence	178/200	1.70	9.14e-30	-	no
PS	4	PO:0000230	inflorescence meristem	154/200	1.98	6.29e-29	-	no
PS	4	PO:0009047	stem	159/200	1.88	5.61e-28	-	no
PS	3	PO:0020091	male gametophyte	152/200	1.83	5.39e-24	-	no
PS	4	PO:0000293	guard cell	37/200	3.44	9.74e-12	-	no
PS	4	PO:0000351	guard mother cell	37/200	3.42	1.11e-11	-	no
PS	3	PO:0000070	meristemoid	37/200	3.42	1.17e-11	-	no
PS	5	PO:0006016	leaf epidermis	37/200	3.33	2.56e-11	-	no
PS	5	PO:0006035	shoot epidermis	37/200	3.30	3.14e-11	-	no
PS	5	PO:0000349	epidermal initial	37/200	3.28	3.85e-11	-	no
PS	4	PO:0004011	initial cell	37/200	3.26	4.63e-11	-	no
PS	3	PO:0004010	meristematic cell	37/200	3.26	4.85e-11	-	no
PS	3	PO:0004013	epidermal cell	38/200	3.19	4.94e-11	-	no
PS	4	PO:0005679	epidermis	38/200	3.07	1.49e-10	-	no
PS	3	PO:0009014	dermal tissue	38/200	3.07	1.51e-10	-	no
PS	3	PO:0009005	root	123/200	1.37	9.29e-07	-	no

PG	5	PO:0001185	C globular stage	172/200	2.10	9.76e-41	-	no
PG	5	PO:0001081	F mature embryo stage	168/200	2.11	4.95e-39	-	no
PG	5	PO:0007133	leaf production	171/200	2.03	4.01e-38	-	no
PG	4	PO:0007112	1 main shoot growth	171/200	2.03	4.15e-38	-	no
PG	5	PO:0004507	D bilateral stage	169/200	2.05	1.14e-37	-	no
PG	3	PO:0007134	A vegetative growth	171/200	2.02	1.18e-37	-	no
PG	4	PO:0001054	4 leaf senescence stage	164/200	2.13	1.36e-37	-	no
PG	3	PO:0001050	leaf development stages	164/200	2.13	1.47e-37	-	no
PG	5	PO:0001078	E expanded cotyledon stage	169/200	2.04	3.58e-37	-	no
PG	4	PO:0007631	embryo development stages	174/200	1.93	2.43e-36	-	no
PG	3	PO:0001170	seed development stages	174/200	1.92	4.77e-36	-	no
PG	4	PO:0007616	4 anthesis	175/200	1.80	2.90e-32	-	no
PG	5	PO:0007604	corolla developmental stages	176/200	1.78	5.94e-32	-	no
PG	4	PO:0007600	3 floral organ development stages	177/200	1.74	1.04e-30	-	no
PG	3	PO:0007615	flower development stages	178/200	1.70	1.03e-29	-	no

KW	0	chloroplast	-	68/200	3.85	4.22e-24	-	no
KW	0	thylakoid	-	25/200	11.74	1.15e-20	-	no
KW	0	photosystem	-	16/200	26.60	3.79e-20	-	no
KW	0	components	-	13/200	8.01	1.19e-09	-	no
KW	0	envelope	-	15/200	6.56	1.55e-09	-	no
KW	0	encodes	-	53/200	2.08	4.92e-08	-	no
KW	0	stroma	-	12/200	6.44	5.81e-08	-	no
KW	0	light	-	14/200	5.24	9.33e-08	-	no
KW	0	glucose	-	10/200	6.76	3.30e-07	-	no
KW	0	reductase	-	13/200	4.77	7.34e-07	-	no
KW	0	apoplast	-	10/200	5.96	1.14e-06	-	no
KW	0	chain	-	13/200	4.30	2.50e-06	-	no
KW	0	process	-	40/200	1.95	1.19e-05	-	no
KW	0	mutant	-	10/200	4.59	1.36e-05	-	no
KW	0	subunit	-	20/200	2.73	1.62e-05	-	no
KW	0	membrane	-	47/200	1.77	2.90e-05	-	no
KW	0	catalytic	-	24/200	2.36	3.18e-05	-	no
KW	0	dehydrogenase	-	11/200	3.79	3.93e-05	-	no
KW	0	glycosyl	-	12/200	2.81	3.91e-04	-	no
KW	0	biosynthetic	-	16/200	2.24	8.94e-04	-	no
KW	0	complex	-	18/200	2.13	9.00e-04	-	no
KW	0	hydrolase	-	16/200	2.19	1.12e-03	-	no
KW	0	metabolic	-	22/200	1.92	1.22e-03	-	no
KW	0	response	-	30/200	1.67	1.90e-03	-	no
KW	0	oxidoreductase	-	11/200	2.36	2.70e-03	-	no
KW	0	stimulus	-	10/200	2.32	4.26e-03	-	no
KW	0	transport	-	18/200	1.85	4.26e-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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