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
AT1G67630.1	0.962358	POLA2 (DNA POLYMERASE ALPHA 2)	-	-	-	-
AT3G05740.1	0.953644	RECQI1 (Arabidopsis RecQ helicase l1)	-	-	-	-
AT5G44635.1	0.953437	minichromosome maintenance family protein / MCM family protein	-	-	-	-
AT3G13560.1	0.948323	glycosyl hydrolase family 17 protein	OMAT3P104500	-	-	-
AT5G15580.1	0.945079	LNG1 (LONGIFOLIA1)	OMAT5P104420	-	-	-
AT3G23740.1	0.943575	unknown protein	-	-	-	-
AT3G18524.1	0.939593	MSH2 (MUTS HOMOLOG 2)	-	-	-	-
AT2G40550.1	0.936763	ETG1 (E2F TARGET GENE 1)	OMAT2P010865	-	-	-
AT1G14180.1	0.936077	protein binding / zinc ion binding	OMAT1P004980	-	-	-
AT1G18250.2	0.931204	ATLP-1	OMAT1P105890	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT3G01170.1	-0.791272	structural constituent of ribosome	OMAT3P000060	-	-	-
AT3G29641.1	-0.762008	transposable element gene	-	-	-	-
AT3G66654.1	-0.748698	peptidyl-prolyl cis-trans isomerase cyclophilin-type family protein	OMAT3P002350	-	-	-
AT1G49300.1	-0.742936	RABG3E (RAB GTPASE HOMOLOG G3E)	OMAT1P013520	-	-	-
AT5G53330.1	-0.742914	FUNCTIONS IN: molecular_function unknown	OMAT5P015580	-	-	-
AT5G45130.1	-0.727043	RHA1 (RAB HOMOLOG 1)	OMAT5P012600	-	-	-
AT4G29160.1	-0.721797	SNF7.1	-	-	-	-
AT3G12360.1	-0.720501	ITN1 (INCREASED TOLERANCE TO NACL)	OMAT3P004330	-	-	-
AT3G60590.3	-0.716392	unknown protein	OMAT3P017100	-	-	-
AT1G16240.1	-0.715244	SYP51 (SYNTAXIN OF PLANTS 51)	OMAT1P105390	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 2.16e-29	:20 terms with high significance
2.16e-29 <	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	5	GO:0006259	DNA metabolic process	23/200	11.42	6.77e-19	-	yes
B	5	GO:0007167	enzyme linked receptor protein signaling pathway	15/200	19.19	1.06e-16	-	no
B	4	GO:0007166	cell surface receptor linked signaling pathway	15/200	16.52	1.20e-15	-	no
B	3	GO:0007049	cell cycle	18/200	11.60	2.11e-15	3.96E-16	no
B	3	GO:0007017	microtubule-based process	13/200	20.20	3.81e-15	-	no
B	3	GO:0023033	signaling pathway	20/200	5.92	3.53e-11	-	no
B	3	GO:0022402	cell cycle process	11/200	12.03	1.57e-10	2.65E-17	no
B	3	GO:0006996	organelle organization	19/200	5.69	2.00e-10	-	no
B	4	GO:0051276	chromosome organization	11/200	8.92	4.84e-09	-	no
B	3	GO:0043170	macromolecule metabolic process	66/200	1.71	1.53e-06	-	yes
B	3	GO:0022607	cellular component assembly	10/200	5.71	1.72e-06	-	no
B	4	GO:0044260	cellular macromolecule metabolic process	58/200	1.65	2.46e-05	-	yes
B	5	GO:0006796	phosphate metabolic process	18/200	2.71	4.23e-05	-	no
B	4	GO:0006793	phosphorus metabolic process	18/200	2.71	4.28e-05	-	no
B	3	GO:0044238	primary metabolic process	73/200	1.47	7.96e-05	-	yes
B	5	GO:0006464	protein modification process	23/200	2.21	1.25e-04	-	no
B	3	GO:0051716	cellular response to stimulus	13/200	2.94	1.59e-04	-	no
B	4	GO:0043412	macromolecule modification	24/200	2.12	1.80e-04	-	no
B	5	GO:0090304	nucleic acid metabolic process	29/200	1.93	2.23e-04	-	yes
B	4	GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	30/200	1.78	7.17e-04	-	yes
B	4	GO:0034641	cellular nitrogen compound metabolic process	31/200	1.59	3.46e-03	-	yes
B	4	GO:0019538	protein metabolic process	35/200	1.52	4.56e-03	-	no
B	3	GO:0006807	nitrogen compound metabolic process	31/200	1.56	4.64e-03	-	yes
B	3	GO:0044237	cellular metabolic process	62/200	1.31	6.55e-03	-	yes

C	4	GO:0044427	chromosomal part	15/200	20.28	4.30e-17	-	yes
C	5	GO:0005694	chromosome	15/200	15.12	4.96e-15	5.21E-16	yes
C	3	GO:0043228	non-membrane-bounded organelle	31/200	5.20	9.22e-15	-	yes
C	4	GO:0043232	intracellular non-membrane-bounded organelle	31/200	5.20	9.22e-15	-	yes
C	3	GO:0044464	cell part	140/200	1.53	1.10e-12	2.86E-16	yes
C	5	GO:0005856	cytoskeleton	13/200	11.56	9.18e-12	-	no
C	4	GO:0044430	cytoskeletal part	12/200	12.71	1.45e-11	-	no
C	5	GO:0005634	nucleus	38/200	2.43	9.45e-08	-	yes
C	3	GO:0044446	intracellular organelle part	35/200	2.44	2.76e-07	-	yes
C	3	GO:0044422	organelle part	35/200	2.44	2.81e-07	-	yes
C	3	GO:0043234	protein complex	21/200	3.21	7.70e-07	-	no
C	4	GO:0005886	plasma membrane	30/200	2.42	2.26e-06	-	no
C	3	GO:0043229	intracellular organelle	74/200	1.60	3.09e-06	-	yes
C	4	GO:0044428	nuclear part	13/200	3.91	7.36e-06	4.90E-17	yes
C	3	GO:0030312	external encapsulating structure	13/200	3.89	7.82e-06	-	no
C	3	GO:0044424	intracellular part	78/200	1.53	8.97e-06	-	yes
C	3	GO:0005622	intracellular	79/200	1.48	2.50e-05	-	yes
C	4	GO:0005618	cell wall	12/200	3.61	3.32e-05	-	no
C	4	GO:0043231	intracellular membrane-bounded organelle	64/200	1.46	3.66e-04	-	yes
C	3	GO:0043227	membrane-bounded organelle	64/200	1.46	3.67e-04	-	yes
C	3	GO:0016020	membrane	40/200	1.46	4.98e-03	-	no
C	5	GO:0009536	plastid	29/200	1.57	5.56e-03	-	no

M	5	GO:0030554	adenyl nucleotide binding	41/200	4.53	5.65e-17	-	yes
M	4	GO:0001883	purine nucleoside binding	41/200	4.53	5.65e-17	-	yes
M	3	GO:0001882	nucleoside binding	41/200	4.52	6.20e-17	-	yes
M	4	GO:0017076	purine nucleotide binding	42/200	4.05	1.32e-15	-	yes
M	5	GO:0032555	purine ribonucleotide binding	40/200	4.08	5.16e-15	-	yes
M	4	GO:0032553	ribonucleotide binding	40/200	4.08	5.16e-15	-	yes
M	3	GO:0000166	nucleotide binding	44/200	3.33	2.76e-13	-	yes
M	5	GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	21/200	4.72	8.86e-10	-	yes
M	4	GO:0016817	hydrolase activity, acting on acid anhydrides	21/200	4.67	1.05e-09	-	yes
M	5	GO:0016773	phosphotransferase activity, alcohol group as acceptor	20/200	3.22	1.26e-06	-	no
M	4	GO:0016772	transferase activity, transferring phosphorus-containing groups	25/200	2.73	1.77e-06	-	no
M	3	GO:0016787	hydrolase activity	35/200	2.24	2.06e-06	-	yes
M	5	GO:0016301	kinase activity	22/200	2.73	6.45e-06	-	no
M	4	GO:0003677	DNA binding	28/200	2.02	1.28e-04	2.65E-15	yes
M	3	GO:0005515	protein binding	30/200	1.92	1.98e-04	-	no
M	3	GO:0016740	transferase activity	30/200	1.83	4.23e-04	-	no

PS	5	PO:0009052	pedicel	169/200	2.08	1.61e-38	-	yes
PS	4	PO:0000037	shoot apex	173/200	2.01	1.75e-38	-	yes
PS	3	PO:0009031	sepal	174/200	1.88	1.25e-34	-	yes
PS	4	PO:0009009	embryo	176/200	1.82	2.07e-33	-	yes
PS	5	PO:0008034	leaf whorl	174/200	1.85	3.05e-33	-	yes
PS	4	PO:0008033	phyllome whorl	174/200	1.85	3.05e-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:0006001	phyllome	176/200	1.72	2.16e-29	-	yes
PS	4	PO:0009049	inflorescence	177/200	1.69	6.89e-29	-	yes
PS	5	PO:0009046	flower	176/200	1.69	1.97e-28	-	yes
PS	4	PO:0009025	leaf	166/200	1.81	3.44e-28	-	yes
PS	3	PO:0009006	shoot	179/200	1.65	3.83e-28	-	yes
PS	3	PO:0009032	petal	161/200	1.84	2.95e-27	-	yes
PS	5	PO:0008037	seedling	154/200	1.74	4.99e-22	-	yes
PS	3	PO:0009005	root	155/200	1.72	1.18e-21	1.43E-16	yes
PS	5	PO:0020039	leaf lamina	146/200	1.77	1.68e-20	-	yes
PS	5	PO:0020038	petiole	139/200	1.83	4.46e-20	-	yes
PS	5	PO:0000013	cauline leaf	133/200	1.72	3.77e-16	-	yes
PS	5	PO:0009027	megasporophyll	135/200	1.61	8.67e-14	-	yes
PS	4	PO:0009026	sporophyll	136/200	1.51	1.51e-11	-	yes
PS	3	PO:0000084	sperm cell	66/200	2.03	1.47e-09	-	yes
PS	3	PO:0020097	generative cell	66/200	2.03	1.47e-09	-	yes
PS	3	PO:0020091	male gametophyte	118/200	1.42	1.97e-07	-	yes
PS	5	PO:0009028	microsporophyll	107/200	1.28	3.72e-04	-	yes
PS	3	PO:0009013	meristem	102/200	1.27	7.51e-04	5.93E-18	yes
PS	4	PO:0000230	inflorescence meristem	96/200	1.24	3.36e-03	-	yes
PS	4	PO:0020030	cotyledon	91/200	1.24	4.28e-03	-	yes

PG	5	PO:0001081	F mature embryo stage	171/200	2.15	7.32e-42	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	173/200	2.08	6.32e-41	-	yes
PG	5	PO:0004507	D bilateral stage	171/200	2.08	1.60e-39	-	yes
PG	4	PO:0007631	embryo development stages	175/200	1.94	2.78e-37	-	yes
PG	5	PO:0001185	C globular stage	168/200	2.05	5.09e-37	-	yes
PG	3	PO:0001170	seed development stages	175/200	1.93	5.50e-37	-	yes
PG	4	PO:0007616	4 anthesis	173/200	1.78	1.60e-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	176/200	1.73	7.91e-30	-	yes
PG	3	PO:0007615	flower development stages	178/200	1.70	1.03e-29	-	yes
PG	3	PO:0001050	leaf development stages	139/200	1.81	1.38e-19	-	yes
PG	4	PO:0001054	4 leaf senescence stage	138/200	1.79	4.86e-19	-	yes
PG	3	PO:0007134	A vegetative growth	137/200	1.62	2.18e-14	-	yes
PG	5	PO:0007133	leaf production	135/200	1.60	1.03e-13	-	yes
PG	4	PO:0007112	1 main shoot growth	135/200	1.60	1.05e-13	-	yes

KW	0	replication	-	18/200	22.17	9.46e-21	0	yes
KW	0	microtubule	-	17/200	16.53	2.11e-17	-	no
KW	0	ipr013210	-	18/200	13.67	1.01e-16	-	no
KW	0	ipr001611	-	22/200	7.78	1.46e-14	-	no
KW	0	cycle	-	13/200	9.61	1.09e-10	6.47E-16	no
KW	0	pathway	-	17/200	6.32	2.89e-10	-	no
KW	0	based	-	11/200	10.76	5.73e-10	-	no
KW	0	signaling	-	19/200	5.10	1.32e-09	-	no
KW	0	leucine	-	22/200	4.19	3.57e-09	-	no
KW	0	tyrosine	-	18/200	5.07	3.68e-09	-	no
KW	0	terminal	-	46/200	2.39	6.53e-09	-	no
KW	0	receptor	-	19/200	3.99	7.76e-08	-	no
KW	0	assembly	-	10/200	7.42	1.29e-07	1.47E-16	no
KW	0	ipr000719	-	21/200	3.37	3.40e-07	-	no
KW	0	movement	-	10/200	6.55	4.53e-07	-	no
KW	0	nucleus	-	32/200	2.48	6.22e-07	-	yes
KW	0	ipr011009	-	21/200	3.25	6.31e-07	-	no
KW	0	complex	-	24/200	2.83	1.39e-06	1.40E-15	no
KW	0	serine	-	24/200	2.69	3.44e-06	-	no
KW	0	plasma	-	28/200	2.44	4.05e-06	-	no
KW	0	threonine	-	21/200	2.80	6.93e-06	-	no
KW	0	kinase	-	26/200	2.46	7.39e-06	-	no
KW	0	transmembrane	-	20/200	2.76	1.40e-05	-	no
KW	0	phosphorylation	-	17/200	2.77	5.04e-05	-	no
KW	0	ipr001245	-	10/200	3.92	5.73e-05	-	no
KW	0	repeat	-	27/200	2.08	1.04e-04	-	no
KW	0	region	-	28/200	1.94	2.61e-04	1.08E-15	no
KW	0	amino	-	19/200	2.21	4.29e-04	1.80E-15	no
KW	0	embryo	-	16/200	2.30	6.56e-04	-	no
KW	0	chloroplast	-	31/200	1.76	7.37e-04	-	no
KW	0	ipr017442	-	13/200	2.47	9.06e-04	-	no
KW	0	associated	-	15/200	2.20	1.49e-03	-	no
KW	0	related	-	41/200	1.46	4.55e-03	2.57E-15	no
KW	0	membrane	-	38/200	1.43	8.81e-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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