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
AT3G08680.1	0.978679	leucine-rich repeat transmembrane protein kinase, putative	OMAT3P002980	-	-	-
AT5G22940.1	0.956747	F8H (FRA8 HOMOLOG)	OMAT5P007710	-	-	-
AT3G56370.1	0.952596	leucine-rich repeat transmembrane protein kinase, putative	OMAT3P113830	-	-	-
AT2G44740.1	0.951596	CYCP4	OMAT2P111520	-	-	-
AT3G43960.1	0.951079	cysteine proteinase, putative	OMAT3P109890	-	-	-
AT1G05950.1	0.950955	unknown protein	OMAT1P101650	-	-	-
AT3G62060.1	0.949361	pectinacetylesterase family protein	-	-	-	-
AT2G07690.1	0.947119	minichromosome maintenance family protein / MCM family protein	-	-	-	-
AT1G75710.1	0.947016	zinc finger (C2H2 type) family protein	OMAT1P022130	-	-	-
AT3G17998.1	0.944971	CPuORF30 (Conserved peptide upstream open reading frame 30)	OMAT3P006840	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT4G10860.1	-0.779324	unknown protein	-	-	-	-
AT1G01020.1	-0.777686	ARV1	-	-	-	-
AT5G05870.1	-0.743578	UGT76C1 (UDP-glucosyl transferase 76C1)	OMAT5P001930	-	-	-
AT2G04720.1	-0.738562	pseudogene, GTP-binding protein -related, similar to GTP-binding protein GI:6624302 from (Carica papaya)	-	-	-	-
AT4G01940.1	-0.70941	NFU1	OMAT4P100710	-	OMAT4P000710	-
AT5G23040.1	-0.704595	CDF1 (CELL GROWTH DEFECT FACTOR 1)	OMAT5P106710	-	-	-
AT4G12300.1	-0.704421	CYP706A4	OMAT4P102490	-	-	-
AT2G02180.1	-0.699831	TOM3	OMAT2P000390	-	OMAT2P100480	-
AT3G07790.1	-0.683145	DGCR14-related	OMAT3P002810	-	OMAT3P102680	-
AT2G27050.1	-0.681548	EIL1 (ETHYLENE-INSENSITIVE3-LIKE 1)	OMAT2P005910	-	OMAT2P105220	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 9.12e-25	:20 terms with high significance
9.12e-25 <	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	11/200	5.46	1.01e-06	-	no
B	3	GO:0023033	signaling pathway	13/200	3.85	8.83e-06	5.00E-13	no
B	3	GO:0050794	regulation of cellular process	29/200	1.90	2.88e-04	-	no
B	3	GO:0044238	primary metabolic process	70/200	1.41	4.51e-04	-	no
B	3	GO:0043170	macromolecule metabolic process	55/200	1.42	1.90e-03	-	no
B	3	GO:0050789	regulation of biological process	29/200	1.68	2.16e-03	-	no
B	5	GO:0006508	proteolysis	10/200	2.39	3.49e-03	-	no
B	5	GO:0006796	phosphate metabolic process	13/200	1.96	7.20e-03	-	no
B	4	GO:0006793	phosphorus metabolic process	13/200	1.96	7.26e-03	-	no

C	5	GO:0005856	cytoskeleton	11/200	9.78	1.71e-09	0	yes
C	3	GO:0044464	cell part	129/200	1.41	3.03e-08	-	yes
C	3	GO:0043228	non-membrane-bounded organelle	22/200	3.69	3.70e-08	-	yes
C	4	GO:0043232	intracellular non-membrane-bounded organelle	22/200	3.69	3.70e-08	-	yes
C	5	GO:0031225	anchored to membrane	11/200	7.40	3.85e-08	-	no
C	4	GO:0005886	plasma membrane	25/200	2.02	2.85e-04	3.64E-21	yes
C	3	GO:0030312	external encapsulating structure	10/200	2.99	5.89e-04	-	no
C	4	GO:0031224	intrinsic to membrane	13/200	2.42	1.08e-03	-	no
C	3	GO:0043234	protein complex	14/200	2.14	2.55e-03	5.61E-16	no
C	5	GO:0005634	nucleus	26/200	1.66	3.84e-03	3.64E-21	no
C	3	GO:0044425	membrane part	15/200	1.90	6.15e-03	-	no
C	3	GO:0016020	membrane	39/200	1.42	8.38e-03	3.64E-21	yes

M	3	GO:0016787	hydrolase activity	39/200	2.50	3.05e-08	-	no
M	5	GO:0030554	adenyl nucleotide binding	26/200	2.87	4.08e-07	-	no
M	4	GO:0001883	purine nucleoside binding	26/200	2.87	4.08e-07	-	no
M	3	GO:0001882	nucleoside binding	26/200	2.87	4.30e-07	-	no
M	4	GO:0017076	purine nucleotide binding	28/200	2.70	5.66e-07	-	no
M	5	GO:0032555	purine ribonucleotide binding	26/200	2.65	1.94e-06	-	no
M	4	GO:0032553	ribonucleotide binding	26/200	2.65	1.94e-06	-	no
M	3	GO:0000166	nucleotide binding	29/200	2.20	2.19e-05	9.98E-12	no
M	5	GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	14/200	3.15	4.63e-05	-	no
M	4	GO:0016817	hydrolase activity, acting on acid anhydrides	14/200	3.12	5.15e-05	-	no
M	5	GO:0016773	phosphotransferase activity, alcohol group as acceptor	15/200	2.42	5.45e-04	-	no
M	4	GO:0003677	DNA binding	26/200	1.88	6.78e-04	2.65E-15	no
M	5	GO:0016301	kinase activity	16/200	1.99	3.12e-03	3.95E-16	no
M	3	GO:0005515	protein binding	25/200	1.60	7.41e-03	1.67E-15	no

PS	5	PO:0009052	pedicel	163/200	2.00	2.70e-33	-	yes
PS	3	PO:0009032	petal	164/200	1.87	1.53e-29	-	yes
PS	3	PO:0009031	sepal	167/200	1.81	1.07e-28	-	yes
PS	4	PO:0009001	fruit	170/200	1.73	3.62e-27	-	yes
PS	3	PO:0006342	infructescence	170/200	1.73	3.62e-27	-	yes
PS	4	PO:0009009	embryo	168/200	1.74	1.04e-26	2.90E-16	yes
PS	3	PO:0009006	shoot	177/200	1.63	1.96e-26	1.15E-17	yes
PS	3	PO:0009010	seed	168/200	1.72	6.02e-26	3.72E-17	yes
PS	5	PO:0008034	leaf whorl	165/200	1.75	6.46e-26	-	yes
PS	4	PO:0008033	phyllome whorl	165/200	1.75	6.46e-26	-	yes
PS	5	PO:0009046	flower	172/200	1.65	3.44e-25	1.14E-17	yes
PS	4	PO:0009049	inflorescence	172/200	1.64	8.18e-25	2.20E-18	yes
PS	3	PO:0006001	phyllome	170/200	1.66	1.45e-24	-	yes
PS	4	PO:0000037	shoot apex	154/200	1.79	2.24e-23	-	yes
PS	5	PO:0009027	megasporophyll	141/200	1.68	8.22e-17	-	yes
PS	4	PO:0009025	leaf	148/200	1.61	1.86e-16	4.19E-17	yes
PS	4	PO:0009026	sporophyll	145/200	1.61	7.75e-16	-	yes
PS	5	PO:0020039	leaf lamina	136/200	1.65	5.14e-15	-	yes
PS	5	PO:0020038	petiole	125/200	1.64	7.38e-13	-	yes
PS	5	PO:0000013	cauline leaf	122/200	1.58	4.60e-11	-	yes
PS	5	PO:0008037	seedling	130/200	1.47	8.61e-10	1.16E-17	yes
PS	3	PO:0009005	root	131/200	1.46	1.60e-09	4.20E-22	yes
PS	3	PO:0020091	male gametophyte	122/200	1.47	8.34e-09	-	yes
PS	5	PO:0009028	microsporophyll	116/200	1.38	1.64e-06	-	yes
PS	3	PO:0009013	meristem	111/200	1.38	4.23e-06	5.93E-18	yes
PS	3	PO:0000084	sperm cell	56/200	1.73	8.61e-06	-	yes
PS	3	PO:0020097	generative cell	56/200	1.73	8.61e-06	-	yes
PS	3	PO:0000034	vascular system	11/200	3.37	1.21e-04	-	no
PS	4	PO:0000230	inflorescence meristem	101/200	1.30	3.10e-04	-	yes
PS	4	PO:0005679	epidermis	22/200	1.78	3.17e-03	7.47E-17	yes
PS	3	PO:0009014	dermal tissue	22/200	1.78	3.19e-03	-	yes
PS	5	PO:0006035	shoot epidermis	19/200	1.70	8.84e-03	-	yes

PG	5	PO:0001185	C globular stage	161/200	1.96	3.95e-31	-	yes
PG	4	PO:0007631	embryo development stages	166/200	1.84	1.82e-29	-	yes
PG	3	PO:0001170	seed development stages	166/200	1.84	3.36e-29	-	yes
PG	5	PO:0001081	F mature embryo stage	154/200	1.94	1.27e-27	-	yes
PG	4	PO:0007616	4 anthesis	169/200	1.74	2.93e-27	1.03E-18	yes
PG	5	PO:0004507	D bilateral stage	155/200	1.88	2.03e-26	-	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	172/200	1.64	9.12e-25	-	yes
PG	5	PO:0007604	corolla developmental stages	167/200	1.69	1.18e-24	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	153/200	1.84	1.27e-24	-	yes
PG	3	PO:0001050	leaf development stages	119/200	1.55	5.48e-10	-	yes
PG	4	PO:0001054	4 leaf senescence stage	118/200	1.53	1.27e-09	-	yes
PG	3	PO:0007134	A vegetative growth	123/200	1.45	1.63e-08	6.27E-18	yes
PG	5	PO:0007133	leaf production	122/200	1.45	2.25e-08	4.07E-18	yes
PG	4	PO:0007112	1 main shoot growth	122/200	1.45	2.28e-08	-	yes

KW	0	ipr013210	-	13/200	9.87	7.63e-11	-	no
KW	0	microtubule	-	10/200	9.72	8.06e-09	-	no
KW	0	ipr001611	-	15/200	5.31	3.09e-08	-	no
KW	0	anchored	-	11/200	7.17	5.46e-08	-	no
KW	0	tyrosine	-	15/200	4.23	6.60e-07	-	no
KW	0	terminal	-	38/200	1.97	1.60e-05	5.00E-13	no
KW	0	leucine	-	16/200	3.05	2.38e-05	5.00E-13	no
KW	0	signaling	-	13/200	3.49	2.57e-05	5.00E-13	no
KW	0	serine	-	22/200	2.47	3.24e-05	5.00E-13	no
KW	0	proteolysis	-	10/200	4.09	3.97e-05	-	no
KW	0	inhibitor	-	11/200	3.68	5.27e-05	1.16E-15	no
KW	0	plasma	-	24/200	2.09	2.11e-04	3.64E-21	yes
KW	0	regulation	-	26/200	1.97	3.31e-04	1.97E-15	no
KW	0	receptor	-	13/200	2.73	3.34e-04	2.27E-15	no
KW	0	globular	-	11/200	2.93	4.30e-04	-	no
KW	0	nucleus	-	25/200	1.94	5.26e-04	3.64E-21	no
KW	0	ipr000719	-	15/200	2.41	5.69e-04	-	no
KW	0	region	-	27/200	1.87	5.86e-04	1.08E-15	no
KW	0	development	-	16/200	2.29	6.89e-04	2.18E-15	yes
KW	0	complex	-	18/200	2.13	9.00e-04	1.40E-15	no
KW	0	ipr011009	-	14/200	2.17	2.27e-03	-	no
KW	0	peptidase	-	10/200	2.51	2.36e-03	-	no
KW	0	encodes	-	39/200	1.53	2.51e-03	1.59E-16	yes
KW	0	transmembrane	-	15/200	2.07	2.72e-03	-	no
KW	0	catalytic	-	19/200	1.87	3.10e-03	5.00E-13	no
KW	0	associated	-	14/200	2.05	3.80e-03	3.81E-15	no
KW	0	kinase	-	19/200	1.80	4.71e-03	1.01E-15	no
KW	0	factor	-	28/200	1.60	4.90e-03	2.79E-15	no
KW	0	repeat	-	22/200	1.69	5.61e-03	-	no
KW	0	ipr017442	-	11/200	2.09	7.04e-03	-	no
KW	0	member	-	19/200	1.73	7.04e-03	-	no
KW	0	threonine	-	14/200	1.87	8.71e-03	-	no
KW	0	phosphorylation	-	12/200	1.95	9.24e-03	5.50E-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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