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
AT5G24530.1	0.925522	DMR6 (DOWNY MILDEW RESISTANT 6)	OMAT5P008360,OMAT5P008365,OMAT5P008367,OMAT5P008370	[OMAT5P008360]-, [OMAT5P008365]-, [OMAT5P008367]-, [OMAT5P008370]-	OMAT5P107310	-
AT2G30360.1	0.898934	SIP4 (SOS3-INTERACTING PROTEIN 4)	OMAT2P106280	-	-	-
AT3G54950.1	0.890387	PLA IIIA (PATATIN-LIKE PROTEIN 6)	OMAT3P113300	-	-	-
AT2G16720.1	0.886821	MYB7 (MYB DOMAIN PROTEIN 7)	OMAT2P102120	-	-	-
AT5G49525.1	0.885545	unknown protein	OMAT5P112640	-	-	-
AT1G15800.1	0.872944	unknown protein	OMAT1P105270,OMAT1P105280	[OMAT1P105270]-, [OMAT1P105280]-	-	-
AT1G24190.1	0.872833	SNL3 (SIN3-LIKE 3)	OMAT1P107840	-	-	-
AT3G55880.2	0.871396	unknown protein	OMAT3P015500	-	-	-
AT4G20830.1	0.869787	FAD-binding domain-containing protein	OMAT4P006320	-	OMAT4P105240	-
AT2G47950.1	0.864906	unknown protein	OMAT2P013900	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT2G15290.1	-0.858713	TIC21 (TRANSLOCON AT INNER MEMBRANE OF CHLOROPLASTS 21)	OMAT2P101730	-	-	-
AT3G49510.1	-0.827549	F-box family protein	-	-	-	-
AT3G26483.1	-0.815255	transposable element gene	-	-	-	-
AT2G42130.4	-0.809493	unknown protein	OMAT2P011420	-	-	-
AT3G09860.1	-0.80603	unknown protein	OMAT3P003400	-	-	-
AT1G09625.1	-0.776547	unknown protein	-	-	-	-
AT3G53560.1	-0.772508	chloroplast lumen common family protein	OMAT3P112770	-	-	-
AT3G59190.1	-0.768702	F-box family protein	-	-	-	-
AT3G28760.2	-0.766595	FUNCTIONS IN: molecular_function unknown	-	-	-	-
AT5G42240.1	-0.764343	scpl42 (serine carboxypeptidase-like 42)	OMAT5P011660	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 1.57e-20	:20 terms with high significance
1.57e-20 <	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:0009737	response to abscisic acid stimulus	15/200	8.88	1.86e-11	-	no
B	4	GO:0010033	response to organic substance	27/200	4.04	1.70e-10	-	no
B	4	GO:0009725	response to hormone stimulus	21/200	4.44	2.68e-09	-	no
B	3	GO:0042221	response to chemical stimulus	33/200	2.89	1.06e-08	-	no
B	3	GO:0009719	response to endogenous stimulus	21/200	4.07	1.27e-08	-	no
B	5	GO:0032870	cellular response to hormone stimulus	11/200	7.17	5.46e-08	-	no
B	4	GO:0009755	hormone-mediated signaling pathway	11/200	7.17	5.46e-08	-	no
B	3	GO:0006950	response to stress	33/200	2.66	8.11e-08	-	no
B	5	GO:0009651	response to salt stress	13/200	5.66	9.42e-08	-	no
B	4	GO:0071495	cellular response to endogenous stimulus	11/200	6.51	1.56e-07	-	no
B	4	GO:0006970	response to osmotic stress	13/200	5.18	2.73e-07	-	no
B	5	GO:0071310	cellular response to organic substance	11/200	5.26	1.50e-06	-	no
B	3	GO:0007154	cell communication	10/200	5.38	3.06e-06	-	no
B	4	GO:0070887	cellular response to chemical stimulus	11/200	4.84	3.52e-06	-	no
B	3	GO:0050794	regulation of cellular process	33/200	2.16	8.58e-06	-	no
B	3	GO:0023033	signaling pathway	13/200	3.85	8.83e-06	-	no
B	3	GO:0051716	cellular response to stimulus	15/200	3.39	1.08e-05	-	no
B	3	GO:0009628	response to abiotic stimulus	20/200	2.70	1.89e-05	-	no
B	5	GO:0051252	regulation of RNA metabolic process	16/200	3.06	2.24e-05	-	no
B	3	GO:0019748	secondary metabolic process	10/200	4.32	2.40e-05	-	no
B	5	GO:0032774	RNA biosynthetic process	16/200	2.92	4.05e-05	-	no
B	4	GO:0080090	regulation of primary metabolic process	24/200	2.28	5.63e-05	-	no
B	4	GO:0051171	regulation of nitrogen compound metabolic process	23/200	2.27	8.24e-05	-	no
B	4	GO:0031323	regulation of cellular metabolic process	24/200	2.22	8.58e-05	-	no
B	3	GO:0050789	regulation of biological process	33/200	1.91	1.09e-04	-	no
B	3	GO:0051707	response to other organism	11/200	3.28	1.54e-04	-	no
B	4	GO:0009889	regulation of biosynthetic process	22/200	2.19	1.92e-04	-	no
B	5	GO:0031326	regulation of cellular biosynthetic process	22/200	2.19	1.92e-04	-	no
B	3	GO:0009607	response to biotic stimulus	11/200	3.04	3.07e-04	-	no
B	3	GO:0019222	regulation of metabolic process	24/200	2.04	3.17e-04	-	no
B	5	GO:0010556	regulation of macromolecule biosynthetic process	21/200	2.13	3.76e-04	-	no
B	5	GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	21/200	2.09	4.76e-04	-	no
B	5	GO:0006796	phosphate metabolic process	15/200	2.26	1.11e-03	-	no
B	4	GO:0006793	phosphorus metabolic process	15/200	2.26	1.12e-03	-	no
B	5	GO:0006350	transcription	20/200	1.96	1.44e-03	-	no
B	4	GO:0060255	regulation of macromolecule metabolic process	21/200	1.92	1.49e-03	-	no
B	5	GO:0006464	protein modification process	20/200	1.92	1.83e-03	-	no
B	5	GO:0010468	regulation of gene expression	20/200	1.88	2.41e-03	-	no
B	4	GO:0043412	macromolecule modification	20/200	1.76	4.95e-03	-	no
B	5	GO:0016070	RNA metabolic process	16/200	1.88	5.39e-03	-	no

C	5	GO:0005634	nucleus	27/200	1.73	1.93e-03	-	no

M	5	GO:0042578	phosphoric ester hydrolase activity	10/200	4.57	1.43e-05	-	no
M	3	GO:0005515	protein binding	33/200	2.11	1.46e-05	-	no
M	3	GO:0003700	transcription factor activity	22/200	2.18	2.08e-04	-	no
M	4	GO:0003677	DNA binding	26/200	1.88	6.78e-04	-	no
M	5	GO:0016301	kinase activity	16/200	1.99	3.12e-03	-	no
M	4	GO:0016772	transferase activity, transferring phosphorus-containing groups	17/200	1.85	5.10e-03	-	no

PS	5	PO:0009028	microsporophyll	162/200	1.93	1.27e-30	-	yes
PS	4	PO:0009026	sporophyll	163/200	1.81	3.45e-27	-	yes
PS	4	PO:0009047	stem	156/200	1.85	8.23e-26	-	yes
PS	3	PO:0009005	root	161/200	1.79	9.86e-26	-	yes
PS	4	PO:0009025	leaf	161/200	1.75	1.69e-24	-	yes
PS	3	PO:0020091	male gametophyte	152/200	1.83	5.39e-24	-	yes
PS	3	PO:0006001	phyllome	169/200	1.65	8.00e-24	-	yes
PS	4	PO:0020030	cotyledon	140/200	1.91	2.40e-22	-	yes
PS	5	PO:0008037	seedling	154/200	1.74	4.99e-22	-	yes
PS	5	PO:0009046	flower	167/200	1.61	1.51e-21	-	yes
PS	4	PO:0009049	inflorescence	167/200	1.60	3.38e-21	-	yes
PS	3	PO:0009006	shoot	170/200	1.57	4.23e-21	-	yes
PS	3	PO:0009031	sepal	156/200	1.69	6.46e-21	-	yes
PS	5	PO:0008034	leaf whorl	157/200	1.66	1.87e-20	-	yes
PS	4	PO:0008033	phyllome whorl	157/200	1.66	1.87e-20	-	yes
PS	5	PO:0009027	megasporophyll	147/200	1.75	3.28e-20	-	yes
PS	4	PO:0000230	inflorescence meristem	140/200	1.80	9.86e-20	-	yes
PS	5	PO:0020039	leaf lamina	144/200	1.75	2.55e-19	-	yes
PS	4	PO:0009001	fruit	158/200	1.61	7.33e-19	-	yes
PS	3	PO:0006342	infructescence	158/200	1.61	7.33e-19	-	yes
PS	3	PO:0009013	meristem	141/200	1.75	8.88e-19	-	yes
PS	3	PO:0009010	seed	157/200	1.60	1.57e-18	-	yes
PS	4	PO:0009009	embryo	155/200	1.60	5.51e-18	-	yes
PS	4	PO:0006345	pollen tube	77/200	2.64	1.80e-17	-	no
PS	5	PO:0000013	cauline leaf	135/200	1.75	3.37e-17	-	yes
PS	3	PO:0009032	petal	140/200	1.60	1.88e-14	-	yes
PS	4	PO:0000037	shoot apex	138/200	1.60	3.08e-14	-	yes
PS	5	PO:0020038	petiole	124/200	1.63	2.05e-12	-	yes
PS	5	PO:0009052	pedicel	127/200	1.56	2.09e-11	-	yes
PS	3	PO:0000084	sperm cell	55/200	1.69	1.81e-05	-	no
PS	3	PO:0020097	generative cell	55/200	1.69	1.81e-05	-	no
PS	3	PO:0000034	vascular system	10/200	3.06	4.84e-04	-	no

PG	3	PO:0007134	A vegetative growth	153/200	1.81	1.54e-23	-	yes
PG	5	PO:0007133	leaf production	152/200	1.81	3.00e-23	-	yes
PG	4	PO:0007112	1 main shoot growth	152/200	1.81	3.08e-23	-	yes
PG	4	PO:0007616	4 anthesis	163/200	1.68	7.32e-23	-	yes
PG	3	PO:0007615	flower development stages	168/200	1.60	7.64e-22	-	yes
PG	4	PO:0007600	3 floral organ development stages	164/200	1.61	9.92e-21	-	yes
PG	5	PO:0007604	corolla developmental stages	161/200	1.63	1.57e-20	-	yes
PG	5	PO:0007605	androecium developmental stages	80/200	2.73	4.00e-19	-	no
PG	4	PO:0001054	4 leaf senescence stage	131/200	1.70	2.59e-15	-	yes
PG	3	PO:0001050	leaf development stages	131/200	1.70	2.72e-15	-	yes
PG	4	PO:0007631	embryo development stages	140/200	1.55	2.50e-13	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	133/200	1.60	2.68e-13	-	yes
PG	3	PO:0001170	seed development stages	140/200	1.55	3.75e-13	-	yes
PG	5	PO:0004507	D bilateral stage	131/200	1.59	1.12e-12	-	yes
PG	5	PO:0001081	F mature embryo stage	124/200	1.56	6.58e-11	-	yes
PG	5	PO:0001185	C globular stage	126/200	1.54	1.11e-10	-	yes

KW	0	abscisic	-	14/200	9.99	1.42e-11	-	no
KW	0	response	-	42/200	2.34	5.49e-08	-	no
KW	0	stress	-	18/200	3.84	2.94e-07	-	no
KW	0	ipr001841	-	11/200	3.59	6.74e-05	-	no
KW	0	transcription	-	29/200	2.00	1.23e-04	-	no
KW	0	mediated	-	11/200	3.11	2.52e-04	-	no
KW	0	ipr013083	-	10/200	3.19	3.43e-04	-	no
KW	0	signal	-	12/200	2.73	5.14e-04	-	no
KW	0	nucleus	-	25/200	1.94	5.26e-04	-	no
KW	0	ipr017442	-	13/200	2.47	9.06e-04	-	no
KW	0	ipr008271	-	12/200	2.46	1.35e-03	-	no
KW	0	ipr017441	-	11/200	2.56	1.37e-03	-	no
KW	0	encodes	-	40/200	1.57	1.38e-03	-	no
KW	0	stimulus	-	11/200	2.55	1.41e-03	-	no
KW	0	threonine	-	16/200	2.13	1.50e-03	-	no
KW	0	finger	-	18/200	1.95	2.46e-03	-	no
KW	0	leucine	-	12/200	2.29	2.55e-03	-	no
KW	0	terminal	-	31/200	1.61	3.00e-03	-	no
KW	0	regulation	-	23/200	1.74	3.44e-03	-	no
KW	0	active	-	16/200	1.95	3.70e-03	-	no
KW	0	associated	-	14/200	2.05	3.80e-03	-	no
KW	0	ipr000719	-	13/200	2.09	4.19e-03	-	no
KW	0	plasma	-	20/200	1.74	5.56e-03	-	no
KW	0	ipr011009	-	13/200	2.01	5.76e-03	-	no
KW	0	member	-	19/200	1.73	7.04e-03	-	no
KW	0	class	-	12/200	2.00	7.55e-03	-	no
KW	0	serine	-	16/200	1.80	8.42e-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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