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
AT1G56460.1	0.95746	PAPA-1-like family protein / zinc finger (HIT type) family protein	OMAT1P015790	-	-	-
AT2G47890.1	0.938024	zinc finger (B-box type) family protein	OMAT2P013870	-	-	-
AT1G22050.1	0.919607	MUB6 (MEMBRANE-ANCHORED UBIQUITIN-FOLD PROTEIN 6 PRECURSOR)	OMAT1P008020	-	-	-
AT1G64050.1	0.906393	unknown protein	OMAT1P017550	-	-	-
AT2G32295.1	0.903174	FUNCTIONS IN: molecular_function unknown	OMAT2P007830	-	-	-
AT1G80570.2	0.900696	F-box family protein (FBL14)	OMAT1P024130	-	-	-
AT4G08540.1	0.896916	unknown protein	OMAT4P002110	-	-	-
AT2G34730.1	0.895424	myosin heavy chain-related	OMAT2P008620	-	-	-
AT4G07580.1	0.894096	transposable element gene	-	-	-	-
AT5G28622.1	0.880094	transposable element gene	-	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT2G26250.1	-0.914294	KCS10 (3-KETOACYL-COA SYNTHASE 10)	OMAT2P104930	-	OMAT2P005610	-
AT2G38540.1	-0.856475	LP1	OMAT2P010090	-	OMAT2P109260	-
AT2G32500.1	-0.851684	FUNCTIONS IN: molecular_function unknown	-	-	-	-
AT2G35450.1	-0.83272	catalytic/ hydrolase	OMAT2P107950	-	-	-
AT2G02500.1	-0.821052	ISPD	OMAT2P100520	-	-	-
AT5G26000.1	-0.811575	TGG1 (THIOGLUCOSIDE GLUCOHYDROLASE 1)	OMAT5P107780	-	OMAT5P008870	-
AT1G05190.1	-0.801687	emb2394 (embryo defective 2394)	OMAT1P101390	-	OMAT1P001620	-
AT5G05590.1	-0.797736	PAI2 (PHOSPHORIBOSYLANTHRANILATE ISOMERASE 2)	-	-	-	-
AT1G31330.1	-0.794888	PSAF (photosystem I subunit F)	OMAT1P109880	-	OMAT1P011010	-
AT1G29070.1	-0.794673	ribosomal protein L34 family protein	OMAT1P010230	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 2.71e-08	:20 terms with high significance
2.71e-08 <	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	3	GO:0009628	response to abiotic stimulus	15/200	2.02	3.32e-03	-	no

M	3	GO:0005515	protein binding	28/200	1.79	9.44e-04	6.00E-147	no
M	4	GO:0003677	DNA binding	24/200	1.73	3.06e-03	6.00E-147	no
M	5	GO:0046872	metal ion binding	22/200	1.62	9.34e-03	-	no

PS	4	PO:0009047	stem	137/200	1.62	1.47e-14	-	yes
PS	4	PO:0000230	inflorescence meristem	128/200	1.65	1.74e-13	-	yes
PS	3	PO:0009013	meristem	129/200	1.61	1.06e-12	-	yes
PS	3	PO:0009005	root	134/200	1.49	1.03e-10	-	yes
PS	5	PO:0009028	microsporophyll	127/200	1.51	2.39e-10	-	yes
PS	4	PO:0009026	sporophyll	133/200	1.48	2.68e-10	-	yes
PS	5	PO:0008037	seedling	128/200	1.45	4.92e-09	-	yes
PS	4	PO:0009009	embryo	136/200	1.41	5.67e-09	-	yes
PS	4	PO:0009001	fruit	137/200	1.39	9.88e-09	-	yes
PS	3	PO:0006342	infructescence	137/200	1.39	9.88e-09	-	yes
PS	3	PO:0009010	seed	136/200	1.39	1.52e-08	-	yes
PS	5	PO:0009052	pedicel	119/200	1.46	2.49e-08	-	yes
PS	3	PO:0009031	sepal	130/200	1.41	2.71e-08	-	yes
PS	5	PO:0009046	flower	140/200	1.35	7.21e-08	-	yes
PS	4	PO:0000037	shoot apex	122/200	1.42	1.04e-07	-	yes
PS	4	PO:0009049	inflorescence	140/200	1.34	1.16e-07	-	yes
PS	3	PO:0006001	phyllome	138/200	1.35	1.16e-07	-	yes
PS	3	PO:0009006	shoot	143/200	1.32	1.94e-07	-	yes
PS	5	PO:0009027	megasporophyll	119/200	1.42	2.04e-07	-	yes
PS	5	PO:0000013	cauline leaf	112/200	1.45	2.17e-07	-	yes
PS	4	PO:0009025	leaf	126/200	1.37	4.36e-07	-	yes
PS	3	PO:0009032	petal	120/200	1.37	1.47e-06	-	yes
PS	4	PO:0020030	cotyledon	105/200	1.43	1.84e-06	-	yes
PS	5	PO:0008034	leaf whorl	126/200	1.34	2.27e-06	-	yes
PS	4	PO:0008033	phyllome whorl	126/200	1.34	2.27e-06	-	yes
PS	3	PO:0020091	male gametophyte	114/200	1.37	3.36e-06	-	yes
PS	5	PO:0020039	leaf lamina	112/200	1.36	8.88e-06	-	yes
PS	3	PO:0000084	sperm cell	50/200	1.54	5.13e-04	-	no
PS	3	PO:0020097	generative cell	50/200	1.54	5.13e-04	-	no
PS	5	PO:0020038	petiole	95/200	1.25	2.56e-03	-	yes

PG	5	PO:0004507	D bilateral stage	122/200	1.48	5.18e-09	-	yes
PG	5	PO:0001078	E expanded cotyledon stage	122/200	1.47	8.86e-09	-	yes
PG	5	PO:0007133	leaf production	123/200	1.46	9.92e-09	-	yes
PG	4	PO:0007112	1 main shoot growth	123/200	1.46	1.01e-08	-	yes
PG	5	PO:0007604	corolla developmental stages	137/200	1.39	1.34e-08	-	yes
PG	3	PO:0007134	A vegetative growth	123/200	1.45	1.63e-08	-	yes
PG	4	PO:0007631	embryo development stages	128/200	1.42	2.15e-08	-	yes
PG	3	PO:0001170	seed development stages	128/200	1.42	2.95e-08	-	yes
PG	4	PO:0007616	4 anthesis	134/200	1.38	3.99e-08	-	yes
PG	5	PO:0001185	C globular stage	119/200	1.45	4.58e-08	-	yes
PG	4	PO:0007600	3 floral organ development stages	137/200	1.34	1.55e-07	-	yes
PG	3	PO:0007615	flower development stages	139/200	1.33	2.68e-07	-	yes
PG	5	PO:0001081	F mature embryo stage	114/200	1.43	2.90e-07	-	yes
PG	4	PO:0001054	4 leaf senescence stage	109/200	1.42	1.46e-06	-	yes
PG	3	PO:0001050	leaf development stages	109/200	1.42	1.50e-06	-	yes

KW	0	cellular_component	-	75/200	1.54	1.21e-05	-	no
KW	0	finger	-	22/200	2.38	5.71e-05	-	no
KW	0	nuclear	-	11/200	3.58	6.87e-05	-	no
KW	0	ubiquitin	-	12/200	2.67	6.36e-04	-	no
KW	0	transcription	-	25/200	1.72	2.82e-03	-	no
KW	0	biological_process	-	75/200	1.25	8.35e-03	-	no

(*1)	[B]:Biological process(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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