Other supporting information

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
AT1G09350.1	0.99227	AtGolS3 (Arabidopsis thaliana galactinol synthase 3)	OMAT1P003180	-	-	-
AT3G55580.1	0.988523	regulator of chromosome condensation (RCC1) family protein	OMAT3P015350	-	-	-
AT1G26790.1	0.98584	Dof-type zinc finger domain-containing protein	OMAT1P108370	-	-	-
AT4G32190.1	0.978934	centromeric protein-related	OMAT4P010740	-	OMAT4P109190	-
AT2G22810.1	0.974704	ACS4 (1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 4)	-	-	-	-
AT2G42530.1	0.967965	COR15B (COLD REGULATED 15B)	OMAT2P110820	-	OMAT2P011550	-
AT1G29420.1	0.955638	FUNCTIONS IN: molecular_function unknown	OMAT1P109300	-	-	-
AT1G79660.1	0.950101	unknown protein	OMAT1P023790	-	-	-
AT3G09450.1	0.948778	unknown protein	OMAT3P003240	-	-	-
AT3G27845.1	0.941336	pre-tRNA	-	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT5G43280.1	-0.67165	ATDCI1 (DELTA(3,5),DELTA(2,4)-DIENOYL-COA ISOMERASE 1)	OMAT5P011970	-	-	-
AT3G43710.1	-0.655767	kelch repeat-containing F-box family protein	-	-	-	-
AT2G13300.1	-0.652783	transposable element gene	-	-	-	-
AT2G06150.1	-0.603559	transposable element gene	-	-	-	-
AT3G42710.1	-0.598483	transposable element gene	-	-	-	-
AT5G66710.1	-0.576191	protein kinase, putative	-	-	-	-
AT1G37113.1	-0.574951	unknown protein	-	-	-	-
AT5G19080.1	-0.570467	zinc finger (C3HC4-type RING finger) family protein	-	-	-	-
AT2G10960.1	-0.567874	transposable element gene	-	-	-	-
AT5G37870.1	-0.567573	seven in absentia (SINA) family protein	-	-	-	-

Over-Representation Analysis Result

	p-value	<= 1.00e-06	:20 terms with high significance
1.00e-06 <	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:0009733	response to auxin stimulus	11/200	6.51	1.56e-07	-	no
B	3	GO:0009719	response to endogenous stimulus	14/200	2.72	2.31e-04	-	no
B	4	GO:0009725	response to hormone stimulus	13/200	2.75	3.14e-04	-	no
B	3	GO:0009628	response to abiotic stimulus	17/200	2.29	4.97e-04	-	no
B	4	GO:0010033	response to organic substance	15/200	2.24	1.19e-03	-	no

M	3	GO:0003700	transcription factor activity	21/200	2.08	5.24e-04	-	no
M	4	GO:0003677	DNA binding	23/200	1.66	6.11e-03	0	no

PS	4	PO:0020030	cotyledon	95/200	1.29	6.83e-04	-	no
PS	5	PO:0000013	cauline leaf	97/200	1.26	1.76e-03	-	yes
PS	4	PO:0009025	leaf	109/200	1.19	6.36e-03	-	yes
PS	4	PO:0009047	stem	101/200	1.20	7.20e-03	-	yes

PG	3	PO:0007134	A vegetative growth	105/200	1.24	1.52e-03	-	yes
PG	4	PO:0007112	1 main shoot growth	104/200	1.24	1.83e-03	-	yes
PG	5	PO:0007133	leaf production	103/200	1.22	2.84e-03	-	yes
PG	3	PO:0001050	leaf development stages	93/200	1.21	8.40e-03	-	yes

KW	0	responsive	-	10/200	3.34	2.34e-04	-	no
KW	0	expression	-	12/200	2.48	1.24e-03	-	no
KW	0	carbohydrate	-	10/200	2.55	2.10e-03	-	no
KW	0	stimulus	-	10/200	2.32	4.26e-03	-	no
KW	0	regulation	-	22/200	1.66	6.91e-03	-	no
KW	0	factor	-	27/200	1.54	9.02e-03	1.00E-54	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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