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
AT3G58550.1	0.974157	protease inhibitor/seed storage/lipid transfer protein (LTP) family protein	OMAT3P114510	-	-	-
AT2G37360.1	0.972095	ABC transporter family protein	OMAT2P108750	-	-	-
AT2G18370.1	0.955146	protease inhibitor/seed storage/lipid transfer protein (LTP) family protein	OMAT2P002920	-	-	-
AT1G12010.1	0.945265	1-aminocyclopropane-1-carboxylate oxidase, putative / ACC oxidase, putative	OMAT1P004140	-	-	-
AT3G47790.1	0.943173	ATATH7	OMAT3P012400	-	-	-
AT1G49960.1	0.932086	xanthine/uracil permease family protein	OMAT1P013780	-	-	-
AT5G63560.1	0.922298	transferase family protein	OMAT5P019470	-	-	-
AT2G04025.1	0.917679	unknown protein	OMAT2P100860	-	-	-
AT3G22240.1	0.910399	unknown protein	OMAT3P107400	-	-	-
AT5G10580.1	0.90752	unknown protein	OMAT5P003550	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT1G51990.1	-0.74572	O-methyltransferase family 2 protein	-	-	-	-
AT3G63490.1	-0.718188	ribosomal protein L1 family protein	OMAT3P018190	-	-	-
AT5G07610.1	-0.700399	F-box family protein	-	-	-	-
AT2G31890.1	-0.691887	RAP	OMAT2P106750,OMAT2P106760	[OMAT2P106750]-, [OMAT2P106760]-	-	-
AT5G18570.1	-0.689208	GTP1/OBG family protein	OMAT5P105430	-	-	-
AT4G24770.1	-0.685131	RBP31 (31-KDA RNA BINDING PROTEIN)	OMAT4P106670	-	-	-
AT5G17520.1	-0.677267	RCP1 (ROOT CAP 1)	-	-	-	-
AT3G32150.1	-0.677139	unknown protein	-	-	-	-
AT2G36250.1	-0.667911	FTSZ2-1	OMAT2P108240	-	-	-
AT2G21710.1	-0.661496	EMB2219 (embryo defective 2219)	-	-	-	-

Get whole results

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	4	GO:0044255	cellular lipid metabolic process	14/200	5.21	1.02e-07	-	no
B	4	GO:0008610	lipid biosynthetic process	12/200	5.47	3.79e-07	-	no
B	4	GO:0006629	lipid metabolic process	17/200	3.91	4.48e-07	-	no
B	5	GO:0016053	organic acid biosynthetic process	10/200	4.62	1.29e-05	-	no
B	4	GO:0044283	small molecule biosynthetic process	14/200	3.08	5.80e-05	-	no
B	5	GO:0043436	oxoacid metabolic process	12/200	2.73	5.27e-04	-	no
B	4	GO:0006082	organic acid metabolic process	12/200	2.72	5.41e-04	-	no
B	4	GO:0042180	cellular ketone metabolic process	12/200	2.67	6.29e-04	-	no
B	5	GO:0051252	regulation of RNA metabolic process	12/200	2.30	2.45e-03	-	no
B	5	GO:0031326	regulation of cellular biosynthetic process	19/200	1.89	2.71e-03	-	yes
B	4	GO:0009889	regulation of biosynthetic process	19/200	1.89	2.71e-03	-	yes
B	5	GO:0032774	RNA biosynthetic process	12/200	2.19	3.65e-03	-	no
B	4	GO:0080090	regulation of primary metabolic process	19/200	1.80	4.60e-03	-	yes
B	5	GO:0010556	regulation of macromolecule biosynthetic process	18/200	1.83	4.86e-03	-	yes
B	3	GO:0009058	biosynthetic process	42/200	1.44	5.08e-03	-	yes
B	5	GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	18/200	1.80	5.83e-03	-	yes
B	4	GO:0031323	regulation of cellular metabolic process	19/200	1.76	6.12e-03	-	yes
B	4	GO:0051171	regulation of nitrogen compound metabolic process	18/200	1.78	6.47e-03	-	yes
B	5	GO:0006350	transcription	18/200	1.76	7.01e-03	0	yes
B	4	GO:0044249	cellular biosynthetic process	40/200	1.42	7.89e-03	-	yes
B	3	GO:0044281	small molecule metabolic process	16/200	1.78	9.08e-03	-	no

C	3	GO:0012505	endomembrane system	58/200	2.39	4.24e-11	-	no
C	3	GO:0044464	cell part	122/200	1.33	5.16e-06	-	no
C	4	GO:0031224	intrinsic to membrane	15/200	2.80	1.08e-04	-	no
C	3	GO:0044425	membrane part	16/200	2.02	2.61e-03	-	no

M	3	GO:0016491	oxidoreductase activity	25/200	2.96	3.71e-07	-	no
M	3	GO:0003700	transcription factor activity	20/200	1.98	1.26e-03	-	yes

PS	3	PO:0009005	root	117/200	1.30	4.60e-05	-	yes
PS	4	PO:0009001	fruit	119/200	1.21	1.32e-03	-	yes
PS	3	PO:0006342	infructescence	119/200	1.21	1.32e-03	-	yes
PS	3	PO:0009010	seed	117/200	1.20	2.60e-03	-	yes
PS	5	PO:0008037	seedling	107/200	1.21	3.12e-03	-	yes
PS	4	PO:0009009	embryo	114/200	1.18	5.58e-03	-	yes

KW	0	hypocotyl	-	28/200	12.00	3.61e-23	-	yes
KW	0	stage	-	58/200	3.00	2.61e-15	-	no
KW	0	anthesis	-	44/200	3.35	2.32e-13	-	no
KW	0	petal	-	46/200	3.15	5.43e-13	-	no
KW	0	expansion	-	46/200	3.13	7.07e-13	-	no
KW	0	differentiation	-	46/200	3.04	1.92e-12	-	no
KW	0	endomembrane	-	58/200	2.45	1.39e-11	-	no
KW	0	system	-	58/200	2.39	3.80e-11	-	no
KW	0	globular	-	16/200	4.26	2.73e-07	-	no
KW	0	flower	-	23/200	3.01	7.79e-07	-	no
KW	0	carrier	-	13/200	3.24	5.75e-05	-	no
KW	0	shoot	-	10/200	3.77	8.13e-05	-	no
KW	0	reductase	-	10/200	3.67	1.03e-04	-	no
KW	0	oxidase	-	10/200	3.64	1.11e-04	-	no
KW	0	inhibitor	-	10/200	3.35	2.30e-04	-	no
KW	0	lipid	-	10/200	2.91	7.32e-04	-	no
KW	0	electron	-	10/200	2.81	9.80e-04	-	no
KW	0	transmembrane	-	16/200	2.20	1.06e-03	-	no
KW	0	synthase	-	11/200	2.51	1.65e-03	-	no
KW	0	oxidoreductase	-	11/200	2.36	2.70e-03	-	no
KW	0	membrane	-	40/200	1.50	3.00e-03	-	no
KW	0	process	-	32/200	1.56	4.10e-03	-	no
KW	0	embryo	-	14/200	2.02	4.43e-03	-	no
KW	0	factor	-	28/200	1.60	4.90e-03	0	yes
KW	0	biosynthetic	-	14/200	1.96	5.70e-03	-	no
KW	0	member	-	19/200	1.73	7.04e-03	-	no
KW	0	biological_process	-	75/200	1.25	8.35e-03	-	no

(*1)	[B]:Biological process(Gene ontology), [C]:Cellular component(Gene ontology), [M]:Molecular function(Gene ontology), [PS]:Plant Structure(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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