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
AT3G17640.1	0.894866	leucine-rich repeat family protein	OMAT3P006610	-	-	-
AT3G31415.1	0.853882	terpene synthase/cyclase family protein	-	-	-	-
AT4G08870.1	0.833895	arginase, putative	OMAT4P101740	-	-	-
AT2G18260.1	0.833616	SYP112 (SYNTAXIN OF PLANTS 112)	OMAT2P002870	-	-	-
AT4G35590.1	0.829569	RWP-RK domain-containing protein	-	-	-	-
AT4G10150.1	0.829382	zinc finger (C3HC4-type RING finger) family protein	-	-	-	-
AT4G14770.1	0.820334	TCX2 (TESMIN/TSO1-LIKE CXC 2)	OMAT4P103390	-	-	-
AT1G66430.1	0.817719	pfkB-type carbohydrate kinase family protein	OMAT1P018500	-	-	-
AT1G53520.1	0.816081	chalcone-flavanone isomerase-related	OMAT1P113190	-	-	-
AT5G38140.1	0.815662	NF-YC12 (NUCLEAR FACTOR Y, SUBUNIT C12)	-	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT5G35710.1	-0.6991	transposable element gene	-	-	-	-
AT3G51580.1	-0.696254	unknown protein	OMAT3P111980	-	-	-
AT4G16080.1	-0.670567	unknown protein	-	-	-	-
AT5G16220.1	-0.670362	octicosapeptide/Phox/Bem1p (PB1) domain-containing protein	-	-	-	-
AT4G37120.1	-0.665355	SMP2	OMAT4P012820	-	OMAT4P111160	-
AT4G12440.2	-0.662097	adenine phosphoribosyltransferase, putative	-	-	-	-
AT4G23160.1	-0.644888	protein kinase family protein	-	-	-	-
AT4G24200.1	-0.643793	LOCATED IN: mitochondrion	OMAT4P106480	-	-	-
AT4G14805.1	-0.641643	protease inhibitor/seed storage/lipid transfer protein (LTP)-related	-	-	-	-
AT2G44950.1	-0.636328	HUB1 (HISTONE MONO-UBIQUITINATION 1)	-	-	-	-

Get whole results

Over-Representation Analysis Result

	p-value	<= 3.10e-07	:20 terms with high significance
3.10e-07 <	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:0006633	fatty acid biosynthetic process	17/200	23.36	3.61e-20	-	no
B	5	GO:0006631	fatty acid metabolic process	17/200	14.88	1.40e-16	-	no
B	5	GO:0016053	organic acid biosynthetic process	21/200	9.70	5.91e-16	-	no
B	4	GO:0008610	lipid biosynthetic process	21/200	9.57	7.87e-16	-	no
B	4	GO:0044283	small molecule biosynthetic process	25/200	5.51	8.79e-13	-	no
B	4	GO:0006629	lipid metabolic process	24/200	5.52	2.28e-12	-	no
B	5	GO:0043436	oxoacid metabolic process	24/200	5.45	2.99e-12	-	no
B	4	GO:0006082	organic acid metabolic process	24/200	5.44	3.17e-12	-	no
B	4	GO:0044255	cellular lipid metabolic process	19/200	7.07	4.26e-12	-	no
B	4	GO:0042180	cellular ketone metabolic process	24/200	5.35	4.50e-12	-	no
B	3	GO:0044281	small molecule metabolic process	34/200	3.78	4.95e-12	-	no
B	3	GO:0009058	biosynthetic process	54/200	1.85	1.46e-06	-	yes
B	4	GO:0044249	cellular biosynthetic process	52/200	1.85	2.65e-06	-	yes
B	3	GO:0044238	primary metabolic process	70/200	1.41	4.51e-04	-	yes
B	5	GO:0032774	RNA biosynthetic process	13/200	2.37	1.31e-03	-	no
B	5	GO:0051252	regulation of RNA metabolic process	12/200	2.30	2.45e-03	-	no
B	5	GO:0006350	transcription	19/200	1.86	3.25e-03	0	yes
B	3	GO:0044237	cellular metabolic process	63/200	1.33	4.17e-03	-	yes
B	4	GO:0005975	carbohydrate metabolic process	11/200	2.11	6.45e-03	-	no

C	3	GO:0012505	endomembrane system	55/200	2.26	1.14e-09	-	no
C	3	GO:0044464	cell part	126/200	1.38	3.10e-07	-	yes
C	5	GO:0009532	plastid stroma	11/200	4.45	8.21e-06	-	no
C	5	GO:0009536	plastid	35/200	1.90	7.79e-05	-	no
C	5	GO:0044434	chloroplast part	15/200	2.71	1.56e-04	-	no
C	4	GO:0044435	plastid part	15/200	2.64	2.10e-04	-	no
C	4	GO:0005618	cell wall	10/200	3.01	5.55e-04	-	no
C	3	GO:0030312	external encapsulating structure	10/200	2.99	5.89e-04	-	no

M	3	GO:0016491	oxidoreductase activity	23/200	2.73	4.29e-06	-	no
M	5	GO:0046872	metal ion binding	24/200	1.77	2.35e-03	-	no
M	4	GO:0043169	cation binding	25/200	1.74	2.44e-03	-	no
M	3	GO:0043167	ion binding	25/200	1.74	2.44e-03	0	no

KW	0	fatty	-	17/200	12.79	2.04e-15	-	no
KW	0	biosynthetic	-	29/200	4.06	3.28e-11	-	no
KW	0	system	-	57/200	2.35	1.17e-10	-	no
KW	0	endomembrane	-	55/200	2.33	4.10e-10	-	no
KW	0	process	-	49/200	2.39	1.78e-09	-	no
KW	0	synthase	-	18/200	4.10	1.07e-07	-	no
KW	0	carrier	-	17/200	4.24	1.38e-07	-	no
KW	0	stroma	-	11/200	5.90	4.47e-07	-	no
KW	0	metabolic	-	28/200	2.44	4.21e-06	-	no
KW	0	chloroplast	-	37/200	2.09	5.22e-06	-	no
KW	0	encodes	-	44/200	1.72	9.54e-05	-	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	alpha	-	16/200	2.19	1.12e-03	-	no
KW	0	catalytic	-	20/200	1.97	1.36e-03	-	no
KW	0	putative	-	36/200	1.56	2.55e-03	-	no
KW	0	oxidoreductase	-	11/200	2.36	2.70e-03	-	no

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