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
AT2G42750.1	0.857852	DNAJ heat shock N-terminal domain-containing protein	OMAT2P011630	-	-	-
AT3G10130.1	0.812465	SOUL heme-binding family protein	-	-	-	-
AT3G27110.1	0.802777	peptidase M48 family protein	OMAT3P010190	-	-	-
AT4G17840.1	0.794941	unknown protein	OMAT4P104440	-	-	-
AT4G11570.1	0.788835	haloacid dehalogenase-like hydrolase family protein	OMAT4P002930	-	OMAT4P102290	-
AT5G19540.1	0.761444	unknown protein	OMAT5P006830	-	-	-
AT1G31170.1	0.744266	SRX (SULFIREDOXIN)	OMAT1P010940	-	-	-
AT5G24160.1	0.740279	SQE6 (SQUALENE MONOXYGENASE 6)	OMAT5P107130	-	-	-
AT1G76570.1	0.740185	chlorophyll A-B binding family protein	OMAT1P022490	-	-	-
AT5G43260.1	0.739734	chaperone protein dnaJ-related	OMAT5P110420	-	-	-
Negatively Correlated Genes
Gens	PCC	Definition	Overlap gene	Definition	Overlap gene(antisense)	Definition
AT4G08520.1	-0.90836	clathrin adaptor complex small chain family protein	OMAT4P002090	-	-	-
AT2G17560.1	-0.90065	HMGB4 (HIGH MOBILITY GROUP B 4)	OMAT2P102330	-	-	-
AT5G22790.1	-0.889333	RER1 (RETICULATA-RELATED 1)	OMAT5P106630	-	-	-
AT3G53880.1	-0.885884	aldo/keto reductase family protein	-	-	-	-
AT3G23300.1	-0.877281	dehydration-responsive protein-related	OMAT3P008820	-	-	-
AT3G49080.1	-0.872684	ribosomal protein S9 family protein	OMAT3P111300	-	-	-
AT5G20080.1	-0.869732	NADH-cytochrome b5 reductase, putative	OMAT5P006950	-	-	-
AT5G66680.1	-0.864187	DGL1	OMAT5P118390	-	-	-
AT5G08160.1	-0.863814	ATPK3	OMAT5P102235	-	-	-
AT2G05220.1	-0.863651	40S ribosomal protein S17 (RPS17B)	-	-	-	-

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	3	GO:0009056	catabolic process	10/200	2.10	8.89e-03	-	no

C	5	GO:0009536	plastid	48/200	2.60	1.64e-10	-	yes
C	4	GO:0044444	cytoplasmic part	58/200	1.67	1.57e-05	-	yes
C	4	GO:0005737	cytoplasm	60/200	1.60	3.89e-05	-	yes
C	5	GO:0044434	chloroplast part	14/200	2.53	4.92e-04	-	no
C	4	GO:0044435	plastid part	14/200	2.46	6.47e-04	-	no
C	4	GO:0043231	intracellular membrane-bounded organelle	61/200	1.39	1.84e-03	-	yes
C	3	GO:0043227	membrane-bounded organelle	61/200	1.39	1.85e-03	-	yes
C	3	GO:0043229	intracellular organelle	62/200	1.34	3.86e-03	-	yes

M	3	GO:0016491	oxidoreductase activity	18/200	2.13	8.56e-04	-	no

PS	4	PO:0009047	stem	109/200	1.29	1.70e-04	-	yes
PS	3	PO:0020091	male gametophyte	104/200	1.25	1.03e-03	-	yes
PS	5	PO:0009027	megasporophyll	104/200	1.24	1.69e-03	-	yes
PS	5	PO:0009028	microsporophyll	103/200	1.23	2.52e-03	-	yes
PS	4	PO:0009026	sporophyll	109/200	1.21	2.80e-03	-	yes
PS	4	PO:0020030	cotyledon	91/200	1.24	4.28e-03	-	yes
PS	3	PO:0000084	sperm cell	46/200	1.42	4.79e-03	-	no
PS	3	PO:0020097	generative cell	46/200	1.42	4.79e-03	-	no

KW	0	chloroplast	-	49/200	2.77	9.90e-12	-	yes
KW	0	oxidoreductase	-	12/200	2.57	8.91e-04	-	no
KW	0	group	-	11/200	2.04	8.27e-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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